From 88d23a39def9dfbf0e29836d893c8eb930401af3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 3 Mar 2017 09:20:29 +0200 Subject: [PATCH 001/698] adding easyconfigs: gaussian-09.e.01-AVX.eb, gaussian-16.A.03-AVX2.eb --- .../g/gaussian/gaussian-09.e.01-AVX.eb | 55 +++++++++++++++++++ .../g/gaussian/gaussian-16.A.03-AVX2.eb | 55 +++++++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb create mode 100644 easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb new file mode 100644 index 00000000000..ec627471231 --- /dev/null +++ b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' + +# IMPORTANT!! +# Needs to be installed with --umask=007 + +name = 'gaussian' +version = '09.e.01' +versionsuffix = '-AVX' + +homepage = 'http://www.gaussian.com/' +description = """ +Gaussian 09 is the latest in the Gaussian series of programs. It +provides state-of-the-art capabilities for electronic structure +modeling. Gaussian 09 is licensed for a wide variety of computer +systems. All versions of Gaussian 09 contain every scientific/modeling +feature, and none imposes any artificial limitations on calculations +other than your computing resources and patience. + +This is the official gaussian AVX build. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Gaussian is licensed software. Need to download by hand. +sources = ['09.e.01-AVX-A64-114X.tgz'] + +checksums = [ + '9fd928b0508eb11240c52dcf68baec95', +] + +start_dir = '..' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'ln -s ../g%(version_major)s/g%(version_major)s ../g%(version_major)s/ghelp %(installdir)s/bin', + 'chmod -R o-rwx %(installdir)s/g%(version_major)s', +] + +sanity_check_paths = { + 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], + 'dirs': ['g%(version_major)s/bsd', 'g%(version_major)s/tests', 'g%(version_major)s/basis', 'g%(version_major)s/doc'], +} + +modextravars = { + 'g%(version_major)sroot': '%(installdir)s', + 'G%(version_major)sBASIS': '%(installdir)s/g%(version_major)s/basis', +} + +modextrapaths = { + 'GAUSS_EXEDIR': ['g%(version_major)s', 'g%(version_major)s/bsd'], + 'PATH': ['g%(version_major)s/bsd', 'g%(version_major)s'], + 'LD_LIBRARY_PATH': 'g%(version_major)s', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb new file mode 100644 index 00000000000..c165cdcd008 --- /dev/null +++ b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' + +# IMPORTANT!! +# Needs to be installed with --umask=007 + +name = 'gaussian' +version = '16.A.03' +versionsuffix = '-AVX2' + +homepage = 'http://www.gaussian.com/' +description = """ +Gaussian 09 is the latest in the Gaussian series of programs. It +provides state-of-the-art capabilities for electronic structure +modeling. Gaussian 09 is licensed for a wide variety of computer +systems. All versions of Gaussian 09 contain every scientific/modeling +feature, and none imposes any artificial limitations on calculations +other than your computing resources and patience. + +This is the official gaussian AVX2 build. +""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +# Gaussian is licensed software. Need to download by hand. +sources = ['16.A.03-AVX2-E6B-132X.tbz'] + +checksums = [ + '485f5ff4730a95876a0c37eab1e6b077', +] + +start_dir = '..' + +postinstallcmds = [ + 'mkdir %(installdir)s/bin', + 'ln -s ../g%(version_major)s/g%(version_major)s ../g%(version_major)s/ghelp %(installdir)s/bin', + 'chmod -R o-rwx %(installdir)s/g%(version_major)s', +] + +sanity_check_paths = { + 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], + 'dirs': ['g%(version_major)s/bsd', 'g%(version_major)s/tests', 'g%(version_major)s/basis', 'g%(version_major)s/doc'], +} + +modextravars = { + 'g%(version_major)sroot': '%(installdir)s', + 'G%(version_major)sBASIS': '%(installdir)s/g%(version_major)s/basis', +} + +modextrapaths = { + 'GAUSS_EXEDIR': ['g%(version_major)s', 'g%(version_major)s/bsd'], + 'PATH': ['g%(version_major)s/bsd', 'g%(version_major)s'], + 'LD_LIBRARY_PATH': 'g%(version_major)s', +} + +moduleclass = 'bio' From 91bbf866efc4ae91963ec96f02354df83556d147 Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Thu, 14 Dec 2017 09:07:09 -0500 Subject: [PATCH 002/698] adding easyconfigs: FLUENT-18.2.eb --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb new file mode 100644 index 00000000000..3b43211a37d --- /dev/null +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb @@ -0,0 +1,14 @@ +name = 'FLUENT' +version = '18.2' + +homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed +to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from +air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, +from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +sources = ['FLUIDS_%(version_major)s%(version_minor)s_LINX64.tar'] + +moduleclass = 'cae' From 20f46bc6684ce35aef87b10868a1c4eba7f94ece Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 Jan 2018 14:06:23 +0100 Subject: [PATCH 003/698] Updated comment to not mention version of Gaussian. Updated checksums to sha256. --- easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb | 8 ++------ easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb | 8 ++------ 2 files changed, 4 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb index ec627471231..bb7d50e65cb 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb @@ -9,8 +9,7 @@ versionsuffix = '-AVX' homepage = 'http://www.gaussian.com/' description = """ -Gaussian 09 is the latest in the Gaussian series of programs. It -provides state-of-the-art capabilities for electronic structure +Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations @@ -23,10 +22,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Gaussian is licensed software. Need to download by hand. sources = ['09.e.01-AVX-A64-114X.tgz'] - -checksums = [ - '9fd928b0508eb11240c52dcf68baec95', -] +checksums = ['af1e1cdf7d2799690a642b27ee0779b7cca9695b9a86a48739f3d9fc8c54a98d'] start_dir = '..' diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb index c165cdcd008..b340ff04456 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb @@ -9,8 +9,7 @@ versionsuffix = '-AVX2' homepage = 'http://www.gaussian.com/' description = """ -Gaussian 09 is the latest in the Gaussian series of programs. It -provides state-of-the-art capabilities for electronic structure +Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer systems. All versions of Gaussian 09 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations @@ -23,10 +22,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} # Gaussian is licensed software. Need to download by hand. sources = ['16.A.03-AVX2-E6B-132X.tbz'] - -checksums = [ - '485f5ff4730a95876a0c37eab1e6b077', -] +checksums = ['c83bbcb6ce136d257c8810cb447dfb0880bedf887efe6a4b828635938603384a'] start_dir = '..' From b5d91014f606bb4208d0aceebd302b4f30d3bf45 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 Jan 2018 14:57:33 +0100 Subject: [PATCH 004/698] Reduce line length in dirs directive as per Travis report. --- easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb | 2 +- easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb index bb7d50e65cb..25526a87628 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb @@ -34,7 +34,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], - 'dirs': ['g%(version_major)s/bsd', 'g%(version_major)s/tests', 'g%(version_major)s/basis', 'g%(version_major)s/doc'], + 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc'], } modextravars = { diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb index b340ff04456..b156b40bef1 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb @@ -34,7 +34,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], - 'dirs': ['g%(version_major)s/bsd', 'g%(version_major)s/tests', 'g%(version_major)s/basis', 'g%(version_major)s/doc'], + 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc'], } modextravars = { From a4872ca4a2cacb985b338b1d8c758fbb200efbcc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 Jan 2018 15:55:37 +0100 Subject: [PATCH 005/698] Fix typo. --- easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb | 2 +- easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb index 25526a87628..e036a8343c3 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb @@ -34,7 +34,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], - 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc'], + 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc']], } modextravars = { diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb index b156b40bef1..b8f408218a1 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb @@ -34,7 +34,7 @@ postinstallcmds = [ sanity_check_paths = { 'files': ['g%(version_major)s/g%(version_major)s', 'g%(version_major)s/l9999.exe'], - 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc'], + 'dirs': ['g%%(version_major)s/%s' % x for x in ['bsd', 'tests', 'basis', 'doc']], } modextravars = { From 4d5e124edafbfc913aa76439776d9dd39cd5fcfd Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 6 Feb 2018 16:41:01 +0100 Subject: [PATCH 006/698] We discussed naming schemes for foss + CUDA at EB user meeting, and whether foss + CUDA should maybe be a toolchain. Our preference is at least to include the CUDA version explicitely in the module name. Since I'm away for a long time, I won't be able to make changes, but if we want naming without CUDA version in the official EB repo, feel free to change that part --- .../Boost-1.65.1-foss-2017b-Python-2.7.14.eb | 29 ++++++++++++++++ ...1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 33 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..23b6e6238ed --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,29 @@ +name = 'Boost' +version = '1.65.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), + ('Python', '2.7.14'), +] + +# also build boost_mpi +boost_mpi = True + +# Compile Boost with -std=c++11, see https://gist.github.com/dennycd/5890475 and https://groups.google.com/forum/#!topic/fenics-support/yrseUpq3PSA +# -stdlib is left out, because that is an option for M*X (MacOS) only +# Strangely enough, it does cause the option -std=c++11 to be not recognized anymore.. +buildopts = 'cxxflags="$CXXFLAGS -std=c++11" linkflags="$LDFLAGS -std=c++11" ' + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb new file mode 100644 index 00000000000..288607f0525 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'PyCUDA' +version = '2017.1.1' +cudaver = '9.0.176' +versionsuffix = '-CUDA-{0}-Python-%(pyver)s'.format(cudaver) + +homepage = 'http://mathema.tician.de/software/pycuda' +description = """PyCUDA lets you access Nvidias CUDA parallel computation API from Python.""" + +toolchain = {'name': 'foss', 'version': '2017b'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] + +dependencies = [ + ('Python', '2.7.14'), + ('CUDA', '9.0.176', '', True), + ('Boost', '1.65.1', '-Python-%(pyver)s'), +] + +prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " + +options = {'modulename': '%(namelower)s'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lang' From 8b6a999f6bd441f8d9ebfae84ed9fb6eac9f905a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 10 Feb 2018 22:26:39 +0100 Subject: [PATCH 007/698] {chem}[intel/2017b] Dalton 2016 (REVIEW) --- .../Dalton-2016-fix-bad-includepath-add.patch | 24 ++++++ .../Dalton-2016-fix-cmake-install.patch | 30 +++++++ .../d/Dalton/Dalton-2016-fix-uninits.patch | 78 +++++++++++++++++++ .../d/Dalton/Dalton-2016-intel-2017b.eb | 55 +++++++++++++ ...016-use-EB-install-for-dalton-script.patch | 30 +++++++ .../Dalton-2016_cmake-obey-EB-variables.patch | 76 ++++++++++++++++++ .../d/Dalton/Dalton-2016_intel_lowopt.patch | 21 +++++ 7 files changed, 314 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-bad-includepath-add.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-cmake-install.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-uninits.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016-use-EB-install-for-dalton-script.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch create mode 100644 easybuild/easyconfigs/d/Dalton/Dalton-2016_intel_lowopt.patch diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-bad-includepath-add.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-bad-includepath-add.patch new file mode 100644 index 00000000000..21335dd3f50 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-bad-includepath-add.patch @@ -0,0 +1,24 @@ +commit c1b83a48162d7cef72e5df393999a43e5961ca2d +Author: Ake Sandgren +Date: Tue Jan 17 15:20:17 2017 +0100 + + Don't add detected MPI include paths to the compiler flags. + + The MPI compiler wrappers should be used (and is) and they are much + better at doing this correctly. + +diff --git a/cmake/mpi/ConfigMPI.cmake b/cmake/mpi/ConfigMPI.cmake +index 93237df..c5f1d49 100644 +--- a/cmake/mpi/ConfigMPI.cmake ++++ b/cmake/mpi/ConfigMPI.cmake +@@ -16,7 +16,9 @@ if(ENABLE_MPI) + find_package(MPI) + if(MPI_FOUND) + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${MPI_COMPILE_FLAGS}") +- include_directories(${MPI_INCLUDE_PATH}) ++ # Don't do this!! Let the MPI wrappers handle this. If you ++ # are not using MPI wrappers you are doing it wrong! ++ #include_directories(${MPI_INCLUDE_PATH}) + else() + message(FATAL_ERROR "-- You asked for MPI, but CMake could not find any MPI installation, check $PATH") + endif() diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-cmake-install.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-cmake-install.patch new file mode 100644 index 00000000000..536affecaa8 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-cmake-install.patch @@ -0,0 +1,30 @@ +# Change the install path to use a "bin" directory. +# +# Åke Sandgren +diff -ru DALTON2016.2-Source.orig/cmake/ConfigMakeInstall.cmake DALTON2016.2-Source/cmake/ConfigMakeInstall.cmake +--- DALTON2016.2-Source.orig/cmake/ConfigMakeInstall.cmake 2016-05-13 07:06:33.000000000 +0200 ++++ DALTON2016.2-Source/cmake/ConfigMakeInstall.cmake 2016-11-15 19:35:28.000000000 +0100 +@@ -1,4 +1,4 @@ +-set(INSTALL_DIRECTORY "dalton") ++set(INSTALL_DIRECTORY ".") + + # create install directory + install( +@@ -11,7 +11,7 @@ + foreach(_executable dalton.x) + install( + TARGETS ${_executable} +- DESTINATION ${INSTALL_DIRECTORY} ++ DESTINATION ${INSTALL_DIRECTORY}/bin + PERMISSIONS + OWNER_READ OWNER_WRITE OWNER_EXECUTE + GROUP_READ GROUP_EXECUTE +@@ -23,7 +23,7 @@ + foreach(_script dalton) + install( + FILES ${CMAKE_BINARY_DIR}/${_script} +- DESTINATION ${INSTALL_DIRECTORY} ++ DESTINATION ${INSTALL_DIRECTORY}/bin + PERMISSIONS + OWNER_READ OWNER_WRITE OWNER_EXECUTE + GROUP_READ GROUP_EXECUTE diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-uninits.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-uninits.patch new file mode 100644 index 00000000000..a14d7fc41a5 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-fix-uninits.patch @@ -0,0 +1,78 @@ +# Fix a bunch of uninitialized variables. +# +# Åke Sandgren +diff --git a/DALTON/abacus/dalgnr.F b/DALTON/abacus/dalgnr.F +index c6cea38..b674d18 100644 +--- a/DALTON/abacus/dalgnr.F ++++ b/DALTON/abacus/dalgnr.F +@@ -403,6 +403,7 @@ C /* Deck exeher */ + #include "dftcom.h" + #include "pcmlog.h" + #include "qm3.h" ++#include "nuclei.h" + C + C Run Integral section + C +diff --git a/DALTON/abacus/herpar.F b/DALTON/abacus/herpar.F +index f74c394..1804c40 100644 +--- a/DALTON/abacus/herpar.F ++++ b/DALTON/abacus/herpar.F +@@ -1338,6 +1338,14 @@ C This is a slave in a parallel run; check for programming error + call quit('Failed to allocate memory') + end if + ++#ifdef VAR_MPI ++ ! Make dummy allocation so we don't trip on uninitialized ++ ! variables in call to HER_RVINIT ++ nelement_d = 1 ++ nelement_f = 1 ++ call memallocmpi(nelement_d*8,dmat_p) ++ call memallocmpi(nelement_f*8,fmat_p) ++#endif + ! Receive initialization from master - 1 - common block information + ! ================================================================= + ! +@@ -1362,6 +1370,9 @@ C This is a slave in a parallel run; check for programming error + nelement_f = n2basx*rma_win_info%nmat_max_wo_win + end if + #ifdef VAR_MPI ++ ! Free the dummy allocations before doing the real allocations ++ call memfreempi(fmat_buff) ++ call memfreempi(dmat_buff) + call memallocmpi(nelement_d*8,dmat_p) + call memallocmpi(nelement_f*8,fmat_p) + #endif +diff --git a/DALTON/cc/ccsd_input.F b/DALTON/cc/ccsd_input.F +index 4da8565..04323eb 100644 +--- a/DALTON/cc/ccsd_input.F ++++ b/DALTON/cc/ccsd_input.F +@@ -107,6 +107,7 @@ C + LOGICAL SET, NEWDEF, SIRFF + CHARACTER PROMPT*1, WORD*7, TABLE(NTABLE)*7, WORD1*7 + CHARACTER*(80) LINE ++ INTEGER ITEST + C + SAVE SET + CSONIA/FRAN/TBPEDERSEN +@@ -144,6 +145,8 @@ Cring-CCD for triplet (rTCCD), and SOSEX added + C + IF (SET) RETURN + SET = .TRUE. ++ ++ ITEST = 0 + C + CSPAS:8/11-13: Initialization of CCSDINP, CCLR, CCSDSYM + C and other common blocks is moved to a new routine +diff --git a/DALTON/sirius/sirqmmm.F b/DALTON/sirius/sirqmmm.F +index 48d132d..b0f7f34 100644 +--- a/DALTON/sirius/sirqmmm.F ++++ b/DALTON/sirius/sirqmmm.F +@@ -4339,6 +4339,8 @@ C Receiving data from master + CALL MPIXBCAST(CONMAT,1,'LOGICAL',MASTER) + + KELF = 1 ++ KELFEL = 1 ++ KELFNU = 1 + IF (SPLDIP) THEN + KELFEL = KELF + 3*POLDIM + KELFNU = KELFEL + 3*POLDIM diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb new file mode 100644 index 00000000000..6786804a340 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'Dalton' +version = '2016' + +homepage = 'http://daltonprogram.org/' +description = """The Dalton code is a powerful tool for a wide range of molecular properties + at different levels of theory. + Any published work arising from use of one of the Dalton2016 programs + must acknowledge that by a proper reference, + http://www.daltonprogram.org/www/citation.html.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'i8': True, 'usempi': True} + +# use git clone --recurse-submodules -b release/2016 git@gitlab.com:dalton/dalton.git +# to fetch source, then make the bizpped tarball +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-%(version)s-fix-cmake-install.patch', + '%(name)s-%(version)s-use-EB-install-for-dalton-script.patch', + '%(name)s-%(version)s-fix-uninits.patch', + '%(name)s-%(version)s-fix-bad-includepath-add.patch', + '%(name)s-%(version)s_cmake-obey-EB-variables.patch', + '%(name)s-%(version)s_intel_lowopt.patch', +] +checksums = [ + 'c78bf22293a7fc75465d96079ef39bdaa1f134127766a936763e25eaeb8958a8', # Dalton-2016.tar.bz2 + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch + '570bd128fe0be69ef377c373b69bf64eb8d0908bc960903509cbc68ff275ae13', # Dalton-2016-use-EB-install-for-dalton-script.patch + '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', # Dalton-2016-fix-uninits.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch + 'd7de83216a2090d46d9260f74891ad9ebf8b6038456b5cbc8a2c3a0f9924d3d8', # Dalton-2016_cmake-obey-EB-variables.patch + '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', # Dalton-2016_intel_lowopt.patch +] + +builddependencies = [('CMake', '3.9.5')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DENABLE_MPI=ON ' +configopts += '-DENABLE_OMP=ON ' +configopts += '-DENABLE_64BIT_INTEGERS=ON ' +configopts += '-DENABLE_AUTO_BLAS=OFF ' +configopts += '-DENABLE_AUTO_LAPACK=OFF ' +configopts += '-DEXPLICIT_BLAS_LIB="$LIBBLAS" ' +configopts += '-DEXPLICIT_LAPACK_LIB="$LIBLAPACK" ' + +sanity_check_paths = { + 'files': ['bin/dalton', 'bin/dalton.x'], + 'dirs': ['basis'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-use-EB-install-for-dalton-script.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016-use-EB-install-for-dalton-script.patch new file mode 100644 index 00000000000..95f110e7db2 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-use-EB-install-for-dalton-script.patch @@ -0,0 +1,30 @@ +# Use EasyBuild installation dir for dalton wrapper. +# No need to try to find it in a complicated way. +# +# Åke Sandgren +diff -ru DALTON2016.2-Source.orig/dalton.in DALTON2016.2-Source/dalton.in +--- DALTON2016.2-Source.orig/dalton.in 2016-05-13 18:35:49.000000000 +0200 ++++ DALTON2016.2-Source/dalton.in 2016-11-15 19:17:48.000000000 +0100 +@@ -21,20 +21,10 @@ + DALTON="DALTON" + fi + +- +-# radovan: this is to figure out the location of this script +-# http://stackoverflow.com/questions/59895/can-a-bash-script-tell-what-directory-its-stored-in +-SOURCE="${BASH_SOURCE[0]}" +-while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink +- SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" +- SOURCE="$(readlink "$SOURCE")" +- # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located +- [[ $SOURCE != /* ]] && SOURCE="$SCRIPT_DIR/$SOURCE" +-done +-SCRIPT_DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" ++SCRIPT_DIR="$EBROOTDALTON" + + LSLIB_TEST=$SCRIPT_DIR/lslib_tester.x +-DALTON_EXECUTABLE=$SCRIPT_DIR/$dalton.x ++DALTON_EXECUTABLE=$SCRIPT_DIR/bin/$dalton.x + + which mpirun > /dev/null # check if mpirun exists, if not, then assume mpiexec + if [ $? -eq 0 ]; then diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch new file mode 100644 index 00000000000..5220e7f9a92 --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch @@ -0,0 +1,76 @@ +# Take EasyBuild compiler flags for C, C++, and Fortran +# February 6th, 2018 by B. Hajgato (Free University Brussels - VUB) +diff -ru dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/CFlags.cmake dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/CFlags.cmake +--- dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/CFlags.cmake 2017-08-14 15:00:21.000000000 +0200 ++++ dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/CFlags.cmake 2018-02-06 15:12:30.449237790 +0100 +@@ -37,13 +37,13 @@ + endif() + + if(CMAKE_C_COMPILER_ID MATCHES Intel) +- set(CMAKE_C_FLAGS "-g -wd981 -wd279 -wd383 -vec-report0 -wd1572 -wd1777 -restrict -DRESTRICT=restrict") ++ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -wd981 -wd279 -wd383 -wd1572 -wd1777 -restrict -DRESTRICT=restrict") + if(NOT DEVELOPMENT_CODE) + # suppress warnings in exported code + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -w") + endif() + set(CMAKE_C_FLAGS_DEBUG "-O0") +- set(CMAKE_C_FLAGS_RELEASE "-O3 -ip") ++ set(CMAKE_C_FLAGS_RELEASE " ") + set(CMAKE_C_FLAGS_PROFILE "${CMAKE_C_FLAGS_RELEASE} -g -pg") + set(CMAKE_C_LINK_FLAGS "${CMAKE_C_LINK_FLAGS} -shared-intel") + +diff -ru dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/CXXFlags.cmake dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/CXXFlags.cmake +--- dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/CXXFlags.cmake 2017-08-14 15:00:21.000000000 +0200 ++++ dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/CXXFlags.cmake 2018-02-06 15:12:44.153908053 +0100 +@@ -39,7 +39,7 @@ + endif() + + if (CMAKE_CXX_COMPILER_ID MATCHES Intel) +- set(CMAKE_CXX_FLAGS "-g -wd981 -wd279 -wd383 -vec-report0 -wd1572 -wd177 -fno-rtti -fno-exceptions") ++ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -wd981 -wd279 -wd383 -vec-report0 -wd1572 -wd177 -fno-rtti -fno-exceptions") + if(DEVELOPMENT_CODE) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall") + else() +@@ -47,7 +47,7 @@ + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -w") + endif() + set(CMAKE_CXX_FLAGS_DEBUG "-O0") +- set(CMAKE_CXX_FLAGS_RELEASE "-O3 -ip") ++ set(CMAKE_CXX_FLAGS_RELEASE " ") + set(CMAKE_CXX_FLAGS_PROFILE "${CMAKE_CXX_FLAGS_RELEASE} -g -pg") + set (CMAKE_CXX_LINK_FLAGS "${CMAKE_CXX_LINK_FLAGS} -shared-intel") + +diff -ru dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/FortranFlags.cmake dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/FortranFlags.cmake +--- dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/compilers/FortranFlags.cmake 2017-08-14 15:00:21.000000000 +0200 ++++ dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/compilers/FortranFlags.cmake 2018-02-06 14:50:21.404219685 +0100 +@@ -48,13 +48,13 @@ + + if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) + add_definitions(-DVAR_IFORT) +- set(CMAKE_Fortran_FLAGS "-fpp -assume byterecl -DVAR_IFORT") ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DVAR_IFORT") + if(NOT DEVELOPMENT_CODE) + # suppress warnings in exported code + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w") + endif() + set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -g -traceback") +- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ip -diag-disable 8290 -diag-disable 8291") ++ set(CMAKE_Fortran_FLAGS_RELEASE "-diag-disable 8290 -diag-disable 8291") + set(CMAKE_Fortran_FLAGS_PROFILE "${CMAKE_Fortran_FLAGS_RELEASE} -g -pg") + + if(DEFINED MKL_FLAG) +diff -ru dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/SourcesDALTON.cmake dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/SourcesDALTON.cmake +--- dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake/SourcesDALTON.cmake 2017-08-14 15:00:21.000000000 +0200 ++++ dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917/cmake/SourcesDALTON.cmake 2018-02-06 15:17:06.776589480 +0100 +@@ -790,7 +790,10 @@ + DALTON/pcm/pcm_write.F90 + DALTON/pcm/pcm_utils.F90 + ) +- set(DALTON_FREE_FORTRAN_SOURCES "${DALTON_FREE_FORTRAN_SOURCES} ${DAL_PCM_SOURCES}") ++ set(DALTON_FREE_FORTRAN_SOURCES ++ ${DALTON_FREE_FORTRAN_SOURCES} ++ ${DAL_PCM_SOURCES} ++ ) + endif() + set(DALTON_OWN_BLAS_SOURCES + DALTON/pdpack/gp_blas.F diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016_intel_lowopt.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016_intel_lowopt.patch new file mode 100644 index 00000000000..6a542557b9d --- /dev/null +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016_intel_lowopt.patch @@ -0,0 +1,21 @@ +# Intel compiler breaks some tests (some Cholesky and some R12 calculations). +# For the fortran sources below the too high level optimizations is the problem. +# The optimization level was decreased to O1 for those files. +# Fsplitting those fortran sources (having more subroutines) could help more +# precisely locate the problematic code, but it does not worth to do it for me. +# February 10th 2018 by Balazs Hajgato (Free University Brussels - VUB) +--- dalton/cmake/compilers/FortranFlags.cmake.orig 2018-02-08 07:41:57.000000000 +0100 ++++ dalton/cmake/compilers/FortranFlags.cmake 2018-02-10 20:43:28.980844855 +0100 +@@ -87,6 +87,12 @@ + "${CMAKE_Fortran_FLAGS} -Qoption,ld,-w" + ) + endif() ++ set(O1_OPT_FORTRAN ++ DALTON/choles/cc_chopt.F ++ DALTON/cc/cc_r12ccsd.F ++ ) ++ SET_SOURCE_FILES_PROPERTIES(${O1_OPT_FORTRAN} PROPERTIES COMPILE_FLAGS "-O1") ++ + set(reorder_definitions " --nocollapse ${reorder_definitions}") + endif() + From 7d88ae759a6e9a02496a32b7bea8b275657287d6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 10 Feb 2018 22:35:10 +0100 Subject: [PATCH 008/698] use -fpp for frotran --- .../d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch b/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch index 5220e7f9a92..f1fc893962d 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016_cmake-obey-EB-variables.patch @@ -48,7 +48,7 @@ diff -ru dalton-release-2016-130ffaa0613bb3af6cac766fc8183d6df7d68917.orig/cmake if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) add_definitions(-DVAR_IFORT) - set(CMAKE_Fortran_FLAGS "-fpp -assume byterecl -DVAR_IFORT") -+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -DVAR_IFORT") ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fpp -DVAR_IFORT") if(NOT DEVELOPMENT_CODE) # suppress warnings in exported code set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w") From 238e36fae59b14dd1146b4be95e962bf18ff531c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 10 Feb 2018 22:38:52 +0100 Subject: [PATCH 009/698] checksum --- easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb index 6786804a340..489331ab9e6 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb @@ -30,7 +30,7 @@ checksums = [ '570bd128fe0be69ef377c373b69bf64eb8d0908bc960903509cbc68ff275ae13', # Dalton-2016-use-EB-install-for-dalton-script.patch '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', # Dalton-2016-fix-uninits.patch '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch - 'd7de83216a2090d46d9260f74891ad9ebf8b6038456b5cbc8a2c3a0f9924d3d8', # Dalton-2016_cmake-obey-EB-variables.patch + '69c6d9c110c78c064544052ae5dcb8721f49744f7a5cbf3a0f4d1170d7d22927', # Dalton-2016_cmake-obey-EB-variables.patch '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', # Dalton-2016_intel_lowopt.patch ] From 422d65cb2cfee1793b10043f45cb9c30e9c2baa4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 12 Feb 2018 15:33:30 +0100 Subject: [PATCH 010/698] use ScaLAPACK/BLACS --- .../d/Dalton/Dalton-2016-intel-2017b.eb | 28 +++++++++++-------- 1 file changed, 17 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb index 489331ab9e6..0d553826562 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb @@ -25,13 +25,20 @@ patches = [ '%(name)s-%(version)s_intel_lowopt.patch', ] checksums = [ - 'c78bf22293a7fc75465d96079ef39bdaa1f134127766a936763e25eaeb8958a8', # Dalton-2016.tar.bz2 - '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch - '570bd128fe0be69ef377c373b69bf64eb8d0908bc960903509cbc68ff275ae13', # Dalton-2016-use-EB-install-for-dalton-script.patch - '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', # Dalton-2016-fix-uninits.patch - '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch - '69c6d9c110c78c064544052ae5dcb8721f49744f7a5cbf3a0f4d1170d7d22927', # Dalton-2016_cmake-obey-EB-variables.patch - '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', # Dalton-2016_intel_lowopt.patch + # Dalton-2016.tar.bz2 + 'c78bf22293a7fc75465d96079ef39bdaa1f134127766a936763e25eaeb8958a8', + # Dalton-2016-fix-cmake-install.patch + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', + # Dalton-2016-use-EB-install-for-dalton-script.patch + '570bd128fe0be69ef377c373b69bf64eb8d0908bc960903509cbc68ff275ae13', + # Dalton-2016-fix-uninits.patch + '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', + # Dalton-2016-fix-bad-includepath-add.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', + # Dalton-2016_cmake-obey-EB-variables.patch + '69c6d9c110c78c064544052ae5dcb8721f49744f7a5cbf3a0f4d1170d7d22927', + # Dalton-2016_intel_lowopt.patch + '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', ] builddependencies = [('CMake', '3.9.5')] @@ -41,11 +48,10 @@ separate_build_dir = True configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' configopts += '-DENABLE_MPI=ON ' configopts += '-DENABLE_OMP=ON ' +# Only enable for BLAS/LAPACK having 8 byte integers (basically MKL) adjust the configopts 'i8' option accordingly configopts += '-DENABLE_64BIT_INTEGERS=ON ' -configopts += '-DENABLE_AUTO_BLAS=OFF ' -configopts += '-DENABLE_AUTO_LAPACK=OFF ' -configopts += '-DEXPLICIT_BLAS_LIB="$LIBBLAS" ' -configopts += '-DEXPLICIT_LAPACK_LIB="$LIBLAPACK" ' +configopts += '-DENABLE_SCALAPACK=ON ' +configopts += '-DBLACS_IMPLEMENTATION=intelmpi ' sanity_check_paths = { 'files': ['bin/dalton', 'bin/dalton.x'], From 96a4abc4bf640335cda4464b41460cd4ccb9b49b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Mar 2018 16:45:12 +0100 Subject: [PATCH 011/698] adding easyconfigs: AmberTools-17-foss-2018a.eb --- .../a/AmberTools/AmberTools-17-foss-2018a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb new file mode 100644 index 00000000000..d1917181a5f --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb @@ -0,0 +1,35 @@ +easyblock = 'EB_Amber' + +name = 'AmberTools' +version = '17' + +homepage = 'http://ambermd.org/' +description = """AmberTools consists of several independently developed packages that work well by themselves, + and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, + with either explicit water or generalized Born solvent models.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +toolchainopts = {'usempi': True} + +# download requires registration, see http://ambermd.org/AmberTools17-get.html +sources = ['AmberTools%(version)s.tar.bz2'] +patches = ['Amber-16_fix-hardcoding.patch'] +checksums = [ + '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 + '5e25d0671a173d3347d9e4ddec2faec4caed048918a7c339767d7fb312008c52', # Amber-16_fix-hardcoding.patch +] + +builddependencies = [('pkg-config', '0.29.2')] +dependencies = [ + ('Python', '2.7.14'), + ('netCDF', '4.6.0'), + ('netCDF-Fortran', '4.4.4'), +] + +# fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others, +# all of which are indirect dependencies via netCDF +netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" +preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % netcdf_libs +configopts = "-nosanderapi" + +moduleclass = 'chem' From dd58d3d239d8bf2df69d5d953b413848bf0e04a9 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 22 Mar 2018 19:40:51 +0100 Subject: [PATCH 012/698] added Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb --- ...ome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb new file mode 100644 index 00000000000..926c0dfb444 --- /dev/null +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'CmdCp' + +name = 'Genome_Profiler' +version = '2.1' +versionsuffix = '-Perl-%(perlver)s' + +homepage = 'https://sourceforge.net/projects/genomeprofiler/' +description = """Genome Profiler (GeP) is a program to perform whole-genome multilocus + sequence typing (wgMLST) analysis for bacterial isolates""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://sourceforge.net/projects/genomeprofiler/files/Genome_Profiler_%(version)s/'] +sources = ['GeP.pl'] +checksums = ['212624965f84316663499751b117608e30b2074675c0e8d38aa8c5f8f6a86a99'] + +dependencies = [ + ('Perl', '5.24.0'), +] + +# skip uncompress because this is plain .pl file +skipsteps = ['source'] + +cmds_map = [("GeP.pl", "cp %(source)s .")] + +files_to_copy = [(['GeP.pl'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/GeP.pl'], + 'dirs': [], +} + +postinstallcmds = [ + "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/GeP.pl", # fix shebang line + "chmod +x %(installdir)s/bin/GeP.pl", +] + +modloadmsg = "To launch execute script GeP.pl\n\r" + +moduleclass = 'bio' From 3d80de6055af8e81c2e1cd1989b7954f4600d8c2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 22 Mar 2018 20:43:59 +0100 Subject: [PATCH 013/698] rename downloaded file to add version --- .../Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb index 926c0dfb444..67eba9fb9eb 100644 --- a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -16,7 +16,7 @@ description = """Genome Profiler (GeP) is a program to perform whole-genome mult toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://sourceforge.net/projects/genomeprofiler/files/Genome_Profiler_%(version)s/'] -sources = ['GeP.pl'] +sources = [{'download_file': 'GeP.pl', 'filename': 'GeP-%(version)s.pl'}] checksums = ['212624965f84316663499751b117608e30b2074675c0e8d38aa8c5f8f6a86a99'] dependencies = [ @@ -26,7 +26,7 @@ dependencies = [ # skip uncompress because this is plain .pl file skipsteps = ['source'] -cmds_map = [("GeP.pl", "cp %(source)s .")] +cmds_map = [("GeP*.pl", "cp %(source)s GeP.pl")] files_to_copy = [(['GeP.pl'], 'bin')] From 8d936358ca1fdc9daa1a96401d207ab14f46c4a3 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 22 Mar 2018 22:28:07 +0100 Subject: [PATCH 014/698] {bio} [foss/2016b] Rematch 3.2 --- .../b/BCFtools/BCFtools-1.3.1-foss-2016b.eb | 37 ++++++++++++++++++ .../ReMatCh-3.2-foss-2016b-Python-2.7.12.eb | 38 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb create mode 100644 easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb new file mode 100644 index 00000000000..0d32c2f03d4 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'BCFtools' +version = '1.3.1' + +homepage = 'http://www.htslib.org/' +description = """BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] + +dependencies = [ + ('zlib', '1.2.8'), + ('GSL', '2.3'), +] + +buildopts = " USE_GPL=1 GSL_LIBS='-lgsl -lgslcblas'" + +runtest = 'test' + +files_to_copy = [(["bcftools", "plot-vcfstats", "vcfutils.pl"], "bin"), + "doc", "plugins", "test", "LICENSE", "README", "AUTHORS"] + +sanity_check_paths = { + 'files': ["bin/bcftools"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb new file mode 100644 index 00000000000..ab251956a7b --- /dev/null +++ b/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'Tarball' + +name = 'ReMatCh' +version = '3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/B-UMMI/ReMatCh' +description = "Reads mapping against target sequences, checking mapping and consensus sequences production" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/B-UMMI/ReMatCh/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['60cd3dbdeed519aab397fa19583f84d9e614240dc7525231fcb9ceaf3509ce42'] + +dependencies = [ + ('Python', '2.7.12'), + ('Bowtie2', '2.3.2'), + ('SAMtools', '1.3.1'), + ('BCFtools', '1.3.1'), +] + +# add install dir to PATH +modextrapaths = { + 'PATH': '' +} + +sanity_check_paths = { + 'files': ['rematch.py'], + 'dirs': [], +} + +moduleclass = 'bio' From 1134ce8d5f4992d60b19af24dd6ad66cd4d177f7 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 22 Mar 2018 22:30:19 +0100 Subject: [PATCH 015/698] added extra docs --- .../r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb b/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb index ab251956a7b..ed936ba687a 100644 --- a/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb +++ b/easybuild/easyconfigs/r/ReMatCh/ReMatCh-3.2-foss-2016b-Python-2.7.12.eb @@ -21,8 +21,8 @@ checksums = ['60cd3dbdeed519aab397fa19583f84d9e614240dc7525231fcb9ceaf3509ce42'] dependencies = [ ('Python', '2.7.12'), ('Bowtie2', '2.3.2'), - ('SAMtools', '1.3.1'), - ('BCFtools', '1.3.1'), + ('SAMtools', '1.3.1'), # website says it must be this exact version + ('BCFtools', '1.3.1'), # website says it must be this exact version ] # add install dir to PATH From 3484e719856be288badaeed2ad4ef42f7ea2fa6f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Fri, 23 Mar 2018 08:54:45 +0100 Subject: [PATCH 016/698] update typo in sources --- .../Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb index 67eba9fb9eb..0591e40261b 100644 --- a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -16,7 +16,7 @@ description = """Genome Profiler (GeP) is a program to perform whole-genome mult toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://sourceforge.net/projects/genomeprofiler/files/Genome_Profiler_%(version)s/'] -sources = [{'download_file': 'GeP.pl', 'filename': 'GeP-%(version)s.pl'}] +sources = [{'download_filename': 'GeP.pl', 'filename': 'GeP-%(version)s.pl'}] checksums = ['212624965f84316663499751b117608e30b2074675c0e8d38aa8c5f8f6a86a99'] dependencies = [ From d496bdc71c1c46546c46bf56792a2af17d4fb217 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 25 Mar 2018 11:29:59 -0500 Subject: [PATCH 017/698] cleanups for cuDNN --- .../c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb | 46 +++++++++++++++++++ .../c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb | 46 +++++++++++++++++++ .../c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb | 46 +++++++++++++++++++ .../c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb | 46 +++++++++++++++++++ .../c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb | 46 +++++++++++++++++++ .../c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb | 31 +++++++++---- 6 files changed, 251 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb new file mode 100644 index 00000000000..17960d9a01a --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '5.1.5' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' + +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-8.0-linux-x64-v5.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-8.0-linux-x64-v5.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['a87cb2df2e5e7cc0a05e266734e679ee1a2fadad6f06af82a76ed81a23b102c8'] + +dependencies = [('CUDA', cuda_version)] + +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb new file mode 100644 index 00000000000..67476fc06d1 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '6.0.21' # the version of the libcudnn.so provided +cuda_version = '7.5.18' # the latest matching CUDA +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' + +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-7.0-linux-x64-v6.tgz, rename to cudnn-7.0-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-7.0-linux-x64-v6.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['568d4b070c5f91ab8a15b287b73dd072b99c7267a43edad13f70337cd186c82c'] + +dependencies = [('CUDA', cuda_version)] + +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb new file mode 100644 index 00000000000..7951558cd5e --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '6.0.21' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' + +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-8.0-linux-x64-v6.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-8.0-linux-x64-v6.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c'] + +dependencies = [('CUDA', cuda_version)] + +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb new file mode 100644 index 00000000000..6f8c0065641 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' + +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-8.0-linux-x64-v7.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-8.0-linux-x64-v7.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['9e0b31735918fe33a79c4b3e612143d33f48f61c095a3b993023cdab46f6d66e'] + +dependencies = [('CUDA', cuda_version)] + +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb new file mode 100644 index 00000000000..16d8e230f47 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Stephane Thiell +## +easyblock = 'Tarball' + +name = 'cuDNN' +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '9.0.176' # the latest matching CUDA +cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % cuda_version + +homepage = 'https://developer.nvidia.com/cudnn' + +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# Nvidia developer registration required. +# Download link: https://developer.nvidia.com/rdp/cudnn-download +# Download as cudnn-9.0-linux-x64-v7.tgz, rename to cudnn-9.0-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-9.0-linux-x64-v7.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] + +dependencies = [('CUDA', cuda_version)] + +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + +sanity_check_paths = { + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb index 6318c9eeb44..f0921ee25f5 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb @@ -6,30 +6,41 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '7.0.5' -cuda_version = '9.1.85' - +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '9.1.85' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) - versionsuffix = '-CUDA-%s' % cuda_version homepage = 'https://developer.nvidia.com/cudnn' -description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for - deep neural networks.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +description = """ + The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated + library of primitives for deep neural networks. +""" + +toolchain = {'name': 'dummy', 'version': ''} # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -# Download as cudnn-9.0-linux-x64-v7.tgz, rename to cudnn-9.0-linux-x64-v.tgz +# Download as cudnn-9.1-linux-x64-v7.tgz, rename to cudnn-9.1-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-9.1-linux-x64-v7.tgz with different %(version)s libraries +# so use the checksum to verify and modify as needed. sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] checksums = ['1ead5da7324db35dcdb3721a8d4fc020b217c68cdb3b3daa1be81eb2456bd5e5'] dependencies = [('CUDA', cuda_version)] +postinstallcmds = [ + # toss duplicates and create symlinks instead + 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), + 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), +] + sanity_check_paths = { - 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a'], - 'dirs': ['include', 'lib64'], + 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], + 'dirs': [], } moduleclass = 'numlib' From 965e3ccf502e01ad5614287b59798a8cf9a9e56b Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 25 Mar 2018 12:03:42 -0500 Subject: [PATCH 018/698] missed some style-checks - was cleanups for cuDNN --- easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb | 4 ++-- easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb | 4 ++-- easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb | 4 ++-- easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb | 4 ++-- easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb | 4 ++-- easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb | 4 ++-- 6 files changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb index 17960d9a01a..f3b966f8e73 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '5.1.5' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA +version = '5.1.5' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb index 67476fc06d1..d913751c0af 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '6.0.21' # the version of the libcudnn.so provided -cuda_version = '7.5.18' # the latest matching CUDA +version = '6.0.21' # the version of the libcudnn.so provided +cuda_version = '7.5.18' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb index 7951558cd5e..c9b5c1049ae 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '6.0.21' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA +version = '6.0.21' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb index 6f8c0065641..d56e0073310 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '7.0.5' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '8.0.44' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb index 16d8e230f47..7bb5e9b2f45 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '7.0.5' # the version of the libcudnn.so provided -cuda_version = '9.0.176' # the latest matching CUDA +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '9.0.176' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb index f0921ee25f5..dbdd894cf99 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.1.85.eb @@ -6,8 +6,8 @@ easyblock = 'Tarball' name = 'cuDNN' -version = '7.0.5' # the version of the libcudnn.so provided -cuda_version = '9.1.85' # the latest matching CUDA +version = '7.0.5' # the version of the libcudnn.so provided +cuda_version = '9.1.85' # the latest matching CUDA cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) versionsuffix = '-CUDA-%s' % cuda_version From 385a32ee5abb430e00b2b1041c81242c1ece2743 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Sun, 25 Mar 2018 12:15:31 -0500 Subject: [PATCH 019/698] minor cleanup --- easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb index d913751c0af..c2a3f5a7a18 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb @@ -22,8 +22,8 @@ toolchain = {'name': 'dummy', 'version': ''} # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download -# Download as cudnn-7.0-linux-x64-v6.tgz, rename to cudnn-7.0-linux-x64-v%(version)s.tgz -# Note, NVIDIA may release another cudnn-7.0-linux-x64-v6.tgz with different %(version)s libraries +# Download as cudnn-7.5-linux-x64-v6.tgz, rename to cudnn-7.5-linux-x64-v%(version)s.tgz +# Note, NVIDIA may release another cudnn-7.5-linux-x64-v6.tgz with different %(version)s libraries # so use the checksum to verify and modify as needed. sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] checksums = ['568d4b070c5f91ab8a15b287b73dd072b99c7267a43edad13f70337cd186c82c'] From 96257747d4fd2437185c84abbdd7b7603135d00b Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 27 Mar 2018 21:19:59 +0200 Subject: [PATCH 020/698] added checksums --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb index 0d32c2f03d4..b4d197f457d 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = ['https://github.com/samtools/bcftools/releases/download/%(version)s/'] sources = [SOURCELOWER_TAR_BZ2] +checksums = ['12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924'] dependencies = [ ('zlib', '1.2.8'), From 88b4c6ced11faacb0cae1621966e4f3bbe3c9539 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Thu, 12 Apr 2018 16:33:41 -0700 Subject: [PATCH 021/698] add NAMD-2.12 with gpu support --- .../NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb new file mode 100644 index 00000000000..31a54251323 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -0,0 +1,28 @@ +name = 'NAMD' +version = '2.12' +versionsuffix = '-CUDA-8.0.61' + +homepage = 'http://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': 'NAMD_%(version)s_Source.tar.gz', + 'extract_cmd': "tar xfv %s", # source file is actually not gzipped +}] +checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] + +dependencies = [ + ('Tcl', '8.6.5'), + ('CUDA', '8.0.61_375.26'), +] + +# /bin/csh is required by 'config' script +osdependencies = ['tcsh'] + +charm_arch = "multicore-linux64" # CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance. + +moduleclass = 'chem' From ee443c91a80a8a2110e263330976263f7f366a12 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Thu, 12 Apr 2018 17:20:18 -0700 Subject: [PATCH 022/698] fix line too long --- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb index 31a54251323..a4572c98422 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -23,6 +23,6 @@ dependencies = [ # /bin/csh is required by 'config' script osdependencies = ['tcsh'] -charm_arch = "multicore-linux64" # CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance. +charm_arch = "multicore-linux64" #CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance moduleclass = 'chem' From 172949bbce784e78d5e78abbfceaf468028bbf32 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Thu, 12 Apr 2018 17:48:51 -0700 Subject: [PATCH 023/698] fix style --comment should start with '# '-- --- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb index a4572c98422..b839d35d382 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -23,6 +23,6 @@ dependencies = [ # /bin/csh is required by 'config' script osdependencies = ['tcsh'] -charm_arch = "multicore-linux64" #CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance +charm_arch = 'multicore-linux64' # CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance moduleclass = 'chem' From ab6178bad34cab313a8e3253733e617cc54ea726 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Thu, 12 Apr 2018 18:11:11 -0700 Subject: [PATCH 024/698] remove comment --- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb index b839d35d382..e779b65b09d 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -23,6 +23,6 @@ dependencies = [ # /bin/csh is required by 'config' script osdependencies = ['tcsh'] -charm_arch = 'multicore-linux64' # CUDA builds require non-MPI SMP or multicore Charm++ arch for reasonable performance +charm_arch = 'multicore-linux64' moduleclass = 'chem' From c1d2bdc01d7d6d41bce3f0d9295eb5719819b935 Mon Sep 17 00:00:00 2001 From: Shail Date: Mon, 16 Apr 2018 17:25:57 -0500 Subject: [PATCH 025/698] adding easyconfigs: pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb --- ..._python-4.6.0-intel-2017a-Python-2.7.13.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb new file mode 100644 index 00000000000..f0082c99d44 --- /dev/null +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'pbs_python' +version = '4.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://oss.trac.surfsara.nl/pbs_python' +description = """The pbs_python package is a wrapper class for the Torque C library. With this package you now can + write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by + an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of + the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ...""" + +toolchain = {'name': 'intel', 'version': '2017a'} + +source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +sources = [SOURCE_TAR_GZ] + +patches = [ + 'pbs_python-%(version)s_CC.patch', + 'pbs_python-%(version)s_remove-printf.patch', +] + +dependencies = [('Python', '2.7.13')] + +osdependencies = ['torque-devel'] + +# this is needed for setup.py script +configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' +preinstallopts = prebuildopts + +pythonpath = 'lib/python%(pyshortver)s/site-packages' +modextrapaths = {'PYTHONPATH': pythonpath} + +sanity_check_paths = { + 'files': [], + 'dirs': ["%s/pbs" % pythonpath] +} + +moduleclass = 'tools' From e1ce2269772159f2365eab9f3a9c76d2454ee43a Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 09:42:43 -0500 Subject: [PATCH 026/698] adding easyconfigs: libav-11.10-GCCcore-6.4.0.eb --- .../l/libav/libav-11.10-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..a948fdf2cd0 --- /dev/null +++ b/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libav' +version = '11.10' + +homepage = 'https://libav.org/' + +description = """ + Libav is a friendly and community-driven effort to provide its users with + a set of portable, functional and high-performance libraries for dealing + with multimedia formats of all sorts. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# https://libav.org/releases/libav-11.9.tar.gz +source_urls = ['https://libav.org/releases/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['5437d8861c3c34f0d258105a370ee61e4e2cc72898b1f577c50304d24d79f4e0'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('NASM', '2.13.01'), + ('zlib', '1.2.11'), +] + +moduleclass = 'vis' From 1f1ad47eff3ba7c9f651737b202f15ee885bcaab Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 13:15:31 -0500 Subject: [PATCH 027/698] adding easyconfigs: SDL_image-1.2.12-GCCcore-6.4.0.eb --- .../l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb | 28 ++++++++++++ .../s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb | 45 +++++++++++++++++++ .../SDL_image-1.2.12-GCCcore-6.4.0.eb | 38 ++++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..07e8e291ead --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.8' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] + +builddependencies = [('binutils', '2.28')] + +dependencies = [ + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..6cef40b4f7d --- /dev/null +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb @@ -0,0 +1,45 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'SDL' +version = '1.2.15' + +homepage = 'http://www.libsdl.org/' + +description = """ + SDL: Simple DirectMedia Layer, a cross-platform multimedia library +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +# http://www.libsdl.org/release/SDL-1.2.15.tar.gz +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +patches = ['SDL-1.2.15-91ad7b43317a.patch'] # from: https://bugzilla.libsdl.org/show_bug.cgi?id=1769 +checksums = [ + 'd6d316a793e5e348155f0dd93b979798933fb98aa1edebcc108829d6474aad00', # SDL-1.2.15.tar.gz + '04fa6aaf1ae1043e82d85f367fdb3bea5532e60aa944ce17357030ee93bb856c', # SDL-1.2.15-91ad7b43317a.patch +] + +builddependencies = [ + ('Autotools', '20170619'), + ('binutils', '2.28'), +] + +dependencies = [ + ('X11', '20180131'), +] + +preconfigopts = """ + ./autogen.sh # else we get error: conflicting types for ‘_XData32’ +""" + +sanity_check_paths = { + 'dirs': ['bin', 'include/SDL', 'lib/pkgconfig', 'share/man/man3'], + 'files': ['bin/sdl-config', 'lib/libSDL.%s' % SHLIB_EXT], +} + +moduleclass = 'lib' +# EOF diff --git a/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..b206c5194f8 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb @@ -0,0 +1,38 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'SDL_image' +version = '1.2.12' + +homepage = 'https://www.libsdl.org/projects/SDL_image/release-1.2.html' + +description = """ + SDL_image is an image file loading library. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# https://www.libsdl.org/projects/SDL_image/release/SDL_image-1.2.12.tar.gz +source_urls = ['https://www.libsdl.org/projects/%(name)s/release'] +sources = [SOURCE_TAR_GZ] +checksums = ['0b90722984561004de84847744d566809dbb9daf732a9e503b91a1b5a84e5699'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('SDL', '1.2.15'), +] + +sanity_check_paths = { + 'files': ['include/SDL/SDL_image.h', 'lib/libSDL_image.so', + 'lib/pkgconfig/SDL_image.pc'], + 'dirs': [] +} + +moduleclass = 'vis' From 99d752dbca34c95de0b435d1e54ef43a6aa80bc1 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 13:19:54 -0500 Subject: [PATCH 028/698] adding easyconfigs: SDL2_image-2.0.3-GCCcore-6.4.0.eb --- .../l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb | 28 +++++++++++++ .../s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ .../SDL2_image-2.0.3-GCCcore-6.4.0.eb | 38 +++++++++++++++++ 3 files changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..07e8e291ead --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.8-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.8' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0b74e51595654f958148759cfef0993114ddccccbb6f31aee018f3558e8e2732'] + +builddependencies = [('binutils', '2.28')] + +dependencies = [ + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..27d85839871 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'SDL2' +version = '2.0.8' + +homepage = 'http://www.libsdl.org/' + +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# http://www.libsdl.org/release/SDL2-2.0.8.tar.gz +source_urls = ['http://www.libsdl.org/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['edc77c57308661d576e843344d8638e025a7818bff73f8fbfab09c3c5fd092ec'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('X11', '20180131'), +] + +sanity_check_paths = { + 'files': ['bin/sdl2-config', 'lib/libSDL2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..0adc78ec7f6 --- /dev/null +++ b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb @@ -0,0 +1,38 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'SDL2_image' +version = '2.0.3' + +homepage = 'https://www.libsdl.org/projects/SDL_image/' + +description = """ + SDL_image is an image file loading library. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +# https://www.libsdl.org/projects/SDL_image/release/SDL2_image-2.0.3.tar.gz +source_urls = ['https://www.libsdl.org/projects/SDL_image/release'] +sources = [SOURCE_TAR_GZ] +checksums = ['3510c25da735ffcd8ce3b65073150ff4f7f9493b866e85b83738083b556d2368'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('SDL2', '2.0.8'), +] + +sanity_check_paths = { + 'files': ['include/SDL2/SDL_image.h', 'lib/libSDL2_image.so', + 'lib/pkgconfig/SDL2_image.pc'], + 'dirs': [] +} + +moduleclass = 'vis' From e1e201c5bac716d0201c057b3804e3ca124e0176 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 13:47:30 -0500 Subject: [PATCH 029/698] adding easyconfigs: PCRE-8.42-GCCcore-6.4.0.eb --- .../p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..98d5303a0a2 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.42' + +homepage = 'http://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['69acbc2fbdefb955d42a4c606dfde800c2885711d2979e356c0636efde9ec3b5'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' From 9875abc9b831e46474da46412aa38dd10eefb1f8 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 13:55:19 -0500 Subject: [PATCH 030/698] adding easyconfigs: HTSlib-1.8-GCCcore-6.4.0.eb --- .../c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb | 49 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb | 43 ++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..606c3eb444b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.59.0' + +homepage = 'http://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0e') + ('zlib', '1.2.11'), +] + +configopts = '--with-zlib=$EBROOTZLIB' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8a4b5b4494f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.8' + +homepage = "http://www.htslib.org/" + +description = """ + A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('cURL', '7.59.0'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 49c0ec0916aa77ed8831d1252ea4be033a25edeb Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 14:08:08 -0500 Subject: [PATCH 031/698] update easybuilder URL --- easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb index 27d85839871..f48f27a6cff 100644 --- a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb @@ -1,5 +1,5 @@ ## -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# This file is an EasyBuild reciPY as per http://easybuilders.github.io/easybuild # # Copyright:: Copyright 2012-2014 Uni.Lu, NTUA # Authors:: Fotis Georgatos From bcde99136f4e327c6069deb9315c3a753b6bf24e Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 14:27:22 -0500 Subject: [PATCH 032/698] include patch --- .../s/SDL/SDL-1.2.15-91ad7b43317a.patch | 60 +++++++++++++++++++ .../s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb | 4 +- 2 files changed, 62 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/SDL/SDL-1.2.15-91ad7b43317a.patch diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-91ad7b43317a.patch b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-91ad7b43317a.patch new file mode 100644 index 00000000000..df5d4b37caa --- /dev/null +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-91ad7b43317a.patch @@ -0,0 +1,60 @@ +# From: https://bugzilla.libsdl.org/show_bug.cgi?id=1769 +# +# HG changeset patch +# User Azamat H. Hackimov +# Date 1370184533 -21600 +# Branch SDL-1.2 +# Node ID 91ad7b43317a6387e115ecdf63a49137f47e42c8 +# Parent f7fd5c3951b9ed922fdf696f7182e71b58a13268 +Fix compilation with libX11 >= 1.5.99.902. + +These changes fixes bug #1769 for SDL 1.2 +(http://bugzilla.libsdl.org/show_bug.cgi?id=1769). + +diff -r f7fd5c3951b9 -r 91ad7b43317a configure.in +--- a/configure.in Wed Apr 17 00:56:53 2013 -0700 ++++ b/configure.in Sun Jun 02 20:48:53 2013 +0600 +@@ -1169,6 +1169,17 @@ + if test x$definitely_enable_video_x11_xrandr = xyes; then + AC_DEFINE(SDL_VIDEO_DRIVER_X11_XRANDR) + fi ++ AC_MSG_CHECKING(for const parameter to _XData32) ++ have_const_param_xdata32=no ++ AC_TRY_COMPILE([ ++ #include ++ extern int _XData32(Display *dpy,register _Xconst long *data,unsigned len); ++ ],[ ++ ],[ ++ have_const_param_xdata32=yes ++ AC_DEFINE(SDL_VIDEO_DRIVER_X11_CONST_PARAM_XDATA32) ++ ]) ++ AC_MSG_RESULT($have_const_param_xdata32) + fi + fi + } +diff -r f7fd5c3951b9 -r 91ad7b43317a include/SDL_config.h.in +--- a/include/SDL_config.h.in Wed Apr 17 00:56:53 2013 -0700 ++++ b/include/SDL_config.h.in Sun Jun 02 20:48:53 2013 +0600 +@@ -283,6 +283,7 @@ + #undef SDL_VIDEO_DRIVER_WINDIB + #undef SDL_VIDEO_DRIVER_WSCONS + #undef SDL_VIDEO_DRIVER_X11 ++#undef SDL_VIDEO_DRIVER_X11_CONST_PARAM_XDATA32 + #undef SDL_VIDEO_DRIVER_X11_DGAMOUSE + #undef SDL_VIDEO_DRIVER_X11_DYNAMIC + #undef SDL_VIDEO_DRIVER_X11_DYNAMIC_XEXT +diff -r f7fd5c3951b9 -r 91ad7b43317a src/video/x11/SDL_x11sym.h +--- a/src/video/x11/SDL_x11sym.h Wed Apr 17 00:56:53 2013 -0700 ++++ b/src/video/x11/SDL_x11sym.h Sun Jun 02 20:48:53 2013 +0600 +@@ -165,7 +165,11 @@ + */ + #ifdef LONG64 + SDL_X11_MODULE(IO_32BIT) ++#if SDL_VIDEO_DRIVER_X11_CONST_PARAM_XDATA32 ++SDL_X11_SYM(int,_XData32,(Display *dpy,register _Xconst long *data,unsigned len),(dpy,data,len),return) ++#else + SDL_X11_SYM(int,_XData32,(Display *dpy,register long *data,unsigned len),(dpy,data,len),return) ++#endif + SDL_X11_SYM(void,_XRead32,(Display *dpy,register long *data,long len),(dpy,data,len),) + #endif + diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb index 6cef40b4f7d..df61b21a554 100644 --- a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb @@ -20,7 +20,7 @@ sources = [SOURCE_TAR_GZ] patches = ['SDL-1.2.15-91ad7b43317a.patch'] # from: https://bugzilla.libsdl.org/show_bug.cgi?id=1769 checksums = [ 'd6d316a793e5e348155f0dd93b979798933fb98aa1edebcc108829d6474aad00', # SDL-1.2.15.tar.gz - '04fa6aaf1ae1043e82d85f367fdb3bea5532e60aa944ce17357030ee93bb856c', # SDL-1.2.15-91ad7b43317a.patch + '48e6afdad171e896e81d7d7aa610a54f0f51175423c5093efe083c70b5219151', # SDL-1.2.15-91ad7b43317a.patch ] builddependencies = [ @@ -33,7 +33,7 @@ dependencies = [ ] preconfigopts = """ - ./autogen.sh # else we get error: conflicting types for ‘_XData32’ + ./autogen.sh # else we get error: conflicting types for ‘_XData32’... even with patch above """ sanity_check_paths = { From 54ecc24047f58d6567f24e275bcf6cdfb612fd32 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Thu, 19 Apr 2018 15:44:11 -0500 Subject: [PATCH 033/698] adding easyconfigs: BCFtools-1.8-GCCcore-6.4.0.eb --- .../b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb | 46 +++++++++++++++++ .../c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb | 49 +++++++++++++++++++ .../h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb | 43 ++++++++++++++++ 3 files changed, 138 insertions(+) create mode 100644 easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..31222b15021 --- /dev/null +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'BCFtools' +version = '1.8' + +homepage = 'http://www.htslib.org/' + +description = """ + Samtools is a suite of programs for interacting with high-throughput + sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and + calling/filtering/summarising SNP and short indel sequence variants +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('GSL', '2.4'), + ('HTSlib', '1.8'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-gsl\ + --with-htslib=$EBROOTHTSLIB\ +""" + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/plugins', + 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], + 'dirs': ['lib/plugins'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..606c3eb444b --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.59.0' + +homepage = 'http://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.0e') + ('zlib', '1.2.11'), +] + +configopts = '--with-zlib=$EBROOTZLIB' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8a4b5b4494f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# 1.4 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.8' + +homepage = "http://www.htslib.org/" + +description = """ + A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1'] + +builddependencies = [ + ('binutils', '2.28'), +] + +dependencies = [ + ('bzip2', '1.0.6'), + ('cURL', '7.59.0'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 4675e7adb41a54cf3b70286c6a744b42c97e2d8c Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Tue, 24 Apr 2018 17:06:48 -0700 Subject: [PATCH 034/698] Sista v4.0 with foss-2017b --- .../s/Siesta/Siesta-4.0-foss-2017b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb new file mode 100644 index 00000000000..63df1d1e13e --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb @@ -0,0 +1,18 @@ +name = 'Siesta' +version = '4.0' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'usempi': True} + +sources = [SOURCELOWER_TGZ] +vl = version.split('-') +source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] +checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] + +dependencies = [('netCDF-Fortran', '4.4.4')] + +moduleclass = 'phys' From 4ea5af6742cba1aa0428183d5656304652407056 Mon Sep 17 00:00:00 2001 From: Javier Ruiz Bosch Date: Thu, 26 Apr 2018 17:53:15 -0700 Subject: [PATCH 035/698] add a sha256 checksum and remove v1 --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb index 63df1d1e13e..f6e6f9bea2b 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb @@ -8,10 +8,9 @@ description = """SIESTA is both a method and its computer program implementation toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True} +source_urls = ['https://launchpad.net/siesta/%(version_major_minor)s/%(version)s/+download'] sources = [SOURCELOWER_TGZ] -vl = version.split('-') -source_urls = ['https://launchpad.net/siesta/%s/%%(version)s/+download' % vl[0]] -checksums = ['c4aa5f4cf2eabefaaacd3ef6350ec8fd'] +checksums = ['f974e0a17f622c3522cc287bec1ad9bae1f3306c15b3f375ff9f6b2172467a90'] dependencies = [('netCDF-Fortran', '4.4.4')] From 5182e99d516b43aa46e0542b9020b6ae6274ec76 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 May 2018 10:34:09 +0200 Subject: [PATCH 036/698] {geo}[intel/2017b] ESMValTool 1.1.0 (REVIEW) --- .../c/check/check-0.12.0-GCCore-6.4.0.eb | 31 + .../ESMValTool-1.1.0-Python-2.7.14.eb | 193 ++ .../e/ESMValTool/basemap-1.1.0_GEOS.patch | 15 + ...ecCodes-2.7.3-intel-2017b-Python-2.7.14.eb | 42 + .../libmo_unpack-3.1.2-GCCore-6.4.0.eb | 33 + ...libmo_unpack-3.1.2_cmake_have_stdint.patch | 9 + ....3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 1791 +++++++++++++++++ 7 files changed, 2114 insertions(+) create mode 100644 easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb create mode 100644 easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/e/ESMValTool/basemap-1.1.0_GEOS.patch create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2017b-Python-2.7.14.eb create mode 100644 easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2_cmake_have_stdint.patch create mode 100644 easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb diff --git a/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb b/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb new file mode 100644 index 00000000000..8b3f74b6a9d --- /dev/null +++ b/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'check' +version = '0.12.0' + +homepage = 'https://libcheck.github.io/check/' +description = """Check is a unit testing framework for C. + It features a simple interface for defining unit tests, + putting little in the way of the developer. Tests are run + in a separate address space, so both assertion failures + and code errors that cause segmentation faults or other + signals can be caught. Test results are reportable in + the following: Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/libcheck/check/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['7816b4c38f6e23ff873786f18d966e552837677bfae144041e0587e7c39e04e8'] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.10.1'), +] + +sanity_check_paths = { + 'files': ['include/check.h', 'lib/libcheck.a', 'lib/libcompat.a'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb new file mode 100644 index 00000000000..729b9d77b65 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb @@ -0,0 +1,193 @@ +easyblock = 'PackedBinary' + +name = 'ESMValTool' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' +hdf5ver = '1.8.19' + +homepage = 'https://www.esmvaltool.org/' +description = """The Earth System Model eValuation Tool (ESMValTool) + is a community diagnostics and performance metrics tool + for the evaluation of Earth System Models (ESMs) that + allows for routine comparison of single or multiple models, + either against predecessor versions or against observations.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ESMValGroup/ESMValTool/archive/'] +sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'v%(version)s.tar.gz'}] +checksums = ['457d5a7e72165a31532b335c42b925abaaa48e959d32b123463df77318c73c36'] + +dependencies = [ + ('Python', '2.7.14'), + ('NCL', '6.4.0'), + ('R', '3.4.3', '-X11-20171023-HDF5-%s' % hdf5ver), + ('CDO', '1.9.1'), + ('GEOS', '3.6.2', versionsuffix), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.8'), + ('freetype', '2.8'), + ('PROJ', '4.9.3'), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5ver), + ('GDAL', '2.2.2', '-Python-%%(pyver)s-HDF5-%s' % hdf5ver), + ('libmo_unpack', '3.1.2', '', ('GCCcore', '6.4.0')), + ('ecCodes', '2.7.3', versionsuffix), +] + +# Python deps, order is important! +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', +} + +exts_classmap = {'ncdf4': 'RPackage'} +exts_list = [ + ('olefile', '0.45.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/o/olefile/'], + 'checksums': ['2b6575f5290de8ab1086f8c5490591f7e0885af682c7c1793bdaf6e64078d385'], + }), + ('Pillow', '4.3.0', { + 'modulename': 'PIL', + 'source_urls': ['https://pypi.python.org/packages/source/p/Pillow/'], + 'checksums': ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'], + }), + ('pyproj', '1.9.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj/'], + 'checksums': ['53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8'], + }), + ('pyshp', '1.2.12', { + 'modulename': 'shapefile', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp/'], + 'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('urllib3', '1.22', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], + }), + ('certifi', '2018.4.16', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], + }), + ('requests', '2.18.4', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], + }), + ('OWSLib', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/o/OWSLib/'], + 'checksums': ['ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554'], + }), + ('basemap', '1.1.0', { + 'modulename': 'mpl_toolkits.basemap', + 'patches': ['basemap-1.1.0_GEOS.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/matplotlib/basemap/archive'], + 'checksums': [ + '6acdc3a08bfcebf0a1b52a05d73d51b7aa5e7240fedfa95537c92d16f2ef8778', # v1.1.0.tar.gz + '7988beb0c591d7a42e470e0dea360ebbd29a902d0a2f75bb719271ba0710fdd8', # basemap-1.1.0_GEOS.patch + ], +# 'custom_commands': ["python -c 'from mpl_toolkits.basemap import Basemap'"], + }), + ('netCDF4', '1.3.1', { + 'modulename': 'netCDF4', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4/'], + 'checksums': ['570ea59992aa6d98a9b672c71161d11ba5683f787da53446086077470a869957'], + }), + ('geoval', '0.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/g/geoval/'], + 'checksums': ['7da4a1879f78bb7aac2d41b5c1ee360ff74087bf857c81c532deb8cc31feb36e'], + }), + ('cdo', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cdo/'], + 'checksums': ['b167efbbac7d0a6cbf74f5d211255705c73245f7c2590b6d9eb634347d8b2c1f'], + }), + ('Shapely', '1.6.4.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], + 'checksums': ['30df7572d311514802df8dc0e229d1660bc4cbdcf027a8281e79c5fc2fcf02f2'], + }), + ('Cartopy', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/Cartopy/'], + 'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'], + }), + ('dask', '0.17.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask/'], + 'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'], + }), + ('PyKE', '1.1.1', { + 'source_tmpl': 'pyke-1.1.1.zip', + 'source_urls': ['http://download.sourceforge.net/pyke'], + 'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'], + }), + ('cf_units', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'], + 'checksums': ['abdd2a0937b958322f7ff7ec6866e80f08603c60aa06cef5766b6512c750028a'], + }), + ('pyugrid', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'], + 'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'], + }), + ('mo_pack', '0.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/mo_pack/archive/'], + 'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('tornado', '4.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'], + }), + ('matplotlib', '1.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + 'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'], + }), + ('toolz', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'], + 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], + }), + ('scitools-iris', '2.0.0', { + 'modulename': 'iris', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/iris/archive/'], + 'checksums': ['8605ab92c67d622e83fff6d7169fe154d9f8610edd8463b697b574884c158ba2'], + }), + ('iris-grib', '0.12.0', { + 'modulename': 'iris_grib', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/iris-grib/archive/'], + 'checksums': ['c2e92d25d8bfd2ddff22ae47c4532c884678bac6ea0d935367eced051ae08bb3'], + }), + ('ncdf4', '1.16', { + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', + 'http://cran.r-project.org/src/contrib/', + 'http://cran.freestatistics.org/src/contrib', + ], + 'checksums': ['edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'R_LIBS': '', +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ESMValTool/basemap-1.1.0_GEOS.patch b/easybuild/easyconfigs/e/ESMValTool/basemap-1.1.0_GEOS.patch new file mode 100644 index 00000000000..e485bfd1bc9 --- /dev/null +++ b/easybuild/easyconfigs/e/ESMValTool/basemap-1.1.0_GEOS.patch @@ -0,0 +1,15 @@ +# Pick EB installed GOES location +# May 14th, 2018 by B. Hajgato (Free University Brussels - VUB) +--- basemap-1.1.0/setup.py.orig 2017-05-04 22:53:42.000000000 +0200 ++++ basemap-1.1.0/setup.py 2018-05-14 22:56:12.370184105 +0200 +@@ -38,8 +38,8 @@ + return geos_version + + # get location of geos lib from environment variable if it is set. +-if 'GEOS_DIR' in os.environ: +- GEOS_dir = os.environ.get('GEOS_DIR') ++if 'EBROOTGEOS' in os.environ: ++ GEOS_dir = os.environ.get('EBROOTGEOS') + else: + # set GEOS_dir manually here if automatic detection fails. + GEOS_dir = None diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..c9636f03290 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.7.3-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.7.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +source_urls = ['https://software.ecmwf.int/wiki/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['6fab143dbb34604bb2e04d10143855c0906b00411c1713fd7ff5c35519b871db'] + +builddependencies = [('CMake', '3.10.1')] + +dependencies = [ + ('Python', '2.7.14'), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('JasPer', '1.900.1'), + ('netCDF', '4.4.1.1', '-HDF5-1.8.19'), +] + +separate_build_dir = True + +configopts = '-DENABLE_PNG=ON ' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['bufr_copy', 'bufr_dump', 'bufr_filter', 'bufr_ls', + 'codes_count', 'codes_info', 'codes_split_file', + 'grib_copy', 'grib_dump', 'grib_filter', 'grib_ls']], + 'dirs': [], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb new file mode 100644 index 00000000000..d8688a45528 --- /dev/null +++ b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libmo_unpack' +version = '3.1.2' + +homepage = "https://github.com/SciTools/libmo_unpack" +description = "A library for handling the WGDOS and RLE compression schemes used in UM files." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/SciTools/libmo_unpack/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_cmake_have_stdint.patch'] +checksums = [ + 'e09ef3e6f1075144acc5d6466b4ef70b2fe32ed4ab1840dd4fb7e15a40f3d370', # v3.1.2.tar.gz + 'b130f9944e763c53b21c2b08f6d4954ca7811a556fda1c7fec737a4086aad1f5', # libmo_unpack-3.1.2_cmake_have_stdint.patch +] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.10.1'), + ('check', '0.12.0'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/logerrors.h', 'include/rlencode.h', 'include/wgdosstuff.h', 'lib/libmo_unpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2_cmake_have_stdint.patch b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2_cmake_have_stdint.patch new file mode 100644 index 00000000000..00f2c985aba --- /dev/null +++ b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2_cmake_have_stdint.patch @@ -0,0 +1,9 @@ +# Header only included if HAVE_STEDINT_H macro is set +# May 8th 2018 by B. Hajgato (Free University Brussels - VUB) +--- libmo_unpack-3.1.2/tests/CMakeLists.txt.orig 2015-10-09 12:44:17.000000000 +0200 ++++ libmo_unpack-3.1.2/tests/CMakeLists.txt 2018-05-08 15:03:00.115085372 +0200 +@@ -6,3 +6,4 @@ + add_executable(test_rle check_rle.c) + target_link_libraries(test_rle ${LIBS}) + add_test(test_rle ${CMAKE_CURRENT_BINARY_DIR}/test_rle) ++set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DHAVE_STDINT_H") diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb new file mode 100644 index 00000000000..b4343f8b311 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -0,0 +1,1791 @@ +name = 'R' +version = '3.4.3' +x11ver = '20171023' +hdf5ver = '1.8.19' +versionsuffix = '-X11-%s-HDF5-%s' % (x11ver, hdf5ver) + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'intel', 'version': '2017b'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] +checksums = ['7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.2.4'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.10'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.20.1'), + ('PCRE', '8.41'), + ('libpng', '1.6.32'), # for plotting in R + ('libjpeg-turbo', '1.5.2'), # for plottting in R + ('LibTIFF', '4.0.8'), + ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.7'), # for tcltk + ('Tk', '8.6.7'), # for tcltk + ('cURL', '7.56.0'), # for RCurl + ('libxml2', '2.9.4'), # for XML + ('GDAL', '2.2.2', '-Python-2.7.14-HDF5-%s' % hdf5ver), # for rgdal + ('PROJ', '4.9.3'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.6'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'http://cran.r-project.org/src/contrib/', # current version of packages + 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on Dec 4th 2017 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-6', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + 'checksums': [ + 'd8fc09ad38264697caa86079885a7a1098921a3116d5a77a62022b9508f8a63a', # Rmpi_0.6-6.tar.gz + 'f753f0b6434295be70fe29d36edb2047c091e465b7ff0cab56b93d55883c8dd3', # Rmpi-0.6-5_impi5.patch + ], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-6', { + 'checksums': ['1b6c3f5bef0ddc28c4b68894051df5d9c0d4985d9e6ad81892369d0f7fe0298d'], + }), + ('geometry', '0.3-6', { + 'patches': ['geometry-0.3-4-icc.patch'], + 'checksums': [ + '2be231ac99171367635cd957f27da77705329df97520ab86f655839c41dc0968', # geometry_0.3-6.tar.gz + 'df0ea118e597f31561093e01d50698dac3345d40d082eee05360bb4f94378377', # geometry-0.3-4-icc.patch + ], + }), + ('bit', '1.1-12', { + 'checksums': ['ce281c87fb7602bf1a599e72f3e25f9ff7a13e390c124a4506087f69ad79d128'], + }), + ('filehash', '2.4-1', { + 'checksums': ['d0e087d338d89372c251c18fc93b53fb24b1750ea154833216ff16aff3b1eaf4'], + }), + ('ff', '2.2-13', { + 'checksums': ['8bfb08afe0651ef3c23aaad49208146d5f929af5af12a25262fe7743fa346ddb'], + }), + ('bnlearn', '4.2', { + 'checksums': ['ca63bee9ceb54a7667b465f3f1ed4cbd3f67787f928d506ecf330ea6d1773fcd'], + }), + ('bootstrap', '2017.2', { + 'checksums': ['44f118c90ee226730175c467a16ac8d5b3169d610424e613da4f73348fd79522'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-37', { + 'checksums': ['aadfadfd85792b129063d02d5604dbd1afa5aacd2a6ec7eff7458edf2b5dc2da'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.5', { + 'checksums': ['874c197ae3720ec11b44984a055655b99a698e1912104eb9034c11fdf6104da7'], + }), + ('gtools', '3.5.0', { + 'checksums': ['86b6a51a92ddb3c78095e0c5dc20414c67f6e28f915bf0ee11406adad3e476f6'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03', { + 'checksums': ['dfb84f92508765c74b170bb5bb2b206a11d10fdb4a74473821b0e51cec5d3ac0'], + }), + ('highr', '0.6', { + 'checksums': ['43e152b2dea596df6e14c44398c74fcd438ece15eaae5bdb84aef8d61b213b59'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-15', { + 'checksums': ['7a4a33ad77ad5dc973413745b5626856485c1c63a984f2182ccf5d0cec7eb8dd'], + }), + ('kernlab', '0.9-25', { + 'checksums': ['b9de072754bb03c02c4d6a5ca20f2290fd090de328b55ab334ac0b397ac2ca62'], + }), + ('mime', '0.5', { + 'checksums': ['fcc72115afb0eb43237da872754464f37ae9ae097f332ec7984149b5e3a82145'], + }), + ('markdown', '0.8', { + 'checksums': ['538fd912b2220f2df344c6cca58304ce11e0960de7bd7bd573b3385105d48fed'], + }), + ('mlbench', '2.1-1', { + 'checksums': ['748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6'], + }), + ('NLP', '0.1-11', { + 'checksums': ['580551a463c14d7186f62e029504f2e95dd9cbbaaef3f979221ddffafb036597'], + }), + ('mclust', '5.4', { + 'checksums': ['7363057845272a1c2b97c77c89704d9d21f3b4eb9b41b95d1c54018c110e7bc4'], + }), + ('RANN', 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['2c9fe648485c6b54c6f95a54b6e00ffe3cf06fa8c5c68f1d669664a7b91a0ede'], + }), + ('memoise', '1.1.0', { + 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], + }), + ('plogr', '0.1-1', { + 'checksums': ['22755c93c76c26252841f43195df31681ea865e91aa89726010bd1b9288ef48f'], + }), + ('bit64', '0.9-7', { + 'checksums': ['7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f'], + }), + ('blob', '1.1.0', { + 'checksums': ['16d6603df3ddba177f0ac4d9469c938f89131c4bf8834345db838defd9ffea16'], + }), + ('pkgconfig', '2.0.1', { + 'checksums': ['ab02b2a4b639ba94dcba882a059fe9cddae5498a4309841f764b62ec46ba5a40'], + }), + ('RSQLite', '2.0', { + 'patches': ['RSQLite-2.0-icc.patch'], + 'checksums': [ + '7f0fe629f34641c6af1e8a34412f3089ee2d184853843209d97ffe29430ceff6', # RSQLite_2.0.tar.gz + '828dd9aeb4f8aaff7bccb8671bee757b8001e049ed349d655044e9c916d1860d', # RSQLite-2.0-icc.patch + ], + }), + ('data.table', '1.10.4-3', { + 'checksums': ['ba8b4f1b96b16e7f9765fc49c5028f21ef2210fc46cf962f4f7ea7901f9d8a89'], + }), + ('BatchJobs', '1.7', { + 'checksums': ['49ef69adfb42f085c7ed143a80d78566d55d794ee9a1e1c83d85dbac2a2aa60c'], + }), + ('sandwich', '2.4-0', { + 'checksums': ['34315b9ced76a3ed109aead7b8f77eea6398a6eb2e1ad71515a48bed9808ccc0'], + }), + ('sfsmisc', '1.1-1', { + 'checksums': ['0eaab03d3023233f4e869616a5cbc58939f8ac8fa0f94ae1d1dd7d4fb95ff54b'], + }), + ('spatial', '7.3-11', { + 'checksums': ['624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11'], + }), + ('VGAM', '1.0-4', { + 'checksums': ['e581985f78ef8b866d0e810b2727061bb9c9bc177b2c9090aebb3a35ae87a964'], + }), + ('waveslim', '1.7.5', { + 'checksums': ['31b698f7b19aadcdc02068ee69bf7676cd9dea2913420ce3caa7e507e3a41a53'], + }), + ('xtable', '1.8-2', { + 'checksums': ['1623a1cde2e130fedb46f98840c3a882f1cbb167b292ef2bd86d70baefc4280d'], + }), + ('profileModel', '0.5-9', { + 'checksums': ['c94f25d222521867ddc86021bd0b9a6b9f7b055212985652a8511054b24c2bdd'], + }), + ('brglm', '0.6.1', { + 'checksums': ['b786db50edc703b1b6a986b1ce13d31aab76fd3c672a6540161b25f5cd57239f'], + }), + ('deSolve', '1.20', { + 'checksums': ['56e945835b0c66d36ebc4ec8b55197b616e387d990788a2e52e924ce551ddda2'], + }), + ('tseriesChaos', '0.1-13', { + 'checksums': ['efabf9c59548e2d22aa9763b340789d8e46e88c741ed4a831e52b1ed3bf35038'], + }), + ('tseries', '0.10-42', { + 'checksums': ['827f79858715c700e8cabd2c27853ba88ad0e05eb043bc94e126b155a75546c4'], + }), + ('fastICA', '1.2-1', { + 'checksums': ['6f2997dd766a544be3a3de2780df48ca67242ac7790a4a2882c417bfaa171f81'], + }), + ('R.methodsS3', '1.7.1', { + 'checksums': ['44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687'], + }), + ('R.oo', '1.21.0', { + 'checksums': ['645ceec2f815ed39650ca72db87fb4ece7357857875a4ec73e18bfaf647f431c'], + }), + ('cgdsr', '1.2.6', { + 'checksums': ['e862f85eec9384082a7755fd66e2a175c33a989cbda83e9a860453f7ce330217'], + }), + ('R.utils', '2.6.0', { + 'checksums': ['5d64993d1209b512a4e97f2edecdbc185f4a369ee5fa2e334ed2cf017486470e'], + }), + ('R.matlab', '3.6.1', { + 'checksums': ['1032579fd152d419eaf1f69bf6035fba7a71ef26e76136c48a6fc619e3887804'], + }), + ('gbm', '2.1.3', { + 'checksums': ['eaf24be931d762f1ccca4f90e15997719d01005f152160a3d20d858a0bbed92b'], + }), + ('Formula', '1.2-2', { + 'checksums': ['8def4600fb7457d38db8083733477501b54528974aa216e4adf8871bff4aa429'], + }), + ('acepack', '1.4.1', { + 'checksums': ['82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9'], + }), + ('proto', '1.0.0', { + 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], + }), + ('assertthat', '0.2.0', { + 'checksums': ['d73ef79b1e75293ed889a99571b237a95829c099f7da094d4763f83ea6fde5f2'], + }), + ('gridExtra', '2.3', { + 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], + }), + ('chron', '2.3-51', { + 'checksums': ['881745b713f93f000aea323fcd04d77c62e920de4b5ac9171c9bdbc45fb45f15'], + }), + ('viridis', '0.4.0', { + 'checksums': ['93d2ded68ed7cec5633c260dbc47051416147aae074f29ebe135cc329250b00e'], + }), + ('yaml', '2.1.15', { + 'checksums': ['14293d84cde0cc0e84f7600b7a55de9236fc93f84d018fa6a080cfe8afe386d8'], + }), + ('jsonlite', '1.5', { + 'checksums': ['6490371082a387cb1834048ad8cdecacb8b6b6643751b50298c741490c798e02'], + }), + ('htmltools', '0.3.6', { + 'checksums': ['44affb82f9c2fd76c9e2b58f9229adb003217932b68c3fdbf1327c8d74c868a2'], + }), + ('htmlwidgets', '0.9', { + 'checksums': ['1154b541ccd868e41d3cf0d7f188f7275ec99f61fe2c7de21c8a05edb19b985e'], + }), + ('knitr', '1.17', { + 'checksums': ['9484a2b2c7b0c2aae24ab7f4eec6db48affbceb0e42bd3d69e34d953fe92f401'], + }), + ('rstudioapi', '0.7', { + 'checksums': ['a541bc76ef082d2c27e42fd683f8262cb195b1497af3509178d2642870397a8c'], + }), + ('bindr', '0.1', { + 'checksums': ['cca166612eeafd6e1c961b34aaf177f9b47f8b4bc37520e277b9920eaa8b2535'], + }), + ('bindrcpp', '0.2', { + 'checksums': ['d0efa1313cb8148880f7902a4267de1dcedae916f28d9a0ef5911f44bf103450'], + }), + ('glue', '1.2.0', { + 'checksums': ['19275b34ee6a1bcad05360b7eb996cebaa1402f189a5dfb084e695d423f2296e'], + }), + ('dplyr', '0.7.4', { + 'checksums': ['7b1fc90750fbb46483423da6721832c545d37b157f4f3355784a65e50fada8c2'], + }), + ('purrr', '0.2.4', { + 'checksums': ['ed8d0f69d29b95c2289ae52be08a0e65f8171abb6d2587de7b57328bf3b2eb71'], + }), + ('tidyselect', '0.2.3', { + 'checksums': ['0c193abc8251a60e1d2a32a99c77651c336bc185e3c2a72e5f8781813d181c2c'], + }), + ('tidyr', '0.7.2', { + 'checksums': ['062cea2e2b57fffd500e4ce31cba6d593e65684fc0897ea49ea38d257c76009c'], + }), + ('htmlTable', '1.11.0', { + 'checksums': ['8ef7cc5c641a8424400d9767475ca9b745f190122d800425fae5bd68facf1874'], + }), + ('Hmisc', '4.0-3', { + 'checksums': ['5d395286d699bcabb6460c91798019d84b1cfa7a033841aa3ac5a02f4407e4fd'], + }), + ('fastcluster', '1.1.24', { + 'checksums': ['82c939b79dbaf00c79b01f19b09a8fadb9a949397b8f65bc861c552e0485b995'], + }), + ('registry', '0.5', { + 'checksums': ['5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb'], + }), + ('pkgmaker', '0.22', { + 'checksums': ['19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f'], + }), + ('rngtools', '1.2.4', { + 'checksums': ['27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9'], + }), + ('doParallel', '1.0.11', { + 'checksums': ['4ccbd2eb46d3e4f5251b0c3de4d93d9168b02bb0be493656d6aea236667ff76a'], + }), + ('gridBase', '0.4-7', { + 'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'], + }), + ('NMF', '0.20.6', { + 'checksums': ['a6539149d7f912057e2f87a78c0fa62dc44109609b3cf6180359c888db70cb7e'], + }), + ('irlba', '2.3.1', { + 'checksums': ['6082f8b5e32e9541747f0ac7d59f9e5a708b291492e9a21a5e4b9753e7ff94b5'], + }), + ('igraph', '1.1.2', { + 'checksums': ['89b16b41bc77949ea208419e52a18b78b5d418c7fedc52cd47d06a51a6e746ec'], + }), + ('GeneNet', '1.2.13', { + 'checksums': ['3798caac3bef7dc87f97b3628eb29eb12365d571ce0837b5b6285b0be655a270'], + }), + ('ape', '5.0', { + 'checksums': ['c32ed22e350b3d7c7ef3de9334155ab1f3086922b5ec9a1643897cae7abda960'], + }), + ('RJSONIO', '1.3-0', { + 'checksums': ['119334b7761c6c1c3cec52fa17dbc1b72eaebb520c53e68d873dea147cf48fb7'], + }), + ('caTools', '1.17.1', { + 'checksums': ['d32a73febf00930355cc00f3e4e71357412e0f163faae6a4bf7f552cacfe9af4'], + }), + ('gplots', '3.0.1', { + 'checksums': ['343df84327ac3d03494992e79ee3afc78ba3bdc08af9a305ee3fb0a38745cb0a'], + }), + ('ROCR', '1.0-7', { + 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], + }), + ('httpuv', '1.3.5', { + 'checksums': ['4336b993afccca2a194aca577b1975b89a35ac863423b18a11cdbb3f8470e4e9'], + }), + ('rjson', '0.2.15', { + 'checksums': ['77d00d8f6a1c936329b46f3b8b0be79a165f8c5f1989497f942ecc53dcf6f2ef'], + }), + ('sourcetools', '0.1.6', { + 'checksums': ['c9f48d2f0b7f7ed0e7fecdf8e730b0b80c4d567f0e1e880d118b0944b1330c51'], + }), + ('shiny', '1.0.5', { + 'checksums': ['20e25f3f72f3608a2151663f7836f2e0c6da32683a555d7541063ae7a935fa42'], + }), + ('seqinr', '3.4-5', { + 'checksums': ['162a347495fd52cbb62e8187a4692e7c50b9fa62123c5ef98f2744c98a05fb9f'], + }), + ('LearnBayes', '2.15', { + 'checksums': ['45c91114b4aaa0314feeb4311dbe78f5b75a3b76bb2d1ca0f8adb2e0f1cbe233'], + }), + ('deldir', '0.1-14', { + 'checksums': ['89d365a980ef8589971e5d311c6bd59fe32c48dbac8000a880b9655032c99289'], + }), + ('gmodels', '2.16.2', { + 'checksums': ['ab018894bdb376c5bd6bc4fbc4fe6e86590f4106795a586ef196fbb6699ec47d'], + }), + ('expm', '0.999-2', { + 'checksums': ['38f1e5bfa90f794486789695d0d9e49158c7eb9445dc171dd83dec3d8fa130d6'], + }), + ('spData', '0.2.6.7', { + 'checksums': ['773df2bd8d820e406402b9480e42219ad4eaa2119191b69ac6b777111d4dcf7b'], + }), + ('spdep', '0.7-4', { + 'checksums': ['9643f1e509e0107c8f8d949b0a6cbb6a274c7ca1e9ba4d474ce42235696653c7'], + }), + ('vegan', '2.4-5', { + 'checksums': ['ca8781ca46d5e014f10e8519b9bf3fdb29a93af9c64a900a27c24add87ddde33'], + }), + ('adegenet', '2.1.0', { + 'checksums': ['7ee44061002b41164bbc09256307ab02e536f4f2ac03f36c7dc8f85f6af4639a'], + }), + ('prettyunits', '1.0.2', { + 'checksums': ['35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c'], + }), + ('progress', '1.1.2', { + 'checksums': ['a9f4abfd9579b80967cd681041643fe9dfcc4eb3beeba45391bb64e9209baabb'], + }), + ('rncl', '0.8.2', { + 'checksums': ['80e1aa00cab4af0093198d0d902c973eb31dbdf4628e229ee9c136a9cc9c369e'], + }), + ('XML', '3.98-1.9', { + 'checksums': ['a3b70169cb2fbd8d61a41ff222d27922829864807e9ecad373f55ba0df6cf3c3'], + }), + ('crayon', '1.3.4', { + 'checksums': ['fc6e9bf990e9532c4fcf1a3d2ce22d8cf12d25a95e4779adfa17713ed836fa68'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('testthat', '1.0.2', { + 'checksums': ['0ef7df0ace1fddf821d329f9d9a5d42296085350ae0d94af62c45bd203c8415e'], + }), + ('rprojroot', '1.2', { + 'checksums': ['28b4d235ce67314528a0c1cc7e98faed42437b42e07fca18a59a80fdc3eefeb9'], + }), + ('rmarkdown', '1.8', { + 'checksums': ['e294b5d4dd6ea52471ba2ad151680fa05588f339d4d50393dbe6f6833a0e3e60'], + }), + ('openssl', '0.9.9', { + 'checksums': ['e7ece774305f1ef99bb645b209395bf02cf85b7ad26440e040f6f50cf47b27c7'], + }), + ('httr', '1.3.1', { + 'checksums': ['22134d7426b2eba37f0cc34b99285499b8bac9fe75a7bc3222fbad179bf8f258'], + }), + ('reshape', '0.8.7', { + 'checksums': ['2fa6c87d1e89f182e51bc5a4fcda3d42d83b8fb4474ca525fa7a8db5081f3992'], + }), + ('xml2', '1.1.1', { + 'checksums': ['00f3e3b66b76760c19da5f6dddc98e6f30de36a96b211e59e1a3f4ff58763116'], + }), + ('triebeard', '0.3.0', { + 'checksums': ['bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3'], + }), + ('urltools', '1.6.0', { + 'checksums': ['6b4e41948cd603b25099577a62df09c848f442d02cea63a12419025a3a42dbef'], + }), + ('httpcode', '0.2.0', { + 'checksums': ['fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a'], + }), + ('crul', '0.4.0', { + 'checksums': ['15d8ad380a171a3ee150d64fd1c1f9959785b15a51d3f4faa691916c873a6178'], + }), + ('bold', '0.5.0', { + 'checksums': ['f40963b847667cf8d69ba7ba3bd479bc117e1bc4df8bd1482a975dadff58b53d'], + }), + ('rredlist', '0.4.0', { + 'checksums': ['9e59d3c5830322ed85762bbb3273b59befe59c3feabfe7d2f32de96fc4525048'], + }), + ('rentrez', '1.1.0', { + 'checksums': ['8dd46c03cbb05d4a3e787b7fc9a1858fcbdf1bb0faf5ee438a4f2ea4dbca9d56'], + }), + ('rotl', '3.0.3', { + 'checksums': ['049a417ee10203339b3543fd97116b59de467344493f234d0d01c4b6ad7fd75d'], + }), + ('solrium', '1.0.0', { + 'checksums': ['0e362d4f3b700997bc417ea3ca21301ddbd7978ab3394affbe6861eb27308ee6'], + }), + ('ritis', '0.7.0', { + 'checksums': ['bb3a3243f83083e7dd874624e8dfb57953c8aea38df16b3e5c0163857e875d38'], + }), + ('worrms', '0.2.0', { + 'checksums': ['66f6238988b3deeecc1dee628979727c98b3db072b046e316ff8962192141bd7'], + }), + ('natserv', '0.1.4', { + 'checksums': ['07501608a2e79b20940cd0e22aca9db6150942eed5b6dad184ec957e153d8e63'], + }), + ('WikipediR', '1.5.0', { + 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], + }), + ('WikidataR', '1.4.0', { + 'checksums': ['64b1d53d7023249b73a77a7146adc3a8957b7bf3d808ebd6734795e9f58f4b2a'], + }), + ('wikitaxa', '0.1.4', { + 'checksums': ['ce646889a59d0f80da0b691dbab89754b1480224e39f4d2f618c02229165de34'], + }), + ('taxize', '0.9.0', { + 'checksums': ['62b45e5ea14c95ef6bbfa9bbdbd0aba6a99ebf12f03cd292b77954cca135251f'], + }), + ('uuid', '0.1-2', { + 'checksums': ['dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be'], + }), + ('RNeXML', '2.0.8', { + 'checksums': ['b2bc118a3982866d12aa880823a17e0247915a0fa265163a383bc26981d96d46'], + }), + ('phylobase', '0.8.4', { + 'checksums': ['d7c1a972c266ffe80345c7150608a85e6e2def4a3f079ac964ad9dbce2281002'], + }), + ('adephylo', '1.1-10', { + 'checksums': ['ccc22dd658aa23a4d12fce8909330da4e964ff59eea8b47d59ad8b2fe8b449c2'], + }), + ('animation', '2.5', { + 'checksums': ['b232fef1b318c79710e5e1923d87baba4c85ffe2c77ddb188130e0911d8cb55f'], + }), + ('bigmemory.sri', '0.1.3', { + 'checksums': ['55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155'], + }), + ('bigmemory', '4.5.31', { + 'patches': ['bigmemory-4.5.19_icpc-wd308.patch'], + 'checksums': [ + 'da51b2a7fa325d6aae481ff74c9c98df333785bccf81e64336aafc6fc8b96073', # bigmemory_4.5.31.tar.gz + 'cf673010f63baff60bf5fe4521a3740aa6891bcfb64c1979a8f1e1aa21532549', # bigmemory-4.5.19_icpc-wd308.patch + ], + }), + ('calibrate', '1.7.2', { + 'checksums': ['78066a564f57f2110f1752d681d6b97915cf73135134330587fff8b46c581604'], + }), + ('clusterGeneration', '1.3.4', { + 'checksums': ['7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa'], + }), + ('raster', '2.6-7', { + 'checksums': ['fb91804fd465a4a6d9d9858e29fd05f41a99b8efdcc5cf4370ea253b68e42b01'], + }), + ('dismo', '1.1-4', { + 'checksums': ['f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8'], + }), + ('extrafontdb', '1.0', { + 'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'], + }), + ('Rttf2pt1', '1.3.4', { + 'checksums': ['58dd29ba4f0c8fc879e7108359768a7b7fcb7d3f6b4ffd28fb3b1cb4d9938ca7'], + }), + ('extrafont', '0.17', { + 'checksums': ['2f6d7d79a890424b56ddbdced361f8b9ddede5edd33e090b816b88a99315332d'], + }), + ('fields', '9.0', { + 'checksums': ['9c7cb036b641731569412c36fa026a738f999fd85593531c1a2ad7fad80b533a'], + }), + ('shapefiles', '0.7', { + 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], + }), + ('fossil', '0.3.7', { + 'checksums': ['3feba6ceecaa6f2f68fdc1ceb0019395ccfadb0cf033e1709dddb690c7f210a1'], + }), + ('geiger', '2.0.6', { + 'checksums': ['e13b2c526378eaf9356b00bbe21b3c2c956327f8062fed638ccc1f49591c3eff'], + }), + ('glmnet', '2.0-13', { + 'checksums': ['f3288dcaddb2f7014d42b755bede6563f73c17bc87f8292c2ef7776cb9b9b8fd'], + }), + ('rgl', '0.98.1', { + 'checksums': ['5f49bed9e092e672f73c8a1a5365cdffcda06db0315ac087e95ab9c9c71a6986'], + }), + ('labdsv', '1.8-0', { + 'checksums': ['dfaeb03a6e1bab6cfd384c00671235b22f2b4254cac1129b24a348cb353b6e65'], + }), + ('stabs', '0.6-3', { + 'checksums': ['e961ae21d45babc1162b6eeda874c4e3677fc286fd06f5427f071ad7a5064a9f'], + }), + ('modeltools', '0.2-21', { + 'checksums': ['07b331475625674ab00e6ddfc479cbdbf0b22d5d237e8c25d83ddf3e0ad1cd7a'], + }), + ('strucchange', '1.5-1', { + 'checksums': ['740e2e20477b9fceeef767ae1002adc5ec397cb0f7daba5289a2c23b0dddaf31'], + }), + ('TH.data', '1.0-8', { + 'checksums': ['478f109fcc1226500ead8e3bd6e047cecde2294fde4df8ec216d38313db79a9d'], + }), + ('multcomp', '1.4-8', { + 'checksums': ['a20876619312310e9523d67e9090af501383ce49dc6113c6b4ca30f9c943a73a'], + }), + ('coin', '1.2-2', { + 'checksums': ['d518065d3e1eb00121cb4e0200e1e4ae6b68eca6e249afc38bbffa35d24105bb'], + }), + ('party', '1.2-3', { + 'checksums': ['6bd24b8f81e3d3b5bedfd41abf6245318f7bdaf42270093ec5f7c5b31c26f7e6'], + }), + ('mboost', '2.8-1', { + 'checksums': ['96a8b7daf5c6bc9240ad2e398867834ec18918c6cbdf64804ddc100a9b717798'], + }), + ('msm', '1.6.4', { + 'checksums': ['1efe0117fe80962eb14ba434a521f5f870185c04e58864925cd4dfad1e4b1040'], + }), + ('nor1mix', '1.2-3', { + 'checksums': ['435e6519e832ef5229c51ccb2619640e6b50dfc7470f70f0c938d18a114273af'], + }), + ('np', '0.60-3', { + 'checksums': ['ef84efa543a4d2de48c00b9c58558e68f8fe75e7722120b576d1b55420ac1f8a'], + }), + ('polynom', '1.3-9', { + 'checksums': ['d35a50925cc5552a6aac0816a91dbc03e9fd77da47e06d27572fde9dcbee9de8'], + }), + ('polspline', '1.1.12', { + 'checksums': ['fc6bd2e0cca8c13cf099c54fe1e740730e26bb9793d439c395cf16ec8c2b0f32'], + }), + ('rms', '5.1-1', { + 'checksums': ['c489948df5c434b40bcf5288844f5b4e08d157f36939d09230c1600f88d1bfe3'], + }), + ('RWekajars', '3.9.1-5', { + 'checksums': ['d0acb19b434b86eb9c0b8768f67e7e2d568c029541cb4ebc42c7009ee491be37'], + }), + ('RWeka', '0.4-36', { + 'checksums': ['69e31386502c3d721608b7b77610521c47b753d4cd47a8f3852153fbcaf6ab76'], + }), + ('slam', '0.1-40', { + 'checksums': ['afaca1d4712aa977028215d968c71c20c7de5663b2ce51cc217091af91c625b6'], + }), + ('tm', '0.7-2', { + 'checksums': ['e25b530eb45a4ed65369fbb031d2fe89c064b27da9cc12838f889f36619a4306'], + }), + ('TraMineR', '2.0-7', { + 'checksums': ['296f7af41dd7bed0413b15aa00a8d5e40fc21712dd9700fa3f2350a19a286c6a'], + }), + ('chemometrics', '1.4.2', { + 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], + }), + ('FNN', '1.1', { + 'checksums': ['b2a2e97af14aa50ef4dce15a170e1d7329aebb7643bab4a6cf35609555acccce'], + }), + ('ipred', '0.9-6', { + 'checksums': ['b8d36438eb9b7209d27b85738dcad03b2e535dcb2f4191432780d9cbf00d3cef'], + }), + ('statmod', '1.4.30', { + 'checksums': ['9d2c1722a85f53623a9ee9f73d835119ae22ae2b8ec7b50d675401e314ea641f'], + }), + ('miscTools', '0.6-22', { + 'checksums': ['d00bb2602d1d31e9e1e13c8868cfe69d432bbe15afa8d4bbb83b3c9e0b9dcfea'], + }), + ('maxLik', '1.3-4', { + 'checksums': ['181ab87721b1e6e3859c60d12eea2f67a7135bfa679db73c20a9ef76d82c4b4a'], + }), + ('mlogit', '0.2-4', { + 'checksums': ['5d9f5d20efd9d654e15875d813d9da3e756c7b8f25d8bb1f5d689a128fa7cd96'], + }), + ('getopt', '1.20.1', { + 'checksums': ['1522c35b13e8546979725a68b75e3bc9d156fb06569067472405f6b8591d8654'], + }), + ('gsalib', '2.1', { + 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], + }), + ('optparse', '1.4.4', { + 'checksums': ['0b1f1d336f1be386260fb5bbdf74f01787c09176d69febf8d563e5af75e5c4b9'], + }), + ('klaR', '0.6-12', { + 'checksums': ['7a8f9fcacc8a0a250811dcd627657bcd7b58c719d585fd5cdcaba9fcc3c2d382'], + }), + ('neuRosim', '0.2-12', { + 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], + }), + ('locfit', '1.5-9.1', { + 'checksums': ['f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51'], + }), + ('GGally', '1.3.2', { + 'checksums': ['f4143f45254fed794be991180aeffe459f6756bfa08acad963707d8e843cfd0a'], + }), + ('beanplot', '1.2', { + 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], + }), + ('clValid', '0.6-6', { + 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], + }), + ('matrixStats', '0.52.2', { + 'checksums': ['39da6aa6b109f89a141dab8913d981abc4fbd3f8be9e206f92e382cc5270d2a5'], + }), + ('DiscriMiner', '0.1-29', { + 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], + }), + ('ellipse', '0.3-8', { + 'checksums': ['508d474c142f0770c25763d6c8f8f8c9dcf8205afd42ffa22e6be1e0360e7f45'], + }), + ('leaps', '3.0', { + 'checksums': ['55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285'], + }), + ('nloptr', '1.0.4', { + 'checksums': ['84225b993cb1ef7854edda9629858662cc8592b0d1344baadea4177486ece1eb'], + }), + ('lme4', '1.1-14', { + 'checksums': ['8a9638ffbefe3341c700e8e885e49bb2006a1072c8056fbe9f07136046d259ed'], + }), + ('pbkrtest', '0.4-7', { + 'checksums': ['5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea'], + }), + ('car', '2.1-6', { + 'checksums': ['d2426a66f63324d9db34dc89becb728d2d4b6d5f183f2efe02cbf683646a8492'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('FactoMineR', '1.39', { + 'checksums': ['b0bb1d6d7d1f3cb11a4b63c377321e10078a36f29bc78dfa3b80c7c149f4a08a'], + }), + ('flexclust', '1.3-4', { + 'checksums': ['7bbbb63bcf3aca81d8f6cafd674c9cc25dcea0a1b320c405b07cac99ccf32ff5'], + }), + ('flexmix', '2.3-14', { + 'checksums': ['837c7f175a211b3c484b2c7b81ec9729889a614c5c6e7d70c95a2c1d60ff846a'], + }), + ('prabclus', '2.2-6', { + 'checksums': ['41792980e40ba18204fab92d85120dcd468860e2204e52fb42636c6f7aee5a62'], + }), + ('diptest', '0.75-7', { + 'checksums': ['462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b'], + }), + ('trimcluster', '0.1-2', { + 'checksums': ['622fb61580cc19b9061c6ee28ffd751250a127f07904b45a0e1c5438d25b4f53'], + }), + ('fpc', '2.1-10', { + 'checksums': ['5d17c5f475c3f24a4809678cbc6186a357276240cf7fcb00d5670b9e68baa096'], + }), + ('BiasedUrn', '1.07', { + 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + }), + ('TeachingDemos', '2.10', { + 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + }), + ('kohonen', '3.0.4', { + 'patches': ['kohonen-3.0.2_icpc-wd308.patch'], + 'checksums': [ + '429864d72858c29d4187bed48ac1c17cf2ecb08f18090b6bf44dff55174609ab', # kohonen_3.0.4.tar.gz + '3502337a28322c4a84a2f26dbd444626a0913944b58b1bb2281f46ede5b8ec2e', # kohonen-3.0.2_icpc-wd308.patch + ], + }), + ('base64', '2.0', { + 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + }), + ('doRNG', '1.6.6', { + 'checksums': ['939c2282c72c0b89fc7510f4bff901a4e99007dc006f46762c8f594c0ecbd876'], + }), + ('nleqslv', '3.3.1', { + 'checksums': ['87eee7dad496539ede21bdb02bb0bc3793c9a390c000b0cd2bcd9b41ce5d3ad8'], + }), + ('Deriv', '3.8.3', { + 'checksums': ['f6804656e2ed8ff72c6ace4fce7ab8fbb72841089c8d6961436b9db54f6ad99b'], + }), + ('RGCCA', '2.1.2', { + 'checksums': ['20f341fca8f616c556699790814debdf2ac7aa4dd9ace2071100c66af1549d7d'], + }), + ('pheatmap', '1.0.8', { + 'checksums': ['51468765380119c302ee9afd52d0483123c0670297f4b906edc79235939960c6'], + }), + ('openxlsx', '4.0.17', { + 'checksums': ['116b9829c5a85ab1b7368d9f7f34a2248436f54bbf6ad635186c8a70b5a204d7'], + }), + ('pvclust', '2.0-0', { + 'checksums': ['1a4615214992307fd7c786cf4607a3ae2af5c0d4067f5053e1c195798a70d741'], + }), + ('RCircos', '1.2.0', { + 'checksums': ['7fd06e2efc33b5c30fc4ba3945b04021f255ba4ffcc394348df7488b9394444a'], + }), + ('lambda.r', '1.2', { + 'checksums': ['7dc4188ce1d4a6b026a1b128719ff60234ae1e3ffa583941bbcd8473ad18146f'], + }), + ('futile.options', '1.0.0', { + 'checksums': ['ee84ece359397fbb63f145d11af678f5c8618570971e78cc64ac60dc0d14e8c2'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.18', { + 'checksums': ['ea6286dea4b12185c0f81c60a729613a55be32d969be14d232ea6aeacbd47017'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.5.7', { + 'checksums': ['36727bc330c281dab8a028fab2dde92d032345974b15e3dde920ee16dc6db363'], + }), + ('forecast', '8.2', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + 'checksums': [ + 'eb3fab64ed139d068e7d026cd3880f1b623f4153a832fb71845488fa75e8b812', # forecast_8.2.tar.gz + '5100dce59858960fc2ade7c599ecda13f3473984fb2bd90f8fa6598653e7ddc2', # forecast-6.1_icpc-wd308.patch + ], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('maptools', '0.9-2', { + 'checksums': ['3bf88cd06f69168d169727ca90d378dfedca77d80ebd26380b2708b3c6aab41c'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.6-1', { + 'checksums': ['c33aac743f1a4c35d37791486a6628838f5fbff51001b4270aba813163e1bd1f'], + }), + ('goftest', '1.1-1', { + 'checksums': ['db6cb1ff6e18520b172e93fca5d7d953bd2d06f4af73bf90aa0a09df8cad71a0'], + }), + ('spatstat.utils', '1.8-0', { + 'checksums': ['cf412cb4ef44af63e8c9e01ca2aa86d665788cdb128fba5a0d9c499beb317214'], + }), + ('spatstat.data', '1.2-0', { + 'checksums': ['f5f1da10a19b1eb3911d56aadea294e1c428d332076cf2ca8ad50c1b832ffc5b'], + }), + ('spatstat', '1.54-0', { + 'checksums': ['54608457d14d7d39e8e2a379e94c03f7d7ee7a5f16d86b6bff9e74f14dac3fed'], + }), + ('rgdal', '1.2-16', { + 'checksums': ['017fefea4f9a6d4540d128c707197b7025b55e4aff98fc763065366b025b03c9'], + }), + ('gdalUtils', '2.0.1.7', { + 'checksums': ['931138a03b37678f47a41a27dca4ba1938bed07a8a3e869f42feaa76aa380c59'], + }), + ('pracma', '2.1.1', { + 'checksums': ['27a14b17f3c2820c8ce61e035af452b43d5eecece6d51a404d5c31ef67ced4d7'], + }), + ('RCurl', '1.95-4.8', { + 'checksums': ['e72243251bbbec341bc5864305bb8cc23d311d19c5d0d9310afec7eb35aa2bfb'], + }), + ('bio3d', '2.3-3', { + 'checksums': ['f4b45847eb8a4175dacea659f30a8075769ec1ae19daec6842b0d72227b48633'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-22', { + 'checksums': ['d9534a19bde3e141a60aaa9afb6ef12e8fca576edc39a4d4f2e966d735c652f9'], + }), + ('lpSolve', '5.6.13', { + 'checksums': ['d5d41c53212dead4fd8e6425a9d3c5767cdc5feb19d768a4704116d791cf498d'], + }), + ('mediation', '4.4.6', { + 'checksums': ['b17784c001305d5f3b84573a673cef31475520d9baec972e42431be193bf305f'], + }), + ('ModelMetrics', '1.1.0', { + 'checksums': ['487d53fda57da4b29f83a927dda8b1ae6655ab044ee3eec33c38aeb27eed3d85'], + }), + ('CVST', '0.2-1', { + 'checksums': ['a27fd2bfa778fce9b9a68d2b9206c66af27b3c36a973dd45ce673886a267aa9f'], + }), + ('DRR', '0.0.2', { + 'checksums': ['02860f05f97a6020012fb6ebfe0d7738dd9e9db0555326f1ef57199fcde58ee9'], + }), + ('dimRed', '0.1.0', { + 'checksums': ['fb0cef7a21b8a5219c74e5227a282168599dd63e904130366f3d2fed8a625a39'], + }), + ('lubridate', '1.7.1', { + 'checksums': ['898c3f482ab8f5e5b415eecd13d1238769c88faed19b63fcb074ffe5ff57fb5f'], + }), + ('ddalpha', '1.3.1', { + 'checksums': ['707d72464c37726f4a067417d6a8927a232b59cf67fa77aa48eef8414ae29f5d'], + }), + ('gower', '0.1.2', { + 'checksums': ['eb91b2d2784d237c7055abcf3cfa4fc0b2226b855a0c29fc5a4e8eaa689079d5'], + }), + ('RcppRoll', '0.2.2', { + 'checksums': ['51c76812687e2a8572c6037b0c095c0a30ee6a24783edf2c7c717d547ddfbfa7'], + }), + ('psych', '1.7.8', { + 'checksums': ['f328ea602e22b0e7e5f310a8d19f305d8e0a3a86040cdfb64863b68b56d55135'], + }), + ('broom', '0.4.3', { + 'checksums': ['2e261b40006432e787dc208c2a8943c6ae714968879dd3361ba1ee6ea5603785'], + }), + ('recipes', '0.1.1', { + 'checksums': ['04bcbf0c49e5edd0be8034d841b6e2bec1f1966ef1f64978ac8938150f33a445'], + }), + ('withr', '2.1.0', { + 'checksums': ['c8bdd4ed682098306f4bfc4c29f8b83b2ef80d3cd8489d6dd26d5023dd30628b'], + }), + ('caret', '6.0-77', { + 'checksums': ['beec200e18a0bbcefa6ba0380b50bea2faf535ac66c4e7febd56e8630a018515'], + }), + ('adabag', '4.1', { + 'checksums': ['ff938c36122cdf58a71a59a6bf79a3c7816966ee7cc4907c4a0a3c0732e3d028'], + }), + ('parallelMap', '1.3', { + 'checksums': ['a52d93572c1b85281e41d8e3c2db97dda5fce96c222e04171b4489ec5000cd08'], + }), + ('ParamHelpers', '1.10', { + 'checksums': ['80629ba62e93b0b706bf2e451578b94fbb9c5b95ff109ecfb5b011bfe0a0fa5b'], + }), + ('ggvis', '0.4.3', { + 'checksums': ['34d517783016aaa1c4bef8972f4c06df5cd9ca0568035b647e60a8369043ecdc'], + }), + ('mlr', '2.11', { + 'checksums': ['aa1293eb98aa13cc9d7b4cd5b5422c7500192716b04f4ed698e5ccd77f1746bb'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-9', { + 'checksums': ['d4b505ef25cb76ffdd1a4b4c0bd9106c521afd9453f10d3dc75d0ac2bcf7c221'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '0.14', { + 'checksums': ['01112a58f3fbd20e9f77aa1555e9bad6ee3a78a5f4d9d5701fd88650921ed9e2'], + }), + ('tensorA', '0.36', { + 'checksums': ['97b3e72f26ca3a756d045008764d787a32c68f0a276fb7a29b6e1b4592fdecf6'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('shape', '1.4.3', { + 'checksums': ['720f6ca9c70a39a3900af9d074bff864b18ac58013b21d48b779047481b93ded'], + }), + ('whisker', '0.3-2', { + 'checksums': ['484836510fcf123a66ddd13cdc8f32eb98e814cad82ed30c0294f55742b08c7c'], + }), + ('commonmark', '1.4', { + 'checksums': ['865ecf9432763393ca9de52d0106a58c4be9e8d5196da60e068eed0b67ca68ed'], + }), + ('desc', '1.1.1', { + 'checksums': ['32ff99b658db3bf0172cf30d15b7f34021144ffc08a5896afd3d30055fc4074c'], + }), + ('roxygen2', '6.0.1', { + 'checksums': ['d22ddc05cd5308a48b8359b932e1f7f4c23fdf0c857ac8e52c42381b6bfcff76'], + }), + ('git2r', '0.19.0', { + 'checksums': ['380121c31dfb53f3417f9014e841a3b0ff8889f896375295984ea9daec724673'], + }), + ('rversions', '1.0.3', { + 'checksums': ['21d0809f46505de89a2be7be9449e39c39cff5bc77e584dec976ee6c0b884f44'], + }), + ('devtools', '1.13.4', { + 'checksums': ['ab82ca75ea301df098191ab68fa3d812317c07c7dc28310d2715fa0d8ac3e1ab'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-9', { + 'patches': ['Cairo-1.5-9.patch'], + 'checksums': [ + '2a867b6cae96671d6bc3acf9334d6615dc01f6ecf1953a27cde8a43c724a38f4', # Cairo_1.5-9.tar.gz + '3efa99888503949eefe586faf3f6f80566674c5a8cfb2c62b648b42f22466dfa', # Cairo-1.5-9.patch + ], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.2-3', { + 'checksums': ['e974b65d6116d540bc2c934c40c5552f64d7781b77c259a5b7724b1338c9e08e'], + }), + ('distillery', '1.0-4', { + 'checksums': ['3d3a8445471b19a6b652761ca783994b2d2108b64ff539b0597a9db9697d17d4'], + }), + ('extRemes', '2.0-8', { + 'checksums': ['d53d50d0feb6295f72c4f646242e1506ca51911c026f881d443d65f1c68ad75e'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('tkrplot', '0.0-23', { + 'checksums': ['87a4323ce3bc6c852c2dae4727639b9a1c30724327a812379f21d73cecd7deb2'], + }), + ('misc3d', '0.8-4', { + 'checksums': ['75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62'], + }), + ('multicool', '0.1-10', { + 'patches': ['multicool-0.1-10_icpc-wd308.patch'], + 'checksums': [ + '5bb0cb0d9eb64420c862877247a79bb0afadacfe23262ec8c3fa26e5e34d6ff9', # multicool_0.1-10.tar.gz + '2afcb15d37d0e4adc43530e448325cb97bc46ebf4d1da9fe6c07cf0070fe0a0c', # multicool-0.1-10_icpc-wd308.patch + ], + }), + ('ks', '1.10.7', { + 'checksums': ['a505c65e1fd59b7e5e61d0955f1a66b0f568198e97a71f356245565bf6a74507'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-17', { + 'checksums': ['c007d6eaf6335a15c1912b0804276ff39abce27b7a61539a91b8fda653629252'], + }), + ('penalized', '0.9-50', { + 'checksums': ['c12b3259e019f91c7bd02827ea3a27f842d9c15950fa6cc114dff23c89c297d1'], + }), + ('clusterRepro', '0.5-1.1', { + 'checksums': ['b7fcb9db0c762a2e6e22a0a0689affd73504c56f13c13b04272a946630334e6f'], + }), + ('randomForestSRC', '2.5.1', { + 'checksums': ['ad45878dab93cdf5fbdd88cbcf5e6cdcceb7fae6b9dd8d2ccddac2d6ce2faadc'], + }), + ('sm', '2.2-5.4', { + 'checksums': ['49f26c52728ac9dd2152d80ef1d3d59b98269bdc81616f81548fa4ed842ed842'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.5-23.1097', { + 'checksums': ['9aa7c3278f08f46b91fb0357dbdb9539936ba54e11d270d7febce0049efc9d87'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.9-3', { + 'checksums': ['1cefcc1d82431f1b3ed014ff04dd087fd0da3396df5a25144ffa80a8d01fe700'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('visNetwork', '2.0.1', { + 'checksums': ['589791c58f9cae1f581757b26d867c6719efa7c00189bc5b7defabc0ffc976b7'], + }), + ('rgexf', '0.15.3', { + 'checksums': ['2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('hms', '0.4.0', { + 'checksums': ['f41bfec3713a16d17111012e0a31992fe54e00ec76680096e8b4844b5d39501f'], + }), + ('readr', '1.1.1', { + 'checksums': ['1a29b99009a06f2cee18d08bc6201fd4985b6d45c76cefca65084dcc1a2f7cb3'], + }), + ('DiagrammeR', '0.9.2', { + 'checksums': ['dc9d24c5129b29688d1dd74438fe1fc5f02f3537a9a94cd26fd54f496468e63b'], + }), + ('sem', '3.1-9', { + 'checksums': ['4a33780202506543da85877cd2813250114420d6ec5e75457bc67477cd332cb9'], + }), + ('jpeg', '0.1-8', { + 'checksums': ['d032befeb3a414cefdbf70ba29a6c01541c54387cc0a1a98a4022d86cbe60a16'], + }), + ('network', '1.13.0', { + 'checksums': ['7a04ea89261cdf32ccb52222810699d5fca59a849053e306b5ec9dd5c1184f87'], + }), + ('statnet.common', '4.0.0', { + 'checksums': ['206e1967df661b277c6fde68f8b0bf4589508f569ff94f1ec5126c4c56a1867b'], + }), + ('sna', '2.4', { + 'checksums': ['2292b3190e8d879e494527ae9d9d1174c31cb4183749ecb455aedd8d534048cf'], + }), + ('glasso', '1.8', { + 'patches': [('glasso-1.8-ifort-no-fixed.patch', 1)], + 'checksums': [ + 'fc9ba74519388c194e14bae39d41f3fec8c2aade0177df364f61753f0fbf8a3d', # glasso_1.8.tar.gz + '87e966b6651c2d9ccd8a2c2ba842eef8dcbeaa3fdd25085bb1d5aff6e79f409c', # glasso-1.8-ifort-no-fixed.patch + ], + }), + ('huge', '1.2.7', { + 'checksums': ['042b771c334cf4d1a92c5c546ca025238919f772a50457594b7e0bd243498d8c'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('ggm', '2.3', { + 'checksums': ['832ffe81ff87c6f1a6644e689ebbfb172924b4c4584ac8108d1244d153219ed8'], + }), + ('BDgraph', '2.43', { + 'checksums': ['e44123e088ea73acf5aa7f13125d3b049be084bbf0c8eec958897e667e020cf3'], + }), + ('qgraph', '1.4.4', { + 'checksums': ['f62a908a4185f30c2f6924a69f1a569a636fa3053de1e92288367b498b93f841'], + }), + ('HWxtest', '1.1.7', { + 'checksums': ['7cfcf7860d655945f9d3bbda4590374d3100bb5da6b49956f2e701b910a20e0c'], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.15', { + 'checksums': ['35a74a9dfc19394ffb04f53ffed873888a2080547994883d599c4267e3d8d6f5'], + }), + ('phangorn', '2.3.1', { + 'checksums': ['518c31f5b2c5f0a655d02a3c71b00c30caea2794dfc31f9d63f3d505bd7863eb'], + }), + ('geepack', '1.2-1', { + 'checksums': ['7effe67381129a48154c445704490ea3b5f2e1adedb66cb65f61369dd1f8d38d'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.1', { + 'checksums': ['174568a01f68b9601a4ea89ca5857bf4888242f00e4212bfb7a422d6292300d5'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.7', { + 'checksums': ['08b3bb63f04fc0b065cb615b6ca1ef95eb6df7a813eb9eb625bc15c6de332c22'], + }), + ('diagram', '1.6.4', { + 'checksums': ['7c2bc5d5d634c3b8ca7fea79fb463e412962d88f47a77a74c811cc62f375ce38'], + }), + ('FME', '1.3.5', { + 'checksums': ['3619d88df2a41ca8819b93bb7dff3b8233f76ff8ab0ca67c664f530f835935e4'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('readbitmap', '0.1-4', { + 'checksums': ['2d45ddd1ee0eb7482d5d4a9cfe41b3aa645de8af89295b4b205d73b19ac6d821'], + }), + ('imager', '0.40.2', { + 'patches': ['imager-0.40.2_icpc-wd308.patch'], + 'checksums': [ + '12be25495c32883961e2503c8064aa90473fc36046630f582ae28c1c06995c9d', # imager_0.40.2.tar.gz + 'c17ee601d73217a8c177924782f4f6537b3188ff54f4627a521974d07f3870c5', # imager-0.40.2_icpc-wd308.patch + ], + }), + ('pracma', '2.1.1', { + 'checksums': ['27a14b17f3c2820c8ce61e035af452b43d5eecece6d51a404d5c31ef67ced4d7'], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.2', { + 'checksums': ['4aafd7d6330572711c117fa2d6e21e14485f695db38a7ebf5c7b3ba8723666f6'], + }), + ('pastecs', '1.3-18', { + 'checksums': ['5188662294bf91545d0c2e4d7de113296f5a8c2cbf38bdc2a90f3f7d03b3b447'], + }), + ('audio', '0.1-5', { + 'checksums': ['b4e229457a0a399b14136ac145e65bb007d9c8d46e421ae79fd26461450164c3'], + }), + ('fftw', '1.0-4', { + 'checksums': ['80413901ce751c0700ac53283366cfcfe3cbeec2982d29721a0275f9fb9de204'], + }), + ('seewave', '2.0.5', { + 'checksums': ['00da9d86459b7c370396a508e18dd3d474f57228efefac5e07db44b3309380d6'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('oce', '0.9-22', { + 'checksums': ['50da1c1d047b82045f513fd7632e599cdd76d1cdfc1fbff0f813e8922199af73'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.2', { + 'checksums': ['50b7ba4b8b9bb1f50a58f427de088566edd3c7c1c9974dc9d5342ade1b24e0c5'], + }), + ('memuse', '4.0-0', { + 'checksums': ['fbf8716a1388692ee439f69ac99643fa427eb100027d8911ff0fbfdcb5b6c3bc'], + }), + ('pinfsc50', '1.1.0', { + 'checksums': ['b6b9b6365a3f408533264d7ec820494f57eccaf362553e8478a46a8e5b474aba'], + }), + ('vcfR', '1.5.0', { + 'checksums': ['7cd7d352d72120cf6127c9ef86b5134135d66bb4f047945c75aa0b99cc741a22'], + }), + ('glmmML', '1.0.2', { + 'checksums': ['abc9ded054787f5459e0e419697927eb031f221be8e0cfdbf306f776d4b9bb59'], + }), + ('ucminf', '1.1-4', { + 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], + }), + ('ordinal', '2015.6-28', { + 'checksums': ['fa33e29cc82bf241ad94fbbf5bb4dd6c9fe01803ba389957a4194d81e5979351'], + }), + ('Rtsne', '0.13', { + 'patches': ['Rtsne-0.13_icpc-wd308.patch'], + 'checksums': [ + '1c3bffe3bd11733ee4fe01749c293669daafda1af2ec74f9158f6080625b999d', # Rtsne_0.13.tar.gz + '89d435412c6e9e9721b2a5d8a7065fda6faed7db34c06ad05ecad7065b958fd4', # Rtsne-0.13_icpc-wd308.patch + ], + }), + ('cowplot', '0.9.1', { + 'checksums': ['953fd9d6ff370472b9f5a9ee867a423bea3e26e406d08a2192ec1872a2e60047'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('pbapply', '1.3-3', { + 'checksums': ['7379b21d1176db5769f5cac858dd12c975736e80a600870180cec9625cf51047'], + }), + ('RcppProgress', '0.4', { + 'checksums': ['3b1ecc82ced98eb481819a28737dac3658586e11ad16a92abd14c4649ae15e25'], + }), + ('sn', '1.5-1', { + 'checksums': ['fcfc077a2c1eb35b1ed875fea296b225540aefb05564cbb54477f266a0a2f850'], + }), + ('tclust', '1.3-1', { + 'checksums': ['fe4479a73b947d8f6c1cc63587283a8b6223d430d39eee4e5833a06d3d1726d2'], + }), + ('ranger', '0.8.0', { + 'checksums': ['7f0fdee2f2d553a0aec56c2a4a4ff9dd972e1c7284118d9ea570749e0eaaabb9'], + }), + ('hexbin', '1.27.1', { + 'checksums': ['075935a3ae2d90e44aca6ebbd368dc6f7e59d322e36e0e0932dedbf01330ad08'], + }), + ('crosstalk', '1.0.0', { + 'checksums': ['b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51'], + }), + ('pryr', '0.1.3', { + 'checksums': ['6acd88341dde4fe247a5cafd3949b281dc6742b7d60f68b57c1feb84b96739ac'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('forcats', '0.2.0', { + 'checksums': ['b5bce370422d4c0ec9509249ae645373949bfbe9217cdf50dce2bfbdad9f7cd7'], + }), + ('laeken', '0.4.6', { + 'checksums': ['465174263f2d495162bf1ee8ab35b362dae8088e458c162ce517813267d813e6'], + }), + ('VIM', '4.7.0', { + 'checksums': ['cdd64cbdca23c097efa8d5084bfc1c0d1449744e90a41680a5246db979d14cee'], + }), + ('proxy', '0.4-19', { + 'checksums': ['6b27e275018366e6024382704da9a9757c8878535dbcd7d450824b70e2e34d51'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('DT', '0.2', { + 'checksums': ['a1b7f9e5c31a241fdf78ac582499f346e915ff948554980bbc2262c924b806bd'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.6.1', { + 'checksums': ['1ee38f257433d24455426bc9d85c36f588735a54fbf6143935fed9cccb3bf193'], + }), + ('rrcov', '1.4-3', { + 'checksums': ['d89631e0dfb39777af9fe303cc0537bbc82c6f3d2a1ed360de950c13dfc34f4d'], + }), + ('WriteXLS', '4.0.0', { + 'checksums': ['a0541da45e16bc4bf994cdf3f07a0e202c38d52386460c64e27fe6c1cd889d5b'], + }), + ('bst', '0.3-14', { + 'checksums': ['08013994d3ac79ffc78585cb2831d4d2e52f39423ba880f84c6224e4c6b6360b'], + }), + ('mpath', '0.3-4', { + 'checksums': ['2a77539924c1aaf9eece2277b415f1df7146c44f04886b4e96d2d9ad32b6c262'], + }), + ('timereg', '1.9.1', { + 'checksums': ['3b9301ca6915d487b050ef8f2329efbdc5f03d85695497416952e53d225aa3e6'], + }), + ('peperr', '1.1-7', { + 'checksums': ['73e0422c71f2df59cd4a0f820c87dd828f2952b60df2d6c58f62a35559d74605'], + }), + ('heatmap3', '1.1.1', { + 'checksums': ['055e30a2fee0e8b6e499cdc5ccb7e37e5615ed3d52cc7058fc5ca5fc808cf393'], + }), + ('GlobalOptions', '0.0.12', { + 'checksums': ['c09da3f9b1646d0f815056cdbeb5fff7dda29f7dd8742d245f5f6dc7066077a9'], + }), + ('circlize', '0.4.2', { + 'checksums': ['b1555392f5e5e790d5544dfcd886cc2dbb9057a1eb1b618806b116b18b13c85f'], + }), + ('GetoptLong', '0.1.6', { + 'checksums': ['f526f006e3ed8507f1f236430ac9e97341c1ee9c207fbb68f936dd4d377b28b5'], + }), + ('dendextend', '1.6.0', { + 'checksums': ['43a4e3340adf716469f53db4e77fa446564d766dc100f6fba522c48f00842c5e'], + }), + ('RInside', '0.2.14', { + 'checksums': ['8de5340993fe879ca00fa559c5b1b27b408ba78bfc5f67d36d6f0b8d8e8649cf'], + }), + ('limSolve', '1.5.5.3', { + 'checksums': ['2f27c03411e0d771ad50d5412125bf4fa0ba461051610edc77e20d28488e86d2'], + }), + ('cli', '1.0.0', { + 'checksums': ['8fa3dbfc954ca61b8510f767ede9e8a365dac2ef95fe87c715a0f37d721b5a1d'], + }), + ('dbplyr', '1.1.0', { + 'checksums': ['7b1e456a2d1056fa6284582cd82d2df66d06b3eea92e9995f5a91a45f246f69d'], + }), + ('haven', '1.1.0', { + 'checksums': ['089fb4d0955f320abc48d0a3031799f96f3a20b82492474743903fdf12001d19'], + }), + ('modelr', '0.1.1', { + 'checksums': ['25b95198d6aa23e28a0bd97dcdc78264ef168ae403928bff01e1ee81ca021ce7'], + }), + ('rematch', '1.0.1', { + 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], + }), + ('cellranger', '1.1.0', { + 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], + }), + ('readxl', '1.0.0', { + 'checksums': ['fbd62f07fed7946363698a57be88f4ef3fa254ecf456ef292535849c787fc7ad'], + }), + ('callr', '1.0.0', { + 'checksums': ['2c56808c723aba2ea8a8b6bbdc9b8332c96f59b119079861dd52f5988c27f715'], + }), + ('clipr', '0.4.0', { + 'checksums': ['44a2f1ab4fde53e4fe81cf5800aa6ad45b72b5da93d6fe4d3661d7397220e8af'], + }), + ('reprex', '0.1.1', { + 'checksums': ['919ae93039b2d8fb8eace98da9376c031d734d9e75c237efb24d047f35b5ba4b'], + }), + ('selectr', '0.3-1', { + 'checksums': ['db4f7ceea4b522a54c3ae7709787b0b7fcf389c5d945c5a278e3625388218949'], + }), + ('rvest', '0.3.2', { + 'checksums': ['0d6e8837fb1df79b1c83e7b48d8f1e6245f34a10c4bb6952e7bec7867e4abb12'], + }), + ('tidyverse', '1.2.1', { + 'checksums': ['ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b'], + }), + ('R.cache', '0.12.0', { + 'checksums': ['dd47c4690fcae910bf5d71455f2eb25b908ffe02d757fc60e1f0a29cb828dd00'], + }), + ('R.rsp', '0.41.0', { + 'checksums': ['6c6c0490fa40af20068e96ced43f6de089d363cc710a4575abef15b915188406'], + }), + ('listenv', '0.6.0', { + 'checksums': ['a737f08123b8bd67b63bb9843d0b6316408516d831203df8c369f3e32a48d84f'], + }), + ('globals', '0.10.3', { + 'checksums': ['d29e3e824e9746b80616742efd0040fff8e044e09b9a3a65acc3eb6b25ef2caf'], + }), + ('future', '1.6.2', { + 'checksums': ['21e2683746fd4eff44c180bdb46b09ce6c1dafe6f0490a630d4db79d6616af05'], + }), + ('gdistance', '1.2-1', { + 'checksums': ['c1a74a86e31c26b6b1cd49c151c2e0ba362565667ec9971c08efc4194167cff3'], + }), + ('vioplot', '0.2', { + 'checksums': ['601f043630999e0498f0fba213d3d3fefd6ff0abf8fdb22119199b3d8d58939b'], + }), + ('emulator', '1.2-15', { + 'checksums': ['e221f185f610ca34d169c42dc560209094825ed0a4fe35db97892ca4ffc1e7e6'], + }), + ('gmm', '1.6-1', { + 'checksums': ['c1d6ac78cfa302895934fbefbf6d073bfdd5c0c92708bfe4a46fb7775804383e'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.17', { + 'checksums': ['18ec9db0aab1de526b8e57ac1f0223811806a814777149b793722b999e6f7c59'], + }), + ('gap', '1.1-20', { + 'checksums': ['ed3c4031d2ab86f08c648e44837036d6f5909f0319db82ec7ac3e234f9bc9763'], + }), + ('qrnn', '1.1.3', { + 'checksums': ['8e4f0f68f75bf77badd2b8afcdc5b467b732332ae9ab31cfdbf0df43e2570b5e'], + }), + ('DHARMa', '0.1.5', { + 'checksums': ['97e3ad80583eb6612f59e225100a10364e39d23076e9a295c5f75c4aa1bffbd5'], + }), + ('BayesianTools', '0.1.3', { + 'checksums': ['4576245165b748e3ca6fef08dd478617111bf7813b6a43587ddeaa0e8b6e9b0e'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.1', { + 'checksums': ['f1069bf920e9bc3da6bf43542a3a7ccc3142544d759945115ecade69dd5ccde0'], + }), + ('tidyverse', '1.2.1', { + 'checksums': ['ad67a27bb4e89417a15338fe1a40251a7b5dedba60e9b72637963d3de574c37b'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3', { + 'checksums': ['e377effe345987850ece985eabf79750ca1979d75469d17a323c21515ad1dda8'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.4.1', { + 'checksums': ['6f585cb622cc52e2b7f3efddb7a363e91771bff80b8facb554755c2b33b7f402'], + }), + ('Rssa', '1.0', { + 'checksums': ['9cc20a7101d8dff4c6cfb789f9bdc14e2b3bb128d7613a67b0f9633cf006902a'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.31', { + 'checksums': ['9d764092216391c9d7e13bbe1585f5d00c357ed8b04c7e66ed82d229c34119cb'], + }), + ('DistributionUtils', '0.5-1', { + 'checksums': ['e92a29003d5e5974f53e40bdb8417e2bdabe784304e21360d7a1cbec7818853f'], + }), + ('gapfill', '0.9.5-3', { + 'checksums': ['137286aff194b33b1bcd21fdcb5908308a23628e66b62ce5fbe1a70ff5668cc3'], + }), +] + +moduleclass = 'lang' From 2a24c5c01f719cb4283e904be9003a6519191d1c Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 May 2018 13:10:42 +0200 Subject: [PATCH 037/698] Do not unpack binary, fix modloadmsg --- .../e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb index 729b9d77b65..ae7a456a67a 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb @@ -1,4 +1,4 @@ -easyblock = 'PackedBinary' +easyblock = 'Binary' name = 'ESMValTool' version = '1.1.0' @@ -93,7 +93,6 @@ exts_list = [ '6acdc3a08bfcebf0a1b52a05d73d51b7aa5e7240fedfa95537c92d16f2ef8778', # v1.1.0.tar.gz '7988beb0c591d7a42e470e0dea360ebbd29a902d0a2f75bb719271ba0710fdd8', # basemap-1.1.0_GEOS.patch ], -# 'custom_commands': ["python -c 'from mpl_toolkits.basemap import Basemap'"], }), ('netCDF4', '1.3.1', { 'modulename': 'netCDF4', @@ -190,4 +189,6 @@ modextrapaths = { 'R_LIBS': '', } +modloadmsg = "To install ESMValTool in your directory execute: tar zxf $EBROOTESMVALTOOL/ESMValTool-1.1.0.tar.gz\n" + moduleclass = 'geo' From 0ca73405694fa88422bc5f002a12ca874e8f1a03 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 May 2018 13:34:41 +0200 Subject: [PATCH 038/698] easyconfig names fixed --- .../c/check/check-0.12.0-GCCcore-6.4.0.eb | 31 +++ ...ValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 194 ++++++++++++++++++ 2 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..8b3f74b6a9d --- /dev/null +++ b/easybuild/easyconfigs/c/check/check-0.12.0-GCCcore-6.4.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'check' +version = '0.12.0' + +homepage = 'https://libcheck.github.io/check/' +description = """Check is a unit testing framework for C. + It features a simple interface for defining unit tests, + putting little in the way of the developer. Tests are run + in a separate address space, so both assertion failures + and code errors that cause segmentation faults or other + signals can be caught. Test results are reportable in + the following: Subunit, TAP, XML, and a generic logging format.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['https://github.com/libcheck/check/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['7816b4c38f6e23ff873786f18d966e552837677bfae144041e0587e7c39e04e8'] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.10.1'), +] + +sanity_check_paths = { + 'files': ['include/check.h', 'lib/libcheck.a', 'lib/libcompat.a'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..4916732144f --- /dev/null +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -0,0 +1,194 @@ +easyblock = 'Binary' + +name = 'ESMValTool' +version = '1.1.0' +versionsuffix = '-Python-%(pyver)s' +hdf5ver = '1.8.19' + +homepage = 'https://www.esmvaltool.org/' +description = """The Earth System Model eValuation Tool (ESMValTool) + is a community diagnostics and performance metrics tool + for the evaluation of Earth System Models (ESMs) that + allows for routine comparison of single or multiple models, + either against predecessor versions or against observations.""" + +toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ESMValGroup/ESMValTool/archive/'] +sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'v%(version)s.tar.gz'}] +checksums = ['457d5a7e72165a31532b335c42b925abaaa48e959d32b123463df77318c73c36'] + +dependencies = [ + ('Python', '2.7.14'), + ('NCL', '6.4.0'), + ('R', '3.4.3', '-X11-20171023-HDF5-%s' % hdf5ver), + ('CDO', '1.9.1'), + ('GEOS', '3.6.2', versionsuffix), + ('libjpeg-turbo', '1.5.2'), + ('libpng', '1.6.32'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.0.8'), + ('freetype', '2.8'), + ('PROJ', '4.9.3'), + ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5ver), + ('GDAL', '2.2.2', '-Python-%%(pyver)s-HDF5-%s' % hdf5ver), + ('libmo_unpack', '3.1.2'), + ('ecCodes', '2.7.3', versionsuffix), +] + +# Python deps, order is important! +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', +} + +exts_classmap = {'ncdf4': 'RPackage'} +exts_list = [ + ('olefile', '0.45.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/o/olefile/'], + 'checksums': ['2b6575f5290de8ab1086f8c5490591f7e0885af682c7c1793bdaf6e64078d385'], + }), + ('Pillow', '4.3.0', { + 'modulename': 'PIL', + 'source_urls': ['https://pypi.python.org/packages/source/p/Pillow/'], + 'checksums': ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'], + }), + ('pyproj', '1.9.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj/'], + 'checksums': ['53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8'], + }), + ('pyshp', '1.2.12', { + 'modulename': 'shapefile', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp/'], + 'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'], + }), + ('chardet', '3.0.4', { + 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('urllib3', '1.22', { + 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], + 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], + }), + ('certifi', '2018.4.16', { + 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], + 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], + }), + ('requests', '2.18.4', { + 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], + 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], + }), + ('OWSLib', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/o/OWSLib/'], + 'checksums': ['ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554'], + }), + ('basemap', '1.1.0', { + 'modulename': 'mpl_toolkits.basemap', + 'patches': ['basemap-1.1.0_GEOS.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/matplotlib/basemap/archive'], + 'checksums': [ + '6acdc3a08bfcebf0a1b52a05d73d51b7aa5e7240fedfa95537c92d16f2ef8778', # v1.1.0.tar.gz + '7988beb0c591d7a42e470e0dea360ebbd29a902d0a2f75bb719271ba0710fdd8', # basemap-1.1.0_GEOS.patch + ], + }), + ('netCDF4', '1.3.1', { + 'modulename': 'netCDF4', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4/'], + 'checksums': ['570ea59992aa6d98a9b672c71161d11ba5683f787da53446086077470a869957'], + }), + ('geoval', '0.1.5', { + 'source_urls': ['https://pypi.python.org/packages/source/g/geoval/'], + 'checksums': ['7da4a1879f78bb7aac2d41b5c1ee360ff74087bf857c81c532deb8cc31feb36e'], + }), + ('cdo', '1.3.6', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cdo/'], + 'checksums': ['b167efbbac7d0a6cbf74f5d211255705c73245f7c2590b6d9eb634347d8b2c1f'], + }), + ('Shapely', '1.6.4.post1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], + 'checksums': ['30df7572d311514802df8dc0e229d1660bc4cbdcf027a8281e79c5fc2fcf02f2'], + }), + ('Cartopy', '0.16.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/Cartopy/'], + 'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'], + }), + ('dask', '0.17.4', { + 'source_urls': ['https://pypi.python.org/packages/source/d/dask/'], + 'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'], + }), + ('PyKE', '1.1.1', { + 'source_tmpl': 'pyke-1.1.1.zip', + 'source_urls': ['http://download.sourceforge.net/pyke'], + 'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'], + }), + ('cf_units', '1.2.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'], + 'checksums': ['abdd2a0937b958322f7ff7ec6866e80f08603c60aa06cef5766b6512c750028a'], + }), + ('pyugrid', '0.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'], + 'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'], + }), + ('mo_pack', '0.2.0', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/mo_pack/archive/'], + 'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'], + }), + ('cycler', '0.10.0', { + 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('singledispatch', '3.4.0.3', { + 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('backports_abc', '0.5', { + 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], + 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], + }), + ('tornado', '4.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], + 'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'], + }), + ('matplotlib', '1.5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], + 'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'], + }), + ('toolz', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'], + 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], + }), + ('scitools-iris', '2.0.0', { + 'modulename': 'iris', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/iris/archive/'], + 'checksums': ['8605ab92c67d622e83fff6d7169fe154d9f8610edd8463b697b574884c158ba2'], + }), + ('iris-grib', '0.12.0', { + 'modulename': 'iris_grib', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/SciTools/iris-grib/archive/'], + 'checksums': ['c2e92d25d8bfd2ddff22ae47c4532c884678bac6ea0d935367eced051ae08bb3'], + }), + ('ncdf4', '1.16', { + 'source_tmpl': '%(name)s_%(version)s.tar.gz', + 'source_urls': [ + 'http://cran.r-project.org/src/contrib/Archive/ncdf4', + 'http://cran.r-project.org/src/contrib/', + 'http://cran.freestatistics.org/src/contrib', + ], + 'checksums': ['edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'R_LIBS': '', +} + +modloadmsg = "To install ESMValTool in your directory execute: tar zxf $EBROOTESMVALTOOL/ESMValTool-1.1.0.tar.gz\n" + +moduleclass = 'geo' From c3897f5d417ff2aa180f3c326bc17c677f9b02e6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 May 2018 13:35:49 +0200 Subject: [PATCH 039/698] easyconfig names fixed --- .../libmo_unpack-3.1.2-GCCcore-6.4.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..d8688a45528 --- /dev/null +++ b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCcore-6.4.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libmo_unpack' +version = '3.1.2' + +homepage = "https://github.com/SciTools/libmo_unpack" +description = "A library for handling the WGDOS and RLE compression schemes used in UM files." + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/SciTools/libmo_unpack/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_cmake_have_stdint.patch'] +checksums = [ + 'e09ef3e6f1075144acc5d6466b4ef70b2fe32ed4ab1840dd4fb7e15a40f3d370', # v3.1.2.tar.gz + 'b130f9944e763c53b21c2b08f6d4954ca7811a556fda1c7fec737a4086aad1f5', # libmo_unpack-3.1.2_cmake_have_stdint.patch +] + +builddependencies = [ + ('binutils', '2.28'), + ('CMake', '3.10.1'), + ('check', '0.12.0'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['include/logerrors.h', 'include/rlencode.h', 'include/wgdosstuff.h', 'lib/libmo_unpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From f1ea1bcf5bce2effa7c3310baca0d62e176c8686 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 May 2018 13:37:39 +0200 Subject: [PATCH 040/698] delete removed files --- .../c/check/check-0.12.0-GCCore-6.4.0.eb | 31 --- .../ESMValTool-1.1.0-Python-2.7.14.eb | 194 ------------------ .../libmo_unpack-3.1.2-GCCore-6.4.0.eb | 33 --- 3 files changed, 258 deletions(-) delete mode 100644 easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb delete mode 100644 easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb delete mode 100644 easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb b/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb deleted file mode 100644 index 8b3f74b6a9d..00000000000 --- a/easybuild/easyconfigs/c/check/check-0.12.0-GCCore-6.4.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'check' -version = '0.12.0' - -homepage = 'https://libcheck.github.io/check/' -description = """Check is a unit testing framework for C. - It features a simple interface for defining unit tests, - putting little in the way of the developer. Tests are run - in a separate address space, so both assertion failures - and code errors that cause segmentation faults or other - signals can be caught. Test results are reportable in - the following: Subunit, TAP, XML, and a generic logging format.""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['https://github.com/libcheck/check/archive'] -sources = ['%(version)s.tar.gz'] -checksums = ['7816b4c38f6e23ff873786f18d966e552837677bfae144041e0587e7c39e04e8'] - -builddependencies = [ - ('binutils', '2.28'), - ('CMake', '3.10.1'), -] - -sanity_check_paths = { - 'files': ['include/check.h', 'lib/libcheck.a', 'lib/libcompat.a'], - 'dirs': [], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb deleted file mode 100644 index ae7a456a67a..00000000000 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-Python-2.7.14.eb +++ /dev/null @@ -1,194 +0,0 @@ -easyblock = 'Binary' - -name = 'ESMValTool' -version = '1.1.0' -versionsuffix = '-Python-%(pyver)s' -hdf5ver = '1.8.19' - -homepage = 'https://www.esmvaltool.org/' -description = """The Earth System Model eValuation Tool (ESMValTool) - is a community diagnostics and performance metrics tool - for the evaluation of Earth System Models (ESMs) that - allows for routine comparison of single or multiple models, - either against predecessor versions or against observations.""" - -toolchain = {'name': 'intel', 'version': '2017b'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/ESMValGroup/ESMValTool/archive/'] -sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'v%(version)s.tar.gz'}] -checksums = ['457d5a7e72165a31532b335c42b925abaaa48e959d32b123463df77318c73c36'] - -dependencies = [ - ('Python', '2.7.14'), - ('NCL', '6.4.0'), - ('R', '3.4.3', '-X11-20171023-HDF5-%s' % hdf5ver), - ('CDO', '1.9.1'), - ('GEOS', '3.6.2', versionsuffix), - ('libjpeg-turbo', '1.5.2'), - ('libpng', '1.6.32'), - ('zlib', '1.2.11'), - ('LibTIFF', '4.0.8'), - ('freetype', '2.8'), - ('PROJ', '4.9.3'), - ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5ver), - ('GDAL', '2.2.2', '-Python-%%(pyver)s-HDF5-%s' % hdf5ver), - ('libmo_unpack', '3.1.2', '', ('GCCcore', '6.4.0')), - ('ecCodes', '2.7.3', versionsuffix), -] - -# Python deps, order is important! -exts_defaultclass = 'PythonPackage' -exts_default_options = { - 'source_tmpl': '%(name)s-%(version)s.tar.gz', -} - -exts_classmap = {'ncdf4': 'RPackage'} -exts_list = [ - ('olefile', '0.45.1', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'source_urls': ['https://pypi.python.org/packages/source/o/olefile/'], - 'checksums': ['2b6575f5290de8ab1086f8c5490591f7e0885af682c7c1793bdaf6e64078d385'], - }), - ('Pillow', '4.3.0', { - 'modulename': 'PIL', - 'source_urls': ['https://pypi.python.org/packages/source/p/Pillow/'], - 'checksums': ['a97c715d44efd5b4aa8d739b8fad88b93ed79f1b33fc2822d5802043f3b1b527'], - }), - ('pyproj', '1.9.5.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyproj/'], - 'checksums': ['53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8'], - }), - ('pyshp', '1.2.12', { - 'modulename': 'shapefile', - 'source_urls': ['https://pypi.python.org/packages/source/p/pyshp/'], - 'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'], - }), - ('chardet', '3.0.4', { - 'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'], - 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], - }), - ('urllib3', '1.22', { - 'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'], - 'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'], - }), - ('certifi', '2018.4.16', { - 'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'], - 'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'], - }), - ('requests', '2.18.4', { - 'source_urls': ['https://pypi.python.org/packages/source/r/requests/'], - 'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'], - }), - ('OWSLib', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/o/OWSLib/'], - 'checksums': ['ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554'], - }), - ('basemap', '1.1.0', { - 'modulename': 'mpl_toolkits.basemap', - 'patches': ['basemap-1.1.0_GEOS.patch'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/matplotlib/basemap/archive'], - 'checksums': [ - '6acdc3a08bfcebf0a1b52a05d73d51b7aa5e7240fedfa95537c92d16f2ef8778', # v1.1.0.tar.gz - '7988beb0c591d7a42e470e0dea360ebbd29a902d0a2f75bb719271ba0710fdd8', # basemap-1.1.0_GEOS.patch - ], - }), - ('netCDF4', '1.3.1', { - 'modulename': 'netCDF4', - 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4/'], - 'checksums': ['570ea59992aa6d98a9b672c71161d11ba5683f787da53446086077470a869957'], - }), - ('geoval', '0.1.5', { - 'source_urls': ['https://pypi.python.org/packages/source/g/geoval/'], - 'checksums': ['7da4a1879f78bb7aac2d41b5c1ee360ff74087bf857c81c532deb8cc31feb36e'], - }), - ('cdo', '1.3.6', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cdo/'], - 'checksums': ['b167efbbac7d0a6cbf74f5d211255705c73245f7c2590b6d9eb634347d8b2c1f'], - }), - ('Shapely', '1.6.4.post1', { - 'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'], - 'checksums': ['30df7572d311514802df8dc0e229d1660bc4cbdcf027a8281e79c5fc2fcf02f2'], - }), - ('Cartopy', '0.16.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/Cartopy/'], - 'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'], - }), - ('dask', '0.17.4', { - 'source_urls': ['https://pypi.python.org/packages/source/d/dask/'], - 'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'], - }), - ('PyKE', '1.1.1', { - 'source_tmpl': 'pyke-1.1.1.zip', - 'source_urls': ['http://download.sourceforge.net/pyke'], - 'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'], - }), - ('cf_units', '1.2.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'], - 'checksums': ['abdd2a0937b958322f7ff7ec6866e80f08603c60aa06cef5766b6512c750028a'], - }), - ('pyugrid', '0.3.1', { - 'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'], - 'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'], - }), - ('mo_pack', '0.2.0', { - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/SciTools/mo_pack/archive/'], - 'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'], - }), - ('cycler', '0.10.0', { - 'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'], - 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], - }), - ('singledispatch', '3.4.0.3', { - 'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'], - 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], - }), - ('backports_abc', '0.5', { - 'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'], - 'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'], - }), - ('tornado', '4.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'], - 'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'], - }), - ('matplotlib', '1.5.3', { - 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'], - 'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'], - }), - ('toolz', '0.9.0', { - 'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'], - 'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'], - }), - ('scitools-iris', '2.0.0', { - 'modulename': 'iris', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/SciTools/iris/archive/'], - 'checksums': ['8605ab92c67d622e83fff6d7169fe154d9f8610edd8463b697b574884c158ba2'], - }), - ('iris-grib', '0.12.0', { - 'modulename': 'iris_grib', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/SciTools/iris-grib/archive/'], - 'checksums': ['c2e92d25d8bfd2ddff22ae47c4532c884678bac6ea0d935367eced051ae08bb3'], - }), - ('ncdf4', '1.16', { - 'source_tmpl': '%(name)s_%(version)s.tar.gz', - 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/ncdf4', - 'http://cran.r-project.org/src/contrib/', - 'http://cran.freestatistics.org/src/contrib', - ], - 'checksums': ['edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253'], - }), -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'R_LIBS': '', -} - -modloadmsg = "To install ESMValTool in your directory execute: tar zxf $EBROOTESMVALTOOL/ESMValTool-1.1.0.tar.gz\n" - -moduleclass = 'geo' diff --git a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb b/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb deleted file mode 100644 index d8688a45528..00000000000 --- a/easybuild/easyconfigs/l/libmo_unpack/libmo_unpack-3.1.2-GCCore-6.4.0.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libmo_unpack' -version = '3.1.2' - -homepage = "https://github.com/SciTools/libmo_unpack" -description = "A library for handling the WGDOS and RLE compression schemes used in UM files." - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/SciTools/libmo_unpack/archive'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_cmake_have_stdint.patch'] -checksums = [ - 'e09ef3e6f1075144acc5d6466b4ef70b2fe32ed4ab1840dd4fb7e15a40f3d370', # v3.1.2.tar.gz - 'b130f9944e763c53b21c2b08f6d4954ca7811a556fda1c7fec737a4086aad1f5', # libmo_unpack-3.1.2_cmake_have_stdint.patch -] - -builddependencies = [ - ('binutils', '2.28'), - ('CMake', '3.10.1'), - ('check', '0.12.0'), -] - -separate_build_dir = True - -sanity_check_paths = { - 'files': ['include/logerrors.h', 'include/rlencode.h', 'include/wgdosstuff.h', 'lib/libmo_unpack.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'tools' From 5f494cc50462049d6b6f438cbbc3e1b9a735b0e2 Mon Sep 17 00:00:00 2001 From: ~Stack~ Date: Thu, 17 May 2018 21:00:34 -0500 Subject: [PATCH 041/698] Update Readme instructions --- easybuild/easyconfigs/m/MATLAB/README | 165 ----------------------- easybuild/easyconfigs/m/MATLAB/README.md | 32 +++++ 2 files changed, 32 insertions(+), 165 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB/README create mode 100644 easybuild/easyconfigs/m/MATLAB/README.md diff --git a/easybuild/easyconfigs/m/MATLAB/README b/easybuild/easyconfigs/m/MATLAB/README deleted file mode 100644 index f59fbb5c405..00000000000 --- a/easybuild/easyconfigs/m/MATLAB/README +++ /dev/null @@ -1,165 +0,0 @@ -Adjust the 'license_server', 'license_server_port' and 'key' values in the example easyconfig file. - -Steps to produce a 'source' tarball that EasyBuild can handle (example for 2012b): - -* create a directory 2012b -* copy matlab-2012b.tar.gz in 2012b -* copy the 'archives' directory containing installation files for toolboxes into '2012b' -* unzip the matlab-2012b.tar.gz in 2012b -* remove matlab-2012b.tar.gz -* run 'chmod -R 755 *' (overkill, yes, but it does the trick) -* check whether bin/glnxa64/libstdc++.so.6 is correct, fix if required -* tar the 2012b directory: 'tar cfvz matlab-2012b.tar.gz 2012b' - -example layout of 2012b subdirectories: - -$ find -maxdepth 3 -. -./sys -./sys/java -./sys/java/jre -./archives -./archives/Robust_Control_Toolbox42_common.zip -./archives/Fuzzy_Logic_Toolbox2216_common.zip -./archives/Bioinformatics_Toolbox42_common.zip -./archives/Simulink_Design_Optimization22_common.zip -./archives/Parallel_Computing_Toolbox61_common.zip -./archives/Simulink_Control_Design36_common.zip -./archives/DSP_System_Toolbox83_common.zip -./archives/Simulink_Coder83_common.zip -./archives/Model_Predictive_Control_Toolbox411_common.zip -./archives/glnxa64 -./archives/glnxa64/Symbolic_Math_Toolbox59_glnxa64.zip -./archives/glnxa64/License_Manager119_glnxa64.zip -./archives/glnxa64/Robust_Control_Toolbox42_glnxa64.zip -./archives/glnxa64/Wavelet_Toolbox410_glnxa64.zip -./archives/glnxa64/System_Identification_Toolbox81_glnxa64.zip -./archives/glnxa64/Control_System_Toolbox94_glnxa64.zip -./archives/glnxa64/Parallel_Computing_Toolbox61_glnxa64.zip -./archives/glnxa64/Statistics_Toolbox81_glnxa64.zip -./archives/glnxa64/Simulink_Control_Design36_glnxa64.zip -./archives/glnxa64/Model_Predictive_Control_Toolbox411_glnxa64.zip -./archives/glnxa64/DSP_System_Toolbox83_glnxa64.zip -./archives/glnxa64/Simulink_Coder83_glnxa64.zip -./archives/glnxa64/MATLAB80_glnxa64.zip -./archives/glnxa64/Simulink_Design_Optimization22_glnxa64.zip -./archives/glnxa64/Simulink80_glnxa64.zip -./archives/glnxa64/MATLAB_Compiler418_glnxa64.zip -./archives/glnxa64/Bioinformatics_Toolbox42_glnxa64.zip -./archives/glnxa64/Fuzzy_Logic_Toolbox2216_glnxa64.zip -./archives/glnxa64/Curve_Fitting_Toolbox33_glnxa64.zip -./archives/glnxa64/Image_Acquisition_Toolbox44_glnxa64.zip -./archives/glnxa64/Neural_Network_Toolbox80_glnxa64.zip -./archives/glnxa64/Database_Toolbox40_glnxa64.zip -./archives/glnxa64/Optimization_Toolbox621_glnxa64.zip -./archives/glnxa64/Communications_System_Toolbox53_glnxa64.zip -./archives/glnxa64/Partial_Differential_Equation_Toolbox11_glnxa64.zip -./archives/glnxa64/MATLAB_Coder23_glnxa64.zip -./archives/glnxa64/Global_Optimization_Toolbox322_glnxa64.zip -./archives/glnxa64/Image_Processing_Toolbox81_glnxa64.zip -./archives/glnxa64/Signal_Processing_Toolbox618_glnxa64.zip -./archives/Curve_Fitting_Toolbox33_common.zip -./archives/common -./archives/common/License_Manager119_common.zip -./archives/Image_Processing_Toolbox81_common.zip -./archives/Wavelet_Toolbox410_common.zip -./archives/Control_System_Toolbox94_common.zip -./archives/Communications_System_Toolbox53_common.zip -./archives/MATLAB80_common.zip -./archives/Signal_Processing_Toolbox618_common.zip -./archives/Statistics_Toolbox81_common.zip -./archives/Image_Acquisition_Toolbox44_common.zip -./archives/MATLAB_Coder23_common.zip -./archives/Partial_Differential_Equation_Toolbox11_common.zip -./archives/Simulink80_common.zip -./archives/Optimization_Toolbox621_common.zip -./archives/Neural_Network_Toolbox80_common.zip -./archives/Database_Toolbox40_common.zip -./archives/System_Identification_Toolbox81_common.zip -./archives/Symbolic_Math_Toolbox59_common.zip -./archives/Global_Optimization_Toolbox322_common.zip -./archives/MATLAB_Compiler418_common.zip -./etc -./etc/glnxa64 -./etc/glnxa64/MLM -./etc/glnxa64/lmgrd -./etc/glnxa64/lmutil -./etc/LicenseAdministration.pdf -./activate.ini -./license.txt -./install_guide.pdf -./bin -./bin/glnxa64 -./bin/glnxa64/libnativewebproxy.so -./bin/glnxa64/libstdc++.so.6 -./bin/glnxa64/libmwcpp11compat.so -./bin/glnxa64/libmwinstall.so -./bin/glnxa64/libinstutil.so -./bin/glnxa64/libgcc_s.so.1 -./bin/glnxa64/libstdc++.so.6.0.13 -./readme.txt -./java -./java/jar -./java/jar/wizard.jar -./java/jar/matlabinstaller.jar -./java/jar/installwizard.jar -./java/jar/professionalinstaller.jar -./java/jar/activationclient.jar -./java/jar/webproxy.jar -./java/jar/instutil.jar -./java/jar/deactivation.jar -./java/jar/instwiz.jar -./java/jar/net.jar -./java/jar/vrd.jar -./java/jar/install.jar -./java/jar/mlwebservices.jar -./java/splash.png -./java/jarext -./java/jarext/glazedlists_java15.jar -./java/jarext/access-bridge.jar -./java/jarext/commons-io.rights -./java/jarext/lucene-analyzers-2.0.0.jar -./java/jarext/axis2 -./java/jarext/commons-compress.jar -./java/jarext/commons-lang.jar -./java/jarext/jdom.jar -./java/jarext/jdom.rights -./java/jarext/jgoodies-forms.jar -./java/jarext/commons-io.jar -./java/jarext/mwaws_client.jar -./java/jarext/dws_client.jar -./java/jarext/jaccess-1_4.jar -./java/jarext/glazedlists_java15.rights -./java/jarext/xercesImpl.jar -./java/jarext/lucene-core-2.0.0.jar -./java/jarext/webservices -./java/jarext/commons-logging.jar -./java/jarext/xerces.rights -./java/jarext/commons-codec.jar -./java/jarext/guice -./install -./installer_input.txt -./help -./help/basecodes.properties -./help/includes -./help/includes/product -./help/templates -./help/templates/documentation-center.xsl -./help/templates/searchresults.html -./help/install -./help/install/docstyle.css -./help/install/b_prev.gif -./help/install/docscripts.js -./help/install/doccenter.properties -./help/install/pixelclear.gif -./help/install/csh -./help/install/ug -./help/install/network-license-administration.html -./help/install/sv -./help/install/more_arrows.gif -./help/install/index.html -./help/install/b_next.gif -./help/install/doccentertoc.html -./help/install/standard-installation-procedure.html -./help/install/helptargets.map -./help/install/group-license-administration.html diff --git a/easybuild/easyconfigs/m/MATLAB/README.md b/easybuild/easyconfigs/m/MATLAB/README.md new file mode 100644 index 00000000000..6f033643659 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/README.md @@ -0,0 +1,32 @@ +This example uses Matlab 2018a and MATLAB-2018a.eb +Steps to install Matlab: +1. Install the appropriate Java install which requires manual configuration. See Java documentation for install. +1. Matlab needs a "File Installation Key". There are a few options available: + 1. Your Matlab license should have a "File Installation Key" in under "Advanced Options" in the "Install and Activate" tab of your "License Center". This will only install the products associated with this license. + 1. If you need to install all of the toolboxes to support multiple licenses Mathworks can enable a "All Product File Installation Key". This will install all of the client products but will not install server products like MDCS. A second manual installation on top of the first will be required. + 1. If you have a server product key, like MDCS, the "File Installation Key" may not install client products like Matlab Compilers. A second manual installation on top of the first will be required. +1. Edit the EasyBuild script. + 1. Update the version of Java to match the version installed in step 1. + 1. Add the following three lines + ``` + # This string could be really long + key = 'XXXXX-XXXXX-XXXXX-XXXXX-XXXXX-XXXXX' + license_server = '' + license_server_port = '' + ``` +1. Download both ISO files from Mathworks. +1. Create the tar file needed for install. + ``` + $ mkdir R2018a + $ mount -o loop,ro R2018a_glnxa64_dvd1.iso /mnt/ + $ rsync -avHlP /mnt/ R2018a/ + $ umount /mnt + $ mount -o loop,ro R2018a_glnxa64_dvd2.iso /mnt/ + $ rsync -avHlP /mnt/ R2018a/ + $ umount /mnt + $ tar -zcvf /my/easybuild/download/path/matlab-2018a.tar.gz R2018a + ``` +1. Install with EasyBuild + ``` + $ eb MATLAB-2018a.eb -r + ``` From 96242ed907c905fbe7664a412752fca1cf011182 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 May 2018 11:37:57 +0200 Subject: [PATCH 042/698] fixed hard-coded version --- .../ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 4916732144f..bd47e399fc7 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -189,6 +189,9 @@ modextrapaths = { 'R_LIBS': '', } -modloadmsg = "To install ESMValTool in your directory execute: tar zxf $EBROOTESMVALTOOL/ESMValTool-1.1.0.tar.gz\n" +modloadmsg = ( + "To install ESMValTool in your directory execute: " + "tar zxf $EBROOTESMVALTOOL/ESMValTool-%(version)s.tar.gz\n" +) moduleclass = 'geo' From f8801b2aa697d79b0d91d9cf53c0f705a17f5ffe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 May 2018 13:32:10 +0200 Subject: [PATCH 043/698] add tcsh as build dep for AmberTools --- .../easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb index d1917181a5f..b50569eb2d2 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb @@ -19,7 +19,10 @@ checksums = [ '5e25d0671a173d3347d9e4ddec2faec4caed048918a7c339767d7fb312008c52', # Amber-16_fix-hardcoding.patch ] -builddependencies = [('pkg-config', '0.29.2')] +builddependencies = [ + ('pkg-config', '0.29.2'), + ('tcsh', '6.20.00'), +] dependencies = [ ('Python', '2.7.14'), ('netCDF', '4.6.0'), From 6612d3352c996da3d8264f24fc24c93083d33cdb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 24 May 2018 11:34:55 +0200 Subject: [PATCH 044/698] adding easyconfigs: HyPhy-2.3.13-foss-2016b.eb --- .../h/HyPhy/HyPhy-2.3.13-foss-2016b.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb diff --git a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb new file mode 100644 index 00000000000..3298eaa084a --- /dev/null +++ b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = "CMakeMake" + +name = 'HyPhy' +version = '2.3.13' + +homepage = 'https://veg.github.io/hyphy-site/' +description = """HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package + for the analysis of genetic sequences (in particular the inference of natural selection) + using techniques in phylogenetics, molecular evolution, and machine learning""" + +toolchain = {'name': 'foss', 'version': '2016b'} + +source_urls = ['https://github.com/veg/hyphy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['29b72574302c98d38a92d5316b9283caa80a54c3e74c5e278c5bc9ae3d3df499'] + +builddependencies = [('CMake', '3.4.3')] + +configopts = '-DINSTALL_PREFIX=%(installdir)s' + +dependencies = [ + ('cURL', '7.40.0', '', True), +] + +sanity_check_paths = { + 'files': ['bin/HYPHYMP', 'bin/HYPHYMPI'], + 'dirs': [], +} + +moduleclass = 'bio' From 0ccb8aab2c941aabb1e6d33b755c934fbc5377ec Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 12:50:32 +0200 Subject: [PATCH 045/698] {cae}[intel/2018a] Nek5000 v17.0 (REVIREW) --- .../n/Nek5000/Nek5000-17.0-intel-2018a.eb | 45 +++++++++++++++++++ .../n/Nek5000/Nek5000-17.0_hypre_blas.patch | 33 ++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb create mode 100644 easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb new file mode 100644 index 00000000000..07f3071a497 --- /dev/null +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -0,0 +1,45 @@ +easyblock = 'PackedBinary' + +name = 'Nek5000' +version = '17.0' + +homepage = 'https://nek5000.mcs.anl.gov/' +description = "a fast and scalable high-order solver for computational fluid dynamics" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'pic': True, 'usempi': True} + +sources = ['v%(version)s.tar.gz'] +source_urls = ['https://github.com/Nek5000/Nek5000/archive/'] +patches = ['%(name)s-%(version)s_hypre_blas.patch'] + +builddependencies = [('CMake', '3.10.2')] + +dependencies = [('X11', '20180131')] + +buildininstalldir = True + +install_cmd = ( + 'mv %(name)s-%(version)s/{*,.[^.]*} . && rmdir %(name)s-%(version)s && cd tools && ./maketools all &&' + 'cd ../3rd_party/gslib && env GSLIB_OPT="USREXIT=1 BLAS=2 PREFIX=gslib_ FPREFIX=fgslib_" ./install &&' + 'cd ../cvode && ./install' +) + +postinstallcmds = [ + 'sed -i -e "s|^#FC=.*|FC=$FC|" bin/makenek', + 'sed -i -e "s|^#CC=.*|CC=$CC|" bin/makenek', + 'sed -i -e "s|^#FFLAGS=.*|FFLAGS=\\"$FFLAGS\\"|" bin/makenek', + 'sed -i -e "s|^#CFLAGS=.*|CFLAGS=\\"$CFLAGS\\"|" bin/makenek', +] + +sanity_check_paths = { + 'files': ['bin/amg_hypre', 'bin/genmap', 'bin/nekmerge', 'bin/prex', 'bin/genbox', 'bin/n2to3', 'bin/postx', + 'bin/reatore2', 'bin/re2torea'], + 'dirs': [] +} + +modextrapaths = { + 'SOURCE_ROOT': '', +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch new file mode 100644 index 00000000000..2ee2833a72f --- /dev/null +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch @@ -0,0 +1,33 @@ +diff -ru Nek5000-17.0.org/tools/amg_hypre/hypre/install Nek5000-17.0/tools/amg_hypre/hypre/install +--- Nek5000-17.0.org/tools/amg_hypre/hypre/install 2017-12-17 10:08:30.000000000 +0100 ++++ Nek5000-17.0/tools/amg_hypre/hypre/install 2018-05-30 15:51:20.546161373 +0200 +@@ -9,5 +9,5 @@ + + tar -zxf *.tar.gz + cd hypre*/src +-./configure --prefix=`pwd`/../.. --without-MPI ++./configure --prefix=`pwd`/../.. --without-MPI --with-blas-libs="$LIBBLAS" --with-blas-lib-dirs=$BLAS_LAPACK_LIB_DIR --with-lapack-libs="$LIBLAPACK" --with-lapack-lib-dirs=$BLAS_LAPACK_LIB_DIR + make -j4 install +diff -ru Nek5000-17.0.org/tools/amg_hypre/makefile Nek5000-17.0/tools/amg_hypre/makefile +--- Nek5000-17.0.org/tools/amg_hypre/makefile 2017-12-17 10:08:30.000000000 +0100 ++++ Nek5000-17.0/tools/amg_hypre/makefile 2018-05-30 15:54:35.428174247 +0200 +@@ -1,16 +1,16 @@ + PREFIX = $(bin_nek_tools) +-LIBS = ./hypre/lib/libHYPRE.a ++#LIBS = ./hypre/lib/libHYPRE.a + + all: lib amg_hypre + + amg_hypre: amg_hypre.o +- $(CC) -o $(PREFIX)/$@ $^ $(LIBS) $(LDFLAGS) -lm ++ $(CC) -o $(PREFIX)/$@ $^ ./hypre/lib/libHYPRE.a $(LDFLAGS) $(LIBBLAS) -lm + + %.o: %.c + $(CC) -DHAVE_CONFIG_H -DHYPRE_TIMING $(CFLAGS) -I./hypre/include -c $< + + lib: +- @cd hypre; env CC="$(CC)" CFLAGS="$(BIGMEM)" FC="$(FC)" FFLAGS="$(BIGMEM)" ./install ++ @cd hypre; env CC="$(CC)" CFLAGS="$(CFLAGS)" FC="$(FC)" FFLAGS="$(FFLAGS)" ./install + + clean: + @rm -rf amg_hypre *.o hypre/lib hypre/include hypre/hypre* From 5c557bc77d1c34be7dd162a68944ca57ce9b59d2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 12:56:16 +0200 Subject: [PATCH 046/698] add checksums --- easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb | 6 +++++- .../easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch | 2 ++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index 07f3071a497..933e45cd1a9 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -9,9 +9,13 @@ description = "a fast and scalable high-order solver for computational fluid dyn toolchain = {'name': 'intel', 'version': '2018a'} toolchainopts = {'pic': True, 'usempi': True} -sources = ['v%(version)s.tar.gz'] source_urls = ['https://github.com/Nek5000/Nek5000/archive/'] +sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-%(version)s_hypre_blas.patch'] +checksums = [ + '4d8d4793ce3c926c54e09a5a5968fa959fe0ba46bd2e6b8043e099528ee35a60', # v17.0.tar.gz + '55d66818151b63826b55545051145a0b0d806d4df7fcf5cf57cf2c75f461f441', # Nek5000-17.0_hypre_blas.patch +] builddependencies = [('CMake', '3.10.2')] diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch index 2ee2833a72f..76400c683a3 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch @@ -1,3 +1,5 @@ +# Make hyopre to use optimized BLAS/LAPACK and use EB provided compiler flags. Delete LIB as interferes with build in EB +# 01 June 2018 by B. Hajgato (Free University Brussel - VUB) diff -ru Nek5000-17.0.org/tools/amg_hypre/hypre/install Nek5000-17.0/tools/amg_hypre/hypre/install --- Nek5000-17.0.org/tools/amg_hypre/hypre/install 2017-12-17 10:08:30.000000000 +0100 +++ Nek5000-17.0/tools/amg_hypre/hypre/install 2018-05-30 15:51:20.546161373 +0200 From 885ad0343a95d5e7f076743c4ff603d746bf57ad Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 13:32:09 +0200 Subject: [PATCH 047/698] extra Python extensions added --- ...MValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index bd47e399fc7..bb1cd27d941 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -173,6 +173,24 @@ exts_list = [ 'source_urls': ['https://github.com/SciTools/iris-grib/archive/'], 'checksums': ['c2e92d25d8bfd2ddff22ae47c4532c884678bac6ea0d935367eced051ae08bb3'], }), + ('patsy', '0.5.0', { + 'source_urls': ['https://pypi.python.org/packages/source/p/patsy/'], + 'checksums': ['e05f38d5c38c8d216f0cc2b765b1069b433c92d628b954fb2fee68d13e42883b'], + }), + ('statsmodels', '0.9.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'], + 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], + }), + ('cftime', '1.0.0', { + 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'], + 'checksums': ['f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8'], + }), + ('nc-time-axis', '1.1.0', { + 'modulename': 'nc_time_axis', + 'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'], + 'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'], + }), + ('ncdf4', '1.16', { 'source_tmpl': '%(name)s_%(version)s.tar.gz', 'source_urls': [ From 198b1e5ed683a9983c7e52dcf6afa3a97303309b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 13:34:08 +0200 Subject: [PATCH 048/698] extra line deleted --- .../e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index bb1cd27d941..0b7c6ff5698 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -190,7 +190,6 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'], 'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'], }), - ('ncdf4', '1.16', { 'source_tmpl': '%(name)s_%(version)s.tar.gz', 'source_urls': [ From 3246f493846658fec0259ffb14dcedeb0d4b3814 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 13:39:41 +0200 Subject: [PATCH 049/698] fix download link --- .../e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 0b7c6ff5698..e913c32eca2 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -182,7 +182,7 @@ exts_list = [ 'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'], }), ('cftime', '1.0.0', { - 'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'], + 'source_urls': ['https://pypi.python.org/packages/source/c/cftime/'], 'checksums': ['f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8'], }), ('nc-time-axis', '1.1.0', { From 20cd761463744f1fa01aeaa6f4dcd84bbe51d1fb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 13:47:45 +0200 Subject: [PATCH 050/698] add exts_filter --- .../ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index e913c32eca2..ab75df71ba8 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -37,14 +37,19 @@ dependencies = [ ('ecCodes', '2.7.3', versionsuffix), ] -# Python deps, order is important! exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_tmpl': '%(name)s-%(version)s.tar.gz', } +exts_filter = [ + ("python -c 'import %(ext_name)s'", ''), + ("R -q --no-save", "library(%(ext_name)s)"), +] + exts_classmap = {'ncdf4': 'RPackage'} exts_list = [ + # Python deps, order is important! ('olefile', '0.45.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'source_urls': ['https://pypi.python.org/packages/source/o/olefile/'], @@ -190,6 +195,7 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'], 'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'], }), + # R extension ('ncdf4', '1.16', { 'source_tmpl': '%(name)s_%(version)s.tar.gz', 'source_urls': [ From 952d15ce1ba55ad1013fbadac5941099307f49e7 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 1 Jun 2018 13:59:56 +0200 Subject: [PATCH 051/698] add exts_filter --- .../ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index ab75df71ba8..60dc7beafcb 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -42,10 +42,8 @@ exts_default_options = { 'source_tmpl': '%(name)s-%(version)s.tar.gz', } -exts_filter = [ - ("python -c 'import %(ext_name)s'", ''), - ("R -q --no-save", "library(%(ext_name)s)"), -] +#exts_filter = ("python -c 'import %(ext_name)s'", '') +# ("R -q --no-save", "library(%(ext_name)s)"), exts_classmap = {'ncdf4': 'RPackage'} exts_list = [ From 81bb8448879dfa569ef624d278899cc3f1a4318e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Sat, 2 Jun 2018 13:26:49 +0200 Subject: [PATCH 052/698] fixed comment space --- .../ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 60dc7beafcb..839636b78b4 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -42,8 +42,9 @@ exts_default_options = { 'source_tmpl': '%(name)s-%(version)s.tar.gz', } -#exts_filter = ("python -c 'import %(ext_name)s'", '') -# ("R -q --no-save", "library(%(ext_name)s)"), +# exts_filter = +# ("python -c 'import %(ext_name)s'", '') +# ("R -q --no-save", "library(%(ext_name)s)"), exts_classmap = {'ncdf4': 'RPackage'} exts_list = [ From de43733b25d9b331bc74737e04009097c7cfbedb Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 4 Jun 2018 10:51:34 +0200 Subject: [PATCH 053/698] Workaround for EB test bug --- easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index 933e45cd1a9..81d4b4d8e29 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -32,8 +32,9 @@ install_cmd = ( postinstallcmds = [ 'sed -i -e "s|^#FC=.*|FC=$FC|" bin/makenek', 'sed -i -e "s|^#CC=.*|CC=$CC|" bin/makenek', - 'sed -i -e "s|^#FFLAGS=.*|FFLAGS=\\"$FFLAGS\\"|" bin/makenek', - 'sed -i -e "s|^#CFLAGS=.*|CFLAGS=\\"$CFLAGS\\"|" bin/makenek', + 'sed -i -e "s|^#FFLAGS=.*|FFLAGS=$FFLAGS|" bin/makenek', + 'sed -i -e "s|^#CFLAGS=.*|CFLAGS=$CFLAGS|" bin/makenek', + """sed -i -e 's||"|g' bin/makenek""", ] sanity_check_paths = { From 54beef30ecfbb563302fda7de0c6300b705207e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Jun 2018 18:52:23 +0200 Subject: [PATCH 054/698] adding easyconfigs: CFDEMcoupling-3.8.0-foss-2018a.eb --- .../CFDEMcoupling-3.8.0-foss-2018a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2018a.eb diff --git a/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2018a.eb b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2018a.eb new file mode 100644 index 00000000000..0e99e27f34d --- /dev/null +++ b/easybuild/easyconfigs/c/CFDEMcoupling/CFDEMcoupling-3.8.0-foss-2018a.eb @@ -0,0 +1,38 @@ +name = 'CFDEMcoupling' +version = '3.8.0' + +homepage = 'https://www.cfdem.com/cfdemrcoupling-open-source-cfd-dem-framework' +description = """CFDEMcoupling is an open source CFD-DEM engine. It provides the possibility to couple + the DEM engine LIGGGHTS to a CFD framework.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +sources = [ + { + 'source_urls': ['https://github.com/CFDEMproject/CFDEMcoupling-PUBLIC/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/CFDEMproject/LIGGGHTS-PUBLIC/archive/'], + 'download_filename': '%(version)s.tar.gz', + 'filename': 'LIGGGHTS-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/CFDEMproject/LPP/archive/'], + 'download_filename': '633058e.tar.gz', + 'filename': 'LPP-20170223.tar.gz', + }, +] +checksums = [ + '3c90d3178c9667ea84db9507221f65f9efec2aab8d22c51769f8a0c94d813ee4', # CFDEMcoupling-3.8.0.tar.gz + '9cb2e6596f584463ac2f80e3ff7b9588b7e3638c44324635b6329df87b90ab03', # LIGGGHTS-3.8.0.tar.gz + '9b191d89e72fba00bd63b327ee8c79425fb73e4e11aa6c165d464ed8a582627a', # LPP-20170223.tar.gz +] + +dependencies = [ + ('OpenFOAM', '5.0-20180108'), + ('VTK', '8.1.0', '-Python-2.7.14'), +] + +moduleclass = 'cae' From 236a4a44043c809319fd775ec497d05f7725f997 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 21 Jun 2018 12:14:35 +0200 Subject: [PATCH 055/698] libepoxy and Mesa --- .../l/libepoxy/libepoxy-1.5.2-foss-2018a.eb | 33 +++++++++ .../m/Mesa/Mesa-18.1.1-foss-2018a.eb | 72 +++++++++++++++++++ .../Mesa-18.1.1_fix-strip-llvm-flags.patch | 14 ++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb new file mode 100644 index 00000000000..15168844f7f --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libepoxy' +version = '1.5.2' + +homepage = 'http://www.linuxfromscratch.org/blfs/view/svn/x/libepoxy.html' +description = "libepoxy is a library for handling OpenGL function pointer management." + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://github.com/anholt/libepoxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1ffc3ffe0567f986ff5731d4ef3a3765e0a4f9d642fffdae303362567eecd689'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Mesa', '18.1.1'), + ('Python', '2.7.14'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': [ + 'include/epoxy/egl.h', 'include/epoxy/gl.h', 'include/epoxy/glx.h', + 'lib/libepoxy.la', 'lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb new file mode 100644 index 00000000000..8a400c0c791 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb @@ -0,0 +1,72 @@ +# Automatically converted from Mesa-17.3.6-foss-2018a.eb +# Original message: +# the purpose of the easyconfig is to build a Mesa for software rendering, +# not hardware rendering. This means you want at least SSE4.2. We build: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# it will try to use the llvmpipe by default. It you want swr, do: +# GALLIUM_DRIVER=swr + +easyblock = 'ConfigureMake' + +name = 'Mesa' +version = '18.1.1' + +homepage = 'http://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'foss', 'version': '2018a'} +# swr detects and builds parts specific for AVX and AVX2. If we use +# -xHost, this always gets overwritten and will fail. +toolchainopts = {'optarch': False} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] +checksums = [ + 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz + '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-18.1.1_fix-strip-llvm-flags.patch +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.0.4'), + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), + ('Mako', '1.0.7', '-Python-2.7.14'), + ('libxml2', '2.9.7'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('nettle', '3.4'), + ('libdrm', '2.4.91'), + ('LLVM', '5.0.1'), + ('X11', '20180131'), +] + +# GLU is not part anymore of Mesa package! +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" +configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, + 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, + 'include/GL/glext.h', 'include/GL/gl_mangle.h', + 'include/GL/glx.h', 'include/GL/osmesa.h', + 'include/GL/gl.h', 'include/GL/glxext.h', + 'include/GL/glx_mangle.h', 'include/GLES/gl.h', + 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch new file mode 100644 index 00000000000..545bee2c946 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch @@ -0,0 +1,14 @@ +strip out '-fp-model source' as a whole, rather than only stripping out '-fp-model' which leads to compilation errors: +"File not found: 'source'" + +author: Kenneth Hoste (HPC-UGent), based on patch for Mesa 17.0.2 by Ward Poelmans (VUB) +--- configure.orig 2017-11-11 19:54:40.966320129 +0100 ++++ configure 2017-11-11 19:59:25.921932866 +0100 +@@ -22540,6 +22540,7 @@ + -e 's/[[:space:]]+-O[^[:space:]]*//g' \ + -e 's/[[:space:]]+-g[^[:space:]]*//g' \ + -e 's/-fno-rtti[[:space:]]/-Fno-rtti /g' \ ++ -e 's/[[:space]]+-fp-model[[:space:]][^[:space:]]*//g' \ + -e 's/[[:space:]]+-f[^[:space:]]*//g' \ + -e 's/-Fno-rtti[[:space:]]/-fno-rtti /g' \ + -e 's/^[[:space:]]//' \ From f94f6ecbf4f143edf5cdb7036c2807129b3ea807 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 21 Jun 2018 12:51:42 +0200 Subject: [PATCH 056/698] use mesa 17, enable dri and egl --- .../m/Mesa/Mesa-17.3.6-foss-2018a.eb | 4 +- .../m/Mesa/Mesa-18.1.1-foss-2018a.eb | 72 ------------------- .../Mesa-18.1.1_fix-strip-llvm-flags.patch | 14 ---- 3 files changed, 2 insertions(+), 88 deletions(-) delete mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb delete mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb index bb7a8ba7acc..224f5e15f98 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb @@ -52,8 +52,8 @@ dependencies = [ ] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " buildopts = 'V=1' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb deleted file mode 100644 index 8a400c0c791..00000000000 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1-foss-2018a.eb +++ /dev/null @@ -1,72 +0,0 @@ -# Automatically converted from Mesa-17.3.6-foss-2018a.eb -# Original message: -# the purpose of the easyconfig is to build a Mesa for software rendering, -# not hardware rendering. This means you want at least SSE4.2. We build: -# - llvmpipe: the high-performance Gallium LLVM driver -# - swr: Intel's OpenSWR -# it will try to use the llvmpipe by default. It you want swr, do: -# GALLIUM_DRIVER=swr - -easyblock = 'ConfigureMake' - -name = 'Mesa' -version = '18.1.1' - -homepage = 'http://www.mesa3d.org/' -description = """Mesa is an open-source implementation of the OpenGL specification - - a system for rendering interactive 3D graphics.""" - -toolchain = {'name': 'foss', 'version': '2018a'} -# swr detects and builds parts specific for AVX and AVX2. If we use -# -xHost, this always gets overwritten and will fail. -toolchainopts = {'optarch': False} - -source_urls = [ - 'https://mesa.freedesktop.org/archive/', - 'https://mesa.freedesktop.org/archive/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', - 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', -] -sources = [SOURCELOWER_TAR_XZ] -patches = ['Mesa-%(version)s_fix-strip-llvm-flags.patch'] -checksums = [ - 'd3312a2ede5aac14a47476b208b8e3a401367838330197c4588ab8ad420d7781', # mesa-18.1.1.tar.xz - '5aa4e92ed96e3d47ffbecd1ec3a1642407dff11995c5585eb5e06c396654ee30', # Mesa-18.1.1_fix-strip-llvm-flags.patch -] - -builddependencies = [ - ('flex', '2.6.4'), - ('Bison', '3.0.4'), - ('Autotools', '20170619'), - ('pkg-config', '0.29.2'), - ('Mako', '1.0.7', '-Python-2.7.14'), - ('libxml2', '2.9.7'), -] - -dependencies = [ - ('zlib', '1.2.11'), - ('nettle', '3.4'), - ('libdrm', '2.4.91'), - ('LLVM', '5.0.1'), - ('X11', '20180131'), -] - -# GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" -configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " - -buildopts = 'V=1' - -sanity_check_paths = { - 'files': ['lib/libGL.%s' % SHLIB_EXT, 'lib/libOSMesa.%s' % SHLIB_EXT, - 'lib/libGLESv1_CM.%s' % SHLIB_EXT, 'lib/libGLESv2.%s' % SHLIB_EXT, - 'include/GL/glext.h', 'include/GL/gl_mangle.h', - 'include/GL/glx.h', 'include/GL/osmesa.h', - 'include/GL/gl.h', 'include/GL/glxext.h', - 'include/GL/glx_mangle.h', 'include/GLES/gl.h', - 'include/GLES2/gl2.h', 'include/GLES3/gl3.h'], - 'dirs': [] -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch b/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch deleted file mode 100644 index 545bee2c946..00000000000 --- a/easybuild/easyconfigs/m/Mesa/Mesa-18.1.1_fix-strip-llvm-flags.patch +++ /dev/null @@ -1,14 +0,0 @@ -strip out '-fp-model source' as a whole, rather than only stripping out '-fp-model' which leads to compilation errors: -"File not found: 'source'" - -author: Kenneth Hoste (HPC-UGent), based on patch for Mesa 17.0.2 by Ward Poelmans (VUB) ---- configure.orig 2017-11-11 19:54:40.966320129 +0100 -+++ configure 2017-11-11 19:59:25.921932866 +0100 -@@ -22540,6 +22540,7 @@ - -e 's/[[:space:]]+-O[^[:space:]]*//g' \ - -e 's/[[:space:]]+-g[^[:space:]]*//g' \ - -e 's/-fno-rtti[[:space:]]/-Fno-rtti /g' \ -+ -e 's/[[:space]]+-fp-model[[:space:]][^[:space:]]*//g' \ - -e 's/[[:space:]]+-f[^[:space:]]*//g' \ - -e 's/-Fno-rtti[[:space:]]/-fno-rtti /g' \ - -e 's/^[[:space:]]//' \ From b922df9e51c48229cad2c16b248fda14d8a41226 Mon Sep 17 00:00:00 2001 From: RvDijk Date: Thu, 21 Jun 2018 13:04:39 +0200 Subject: [PATCH 057/698] also change Mesa version in libepoxy eb file --- easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb index 15168844f7f..0db3afaae7b 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb @@ -17,7 +17,7 @@ builddependencies = [ ] dependencies = [ - ('Mesa', '18.1.1'), + ('Mesa', '17.3.6'), ('Python', '2.7.14'), ] From 77d25ff7326c45194533a376f4aa2974144cfc45 Mon Sep 17 00:00:00 2001 From: Jack Perdue Date: Wed, 4 Jul 2018 09:19:07 -0500 Subject: [PATCH 058/698] adding easyconfigs: Bsoft-2.0.2-foss-2017b.eb --- .../b/Bsoft/Bsoft-2.0.2-foss-2017b.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb diff --git a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb new file mode 100644 index 00000000000..3a4495306e2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb @@ -0,0 +1,63 @@ +# Authors: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'Bsoft' +version = '2.0.2' + +homepage = 'http://lsbr.niams.nih.gov/bsoft/' + +description = """ + Bsoft is a collection of programs and a platform for development of software + for image and molecular processing in structural biology. Problems in + structural biology are approached with a highly modular design, allowing fast + development of new algorithms without the burden of issues such as file I/O. + It provides an easily accessible interface, a resource that can be and has + been used in other packages. +""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'openmp': True} + +# https://lsbr.niams.nih.gov/bsoft/bsoft2_0_2.tgz +source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] +sources = ['%%(namelower)s%s.tgz' % '_'.join(version.split('.'))] + +dependencies = [ + # ('FFTW', '3.3.6'), # FFTW is included in foss/2017b toolchain + ('libjpeg-turbo', '1.5.3'), + ('libpng', '1.6.34'), + ('LibTIFF', '4.0.9'), + ('libxml2', '2.9.8'), + ('Tk', '8.6.8') +] + +skipsteps = ['configure'] + +prebuildopts = """ + # fix libxml2 include path + sed -e 's,^XMLINC=.*,XMLINC=$EBROOTLIBXML2/include/libxml2,'\ + -i.eb.xmlinc bsoft/bsoft_conf + # fix fftw3 include path + sed -e 's,LIBFFTW/api,LIBFFTW/include,'\ + -i.eb.fftw3inc bsoft/bsoft_conf + # configure + ./bconf --prefix=%(installdir)s --fftw=$EBROOTFFTW --tiff=$EBROOTLIBTIFF\ + --jpeg=$EBROOTLIBJPEGMINTURBO --png=$EBROOTLIBPNG +""" + +# try parallel (EB default) build first then fall back to sequential +buildopts = 'bsoft || make bsoft' + +sanity_check_paths = { + 'files': ['bsoft.bashrc', 'bsetup', 'bin/brun', 'bin/bshow', + 'lib/libbsoft.so', 'lib/libbshow.so'], + 'dirs': [], +} + +modextrapaths = { + 'BSOFT': '', + 'BPARAM': 'parameters', +} + +moduleclass = 'bio' From 2cefd93bf3a6cfede098e5f16a11b57643210c5b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jul 2018 09:36:49 +0200 Subject: [PATCH 059/698] adding easyconfigs: OpenFOAM-2.2.2-intel-2018a.eb --- .../o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb new file mode 100644 index 00000000000..61783f35034 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb @@ -0,0 +1,39 @@ +name = 'OpenFOAM' +version = '2.2.2' + +homepage = 'http://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://downloads.sourceforge.net/foam/%(version)s'] +sources = [ + SOURCE_TGZ, + 'ThirdParty-%(version)s.tgz', +] + +patches = [ + 'cleanup-OpenFOAM-%(version)s.patch', + 'OpenFOAM-2.2.0_libreadline.patch', + ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir +] + +dependencies = [ + ('libreadline', '7.0'), + ('METIS', '5.1.0'), + ('ncurses', '6.0'), + ('SCOTCH', '6.0.5'), + ('Boost', '1.66.0'), +] + + +builddependencies = [ + ('flex', '2.5.39'), + ('Bison', '3.0.4'), + ('CMake', '3.10.2'), +] + +moduleclass = 'cae' From d726ece62b394923733baae28d1359c0c462bc1f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Mon, 23 Jul 2018 15:41:31 +0200 Subject: [PATCH 060/698] trimAl easyconfig for foss and intel --- .../t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb | 38 +++++++++++++++++++ .../t/trimAl/trimAl-1.4.1-intel-2018a.eb | 38 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-intel-2018a.eb diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb new file mode 100644 index 00000000000..4d9c1f4619a --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'http://trimal.cgenomics.org/' +description = 'A tool for automated alignment trimming in large-scale phylogenetic analyses' + +toolchain = {'name': 'goolf', 'version': '1.7.20'} + +source_urls = ['https://github.com/scapella/trimal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +start_dir = 'source' + +buildopts = ' CC=${CXX}' + +files_to_copy = [ + (['trimal', 'statal', 'readal'], 'bin'), + 'AUTHORS', + 'CHANGELOG', + 'dataset', + 'LICENSE', + 'README', +] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/statal', 'bin/readal'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-intel-2018a.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-intel-2018a.eb new file mode 100644 index 00000000000..911b37a4572 --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-intel-2018a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'http://trimal.cgenomics.org/' +description = 'A tool for automated alignment trimming in large-scale phylogenetic analyses' + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://github.com/scapella/trimal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +start_dir = 'source' + +buildopts = ' CC=${CXX}' + +files_to_copy = [ + (['trimal', 'statal', 'readal'], 'bin'), + 'AUTHORS', + 'CHANGELOG', + 'dataset', + 'LICENSE', + 'README', +] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/statal', 'bin/readal'], + 'dirs': [], +} + +moduleclass = 'bio' From 897fb526f936910143add5384bad1bf21d60f869 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 25 Jul 2018 15:52:43 +0200 Subject: [PATCH 061/698] Fortran Unit Test Framework, FRUIT v3.4.3 and dependencies (Ruby-Tk v0.2.0) --- .../FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb | 39 ++++++++++++++++++ .../f/FRUIT/fruit_3.4.3-ifort-external.patch | 41 +++++++++++++++++++ ..._processor-3.4.3-intel-2018a-Ruby-2.5.1.eb | 35 ++++++++++++++++ .../Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb | 30 ++++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb create mode 100644 easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch create mode 100644 easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb create mode 100644 easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb new file mode 100644 index 00000000000..a8d3620bf05 --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FRUIT' +version = '3.4.3' + +rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://fortranxunit.sourceforge.io' +description = "FORTRAN Unit Test Framework (FRUIT)" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] +sources = ['fruit_%(version)s.zip'] +patches = ['fruit_3.4.3-ifort-external.patch'] +checksums = [ + '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip + 'a77e1315d41da1f767536252f3afce77dbb58eda7aea138055f03b11c9836bf8', # fruit_3.4.3-ifort-external.patch +] + +builddependencies = [ + ('Ruby', rubyver), + ('FRUIT_processor', '3.4.3', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'rake || ' + +preinstallopts = 'mkdir -p %(installdir)s/include && cp src/*.mod %(installdir)s/include && ' +preinstallopts += 'mkdir -p %(installdir)s/lib && cp src/*.a %(installdir)s/lib || ' + +sanity_check_paths = { + 'files': ['include/fruit.mod', 'include/fruit_util.mod', 'lib/libfruit.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch new file mode 100644 index 00000000000..67626086533 --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch @@ -0,0 +1,41 @@ +diff -Nru fruit_3.4.3-orig/rake_base.rb fruit_3.4.3/rake_base.rb +--- fruit_3.4.3-orig/rake_base.rb 2018-07-20 17:34:13.506622790 +0200 ++++ fruit_3.4.3/rake_base.rb 2018-07-20 18:04:32.166241482 +0200 +@@ -9,11 +9,11 @@ + if RUBY_PLATFORM =~ /(darwin|linux)/i + # Intel FORTRAN compiler tested on Linux + $compiler = 'ifort' +- $option = "-check all -warn all -fpp" ++ $option = "-check all -fpp -fPIC" + $ext_obj = "o" + $dosish_path = false + $gcov = false +- $prof_genx = "-prof-genx" ++ $prof_genx = "-prof-gen=srcpos" + $mpiexec = nil + else + # Intel FORTRAN on Windows +diff -Nru fruit_3.4.3-orig/sample_mpi/rakefile fruit_3.4.3/sample_mpi/rakefile +--- fruit_3.4.3-orig/sample_mpi/rakefile 2018-07-20 17:34:13.507622832 +0200 ++++ fruit_3.4.3/sample_mpi/rakefile 2018-07-23 11:38:34.669769977 +0200 +@@ -46,7 +46,7 @@ + + task :run => [ $goal, "mpi_machine_file" ] do + sleep 3 +- sh "mpiexec -np 2 -machinefile mpi_machine_file #{$goal}" ++ sh "mpiexec -np 2 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal}" + end + + +diff -Nru fruit_3.4.3-orig/self_test_mpi/rakefile fruit_3.4.3/self_test_mpi/rakefile +--- fruit_3.4.3-orig/self_test_mpi/rakefile 2018-07-20 17:34:13.506622790 +0200 ++++ fruit_3.4.3/self_test_mpi/rakefile 2018-07-20 18:50:42.630311001 +0200 +@@ -31,7 +31,7 @@ + + task :run => [ $goal, "mpi_machine_file" ] do + sleep 3 +- sh "mpiexec -np 3 -machinefile mpi_machine_file #{$goal} > stdout" ++ sh "mpiexec -np 3 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal} > stdout" + end + + task :verify => [ :run ] do diff --git a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb new file mode 100644 index 00000000000..6a67ed476fb --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'FRUIT_processor' +version = '3.4.3' + +rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://fortranxunit.sourceforge.io' +description = "FORTRAN Unit Test Framework (FRUIT)" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] + +sources = ['fruit_%(version)s.zip'] +checksums = ['01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862'] + +builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix, toolchain)] + +dependencies = [('Ruby', rubyver)] + +skipsteps = ['configure', 'build'] + +preinstallopts = 'GEM_HOME=%(installdir)s ' +preinstallopts += 'gem install --bindir %(installdir)s/bin --local fruit_processor_gem/pkg/fruit_processor-3.4.3.gem ||' + +modextrapaths = {'GEM_PATH': ''} + +sanity_check_paths = { + 'files': ['gems/fruit_processor-3.4.3/lib/%(namelower)s.rb'], + 'dirs': ['gems/%(namelower)s-%(version)s/lib'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb new file mode 100644 index 00000000000..cc104d58c06 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb @@ -0,0 +1,30 @@ +easyblock = 'RubyGem' + +name = 'Ruby-Tk' +version = '0.2.0' + +rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/ruby/tk' +description = "Ruby/Tk" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['tk-%(version)s.gem'] +checksums = ['0d324ae915c20020bea946b1d0b0b35244f16fd2dacc35cf9647b9ac1ea1fc3f'] + +dependencies = [ + ('Ruby', rubyver), + ('Tk', '8.6.8'), +] + +sanity_check_paths = { + 'files': ['gems/tk-%(version)s/bin/console', + 'gems/tk-%(version)s/bin/setup', + 'gems/tk-%s/lib/tkutil.%s' % (version, SHLIB_EXT)], + 'dirs': ['gems/tk-%(version)s/bin', 'gems/tk-%(version)s/lib/tk'] +} + +moduleclass = 'vis' From 7278921a4544e413114901cd3457830895300498 Mon Sep 17 00:00:00 2001 From: jdemeul Date: Thu, 9 Aug 2018 15:54:32 +0000 Subject: [PATCH 062/698] adding easyconfig R-3.5.1-foss-2018a-X11-20180131-bare.eb --- .../R/R-3.5.1-foss-2018a-X11-20180131-bare.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb new file mode 100644 index 00000000000..b6a4f8cbb10 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb @@ -0,0 +1,69 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +name = 'R' +version = '3.5.1' +x11ver = '20180131' +versionsuffix = '-X11-%s-bare' % x11ver + +homepage = 'http://www.r-project.org/' +description = """R is a free software environment for statistical computing and graphics.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0463bff5eea0f3d93fa071f79c18d0993878fd4f2e18ae6cf22c1639d11457ed'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', x11ver), + ('Mesa', '17.3.6'), + ('libGLU', '9.0.0'), + ('cairo', '1.14.12'), + ('libreadline', '7.0'), + ('ncurses', '6.0'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('zlib', '1.2.11'), + ('SQLite', '3.21.0'), + ('PCRE', '8.41'), + ('libpng', '1.6.34'), # for plotting in R + ('libjpeg-turbo', '1.5.3'), # for plottting in R + ('LibTIFF', '4.0.9'), + ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it + ('Tcl', '8.6.8'), # for tcltk + ('Tk', '8.6.8'), # for tcltk + ('cURL', '7.58.0'), # for RCurl + ('libxml2', '2.9.7'), # for XML + ('GDAL', '2.2.3', '-Python-3.6.4'), # for rgdal + ('PROJ', '5.0.0'), # for rgdal + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.4.2'), # for nloptr + ('FFTW', '3.3.7'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.2h'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_list = [] + +moduleclass = 'lang' From 45ccd1d1fbfbeddd6192654d7223dd15ed816209 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 4 Sep 2018 10:51:06 +0200 Subject: [PATCH 063/698] adding easyconfigs: BDBag-1.4.1-intel-2018a-Python-3.6.4.eb --- .../BDBag-1.4.1-intel-2018a-Python-3.6.4.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..c0955788c59 --- /dev/null +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,50 @@ +easyblock = 'Bundle' + +name = 'BDBag' +version = '1.4.1' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://github.com/fair-research/bdbag' +description = """The bdbag utilities are a collection of software programs for +working with BagIt packages that conform to the Bagit and Bagit/RO profiles.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +# this is a bundle of Python packages +exts_defaultclass = 'PythonPackage' +exts_download_dep_fail = True + +dependencies = [ + ('Python', '3.6.4'), +] + +exts_list = [ + ('tzlocal', '2.0.0b1', { + 'source_urls': ['https://pypi.python.org/packages/source/t/tzlocal'], + 'source_tmpl': 'tzlocal-2.0.0b1.tar.gz', + 'checksums': ['27d58a0958dc884d208cdaf45ef5892bf2a57d21d9611f2ac45e51f1973e8cab'], + }), + ('bagit', '1.6.4', { + 'source_urls': ['https://pypi.python.org/packages/source/b/bagit'], + 'source_tmpl': 'bagit-1.6.4.tar.gz', + 'checksums': ['91c5e253ad4ae0c5a5e795c689cda348c01286c671e9f6ca5cab0018980f9be9'], + }), + (name, version, { + 'source_urls': ['https://github.com/fair-research/bdbag/archive'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['8a18c36fa299e83cdc1974b2f1811242180021b52d23224efa3c286cfe901b76'], + }), +] + + +# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module +full_sanity_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'data' From 73e675daae2cde8d743ba083baff5e63e7cb6db1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 7 Sep 2018 18:46:12 +0200 Subject: [PATCH 064/698] libxcb v1.13 built for GCCcore/6.4.0 --- .../l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb | 27 ++++++++++++++ .../libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb | 28 +++++++++++++++ .../l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb | 36 +++++++++++++++++++ .../easyconfigs/x/xcb-proto/xcb-proto-1.13.eb | 26 ++++++++++++++ 4 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb create mode 100644 easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..159b911a9d1 --- /dev/null +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libXau' +version = '1.0.8' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXau package contains a library implementing the X11 Authorization Protocol. +This is useful for restricting client access to the display.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['lib/libXau.a', 'lib/libXau.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..39e627fae12 --- /dev/null +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libXdmcp' +version = '1.1.2' + +homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is +useful for allowing clients to interact with the X Display Manager. +""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +sources = [SOURCE_TAR_GZ] +source_urls = [XORG_LIB_SOURCE] + +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.1'), +] + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb new file mode 100644 index 00000000000..d27d0fdd901 --- /dev/null +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libxcb' +version = '1.13' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +toolchain = {'name': 'GCCcore', 'version': '6.4.0'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.28'), + ('pkg-config', '0.29.2'), + ('xcb-proto', '1.13', '', True), + ('xproto', '7.0.31'), + ('libpthread-stubs', '0.4'), + ('xorg-macros', '1.19.1'), +] +dependencies = [ + ('libXau', '1.0.8'), + ('libXdmcp', '1.1.2'), +] + +sanity_check_paths = { + 'files': ['lib/libxcb%s.a' % x for x in ['', '-composite', '-damage', '-dpms', '-dri2', '-glx', + '-randr', '-record', '-render', '-res', '-screensaver', + '-shape', '-shm', '-sync', '-xf86dri', '-xfixes', + '-xinerama', '-xtest', '-xv', '-xvmc']], + 'dirs': ['include/xcb', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb new file mode 100644 index 00000000000..226a9dd2d7a --- /dev/null +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'xcb-proto' +version = '1.13' + +homepage = 'http://xcb.freedesktop.org/' +description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, +latency hiding, direct access to the protocol, improved threading support, and extensibility.""" + +# even though xcb-proto is installed with configure-make-make install, nothing is actually built; +# only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://xcb.freedesktop.org/dist/'] +sources = [SOURCELOWER_TAR_GZ] + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) + +sanity_check_paths = { + 'files': ['lib/pkgconfig/xcb-proto.pc'], + 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] +} + +moduleclass = 'devel' From 513e571763d3a4dffeeeeafe3a028185616893a4 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 10 Sep 2018 09:53:42 +0200 Subject: [PATCH 065/698] Add missing checksums for libxcb v1.13 and dependencies [GCCcore/6.4.0] --- easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb | 3 ++- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb | 3 ++- easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb | 1 + easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb | 1 + 4 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb index 159b911a9d1..242381d83e3 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb @@ -9,8 +9,9 @@ This is useful for restricting client access to the display.""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c343b4ef66d66a6b3e0e27aa46b37ad5cab0f11a5c565eafb4a1c7590bc71d7b'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb index 39e627fae12..c7f421b0a38 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb @@ -10,8 +10,9 @@ useful for allowing clients to interact with the X Display Manager. toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCE_TAR_GZ] source_urls = [XORG_LIB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['6f7c7e491a23035a26284d247779174dedc67e34e93cc3548b648ffdb6fc57c0'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb index d27d0fdd901..07567190500 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb'] builddependencies = [ ('binutils', '2.28'), diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb index 226a9dd2d7a..38564e30c77 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'dummy', 'version': 'dummy'} source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7'] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] From 781792c98737fda464ee15d70a88488d0db8401b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 17 Sep 2018 16:01:21 +0200 Subject: [PATCH 066/698] add missing checksums --- .../easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb index 61783f35034..2dd736009f9 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb @@ -14,12 +14,18 @@ sources = [ SOURCE_TGZ, 'ThirdParty-%(version)s.tgz', ] - patches = [ 'cleanup-OpenFOAM-%(version)s.patch', 'OpenFOAM-2.2.0_libreadline.patch', ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir ] +checksums = [ + '097adf813e035d04c9be19ee244632cd76971fde107682d50983f8d5cdcf0210', # OpenFOAM-2.2.2.tgz + '0507ed5c050b87090010f2fe9798caccee30402434f29b867614d452bfd84bd2', # ThirdParty-2.2.2.tgz + '17e7ef6fa04020316e60bf286942f3d30d33e9dfe57f744839131d0511a4e885', # cleanup-OpenFOAM-2.2.2.patch + 'f1c94764fe07a43877d85497d5c7958a3f162d1b5f1370232084912a6d606181', # OpenFOAM-2.2.0_libreadline.patch + 'acae6d27ab8d5197d1df167f986a03188e6404aa58d710f41a693008a11e2583', # cleanup-ThirdParty-2.2.2.patch +] dependencies = [ ('libreadline', '7.0'), From 0784135de11d433e5b5e81b9d916b213410871ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Sep 2018 09:56:07 +0200 Subject: [PATCH 067/698] adding easyconfigs: lavaan-0.6-2-intel-2018a-R-3.4.4.eb --- .../lavaan-0.6-2-intel-2018a-R-3.4.4.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb diff --git a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb new file mode 100644 index 00000000000..3de0a5f8bb0 --- /dev/null +++ b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'lavaan' +version = '0.6-2' +versionsuffix = '-R-%(rver)s' + +homepage = 'http://cran.r-project.org/web/packages/%(name)s' +description = """Fit a variety of latent variable models, including confirmatory factor analysis, structural + equation modeling and latent growth curve models.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['91d5aea1468394f9e2bda773ab51f8a16a198bfc1d8474c1c48bcaba87f9c0be'] + +dependencies = [('R', '3.4.4', '-X11-20180131')] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lavaan'], +} + +moduleclass = 'math' From 3dce0c8d5c2c9df5c07a4c36574fb729f1f972cc Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 21 Sep 2018 11:43:29 +0200 Subject: [PATCH 068/698] Added easyconfig for SeqKit 0.8.1 --- .../easyconfigs/s/SeqKit/SeqKit-0.8.1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb new file mode 100644 index 00000000000..dfe91002e0f --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb @@ -0,0 +1,20 @@ +easyblock = 'PackedBinary' + +name = 'SeqKit' +version = '0.8.1' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['https://github.com/shenwei356/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s_linux_amd64.tar.gz'] +checksums = ['62dc2514d2f114146ff9377ce25abf7bd8159ac914d3ca2b9818828120b2097d'] + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From b9a3afa92795276d6113ada940ebddd8f4f24031 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 15 Oct 2018 20:10:22 +0200 Subject: [PATCH 069/698] {bio}[binary] ORFfinder 0.4.3 (REVIEW) --- .../o/ORFfinder/ORFfinder-0.4.3.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb diff --git a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb new file mode 100644 index 00000000000..b08fef35e1e --- /dev/null +++ b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb @@ -0,0 +1,29 @@ +easyblock = 'PackedBinary' + +name = 'ORFfinder' +version = '0.4.3' + +homepage = 'https://www.ncbi.nlm.nih.gov/orffinder/' +description = """ORF finder searches for open reading frames (ORFs) in the + DNA sequence you enter. The program returns the range of each ORF, + along with its protein translation. Use ORF finder to search newly + sequenced DNA for potential protein encoding segments, verify + predicted protein using newly developed SMART BLAST or regular BLASTP.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = ['http://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] +sources = [{'filename': '%(name)s-%(version)s.gz', 'download_filename': '%(name)s.gz'}] +checksums = ['eff0347277c960c207e7efdf0e5a08889f072dffd12fa6e5a843f06782ee53a8'] + +postinstallcmds = ['mv %(installdir)s/ORFfinder-%(version)s %(installdir)s/ORFfinder &&' + 'chmod +x %(installdir)s/ORFfinder'] + +sanity_check_paths = { + 'files': ['ORFfinder'], + 'dirs': [''], +} + +sanity_check_commands = [('ORFfinder', '-version-full')] + +moduleclass = 'bio' From b309592af3fcb487f0f34cc9a8cc163368764fd4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 17 Oct 2018 10:40:32 +0200 Subject: [PATCH 070/698] Style changes - comment added to determine the version --- easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb index b08fef35e1e..fa96b1674a7 100644 --- a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb +++ b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb @@ -1,6 +1,8 @@ easyblock = 'PackedBinary' name = 'ORFfinder' +# The only way to get the version id to download the software and run "ORFfinder -version" command +# There is no way to download old versions. version = '0.4.3' homepage = 'https://www.ncbi.nlm.nih.gov/orffinder/' @@ -16,14 +18,16 @@ source_urls = ['http://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] sources = [{'filename': '%(name)s-%(version)s.gz', 'download_filename': '%(name)s.gz'}] checksums = ['eff0347277c960c207e7efdf0e5a08889f072dffd12fa6e5a843f06782ee53a8'] -postinstallcmds = ['mv %(installdir)s/ORFfinder-%(version)s %(installdir)s/ORFfinder &&' - 'chmod +x %(installdir)s/ORFfinder'] +postinstallcmds = [ + 'mv %(installdir)s/ORFfinder-%(version)s %(installdir)s/ORFfinder', + 'chmod +x %(installdir)s/ORFfinder' +] sanity_check_paths = { 'files': ['ORFfinder'], - 'dirs': [''], + 'dirs': [], } -sanity_check_commands = [('ORFfinder', '-version-full')] +sanity_check_commands = ["ORFfinder -version-full"] moduleclass = 'bio' From 4ee2899c83011b710e69c6f31344556a712b838d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Nov 2018 15:08:38 +0100 Subject: [PATCH 071/698] adding easyconfigs: Kratos-6.0-intel-2018a-Python-3.6.4.eb and patches: Kratos-6.0_fix-install.patch --- .../Kratos-6.0-intel-2018a-Python-3.6.4.eb | 58 +++++++++++++++++++ .../k/Kratos/Kratos-6.0_fix-install.patch | 48 +++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb create mode 100644 easybuild/easyconfigs/k/Kratos/Kratos-6.0_fix-install.patch diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..6d4886cb21e --- /dev/null +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'Kratos' +version = '6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.cimne.com/kratos' +description = """Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary + simulation software.""" + +toolchain = {'name': 'intel', 'version': '2018a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/KratosMultiphysics/Kratos/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['Kratos-%(version)s_fix-install.patch'] +checksums = [ + '93effdd248d1624ffb5593e3292d429b4fc07764be2a6f2a64779f2951332b33', # v6.0.tar.gz + 'b32e0f0b4d05a524d80479d03a3fbefb8da9c393510694853402ae3efb462ad6', # Kratos-6.0_fix-install.patch +] + +builddependencies = [('CMake', '3.12.1')] +dependencies = [ + ('Python', '3.6.4'), + ('Boost', '1.66.0'), + ('zlib', '1.2.11'), +] + +separate_build_dir = True + +# see configure.sh script for default set of configuration options +configopts = "-DCMAKE_BUILD_TYPE=Release -DKRATOS_INSTALL_PREFIX=%(installdir)s -DBOOST_ROOT=$EBROOTBOOST " +configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DINSTALL_EMBEDDED_PYTHON=ON -DINSTALL_PYTHON_FILES=ON " +configopts += "-DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSTRUCTURAL_MECHANICS_APPLICATION=ON " +configopts += "-DCONVECTION_DIFFUSION_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DFSI_APPLICATION=ON " +configopts += "-DCONSTITUTIVE_MODELS_APPLICATION=ON -DFLUID_DYNAMICS_APPLICATION=ON -DMESH_MOVING_APPLICATION=ON " +configopts += "-DDEM_APPLICATION=OFF -DSWIMMING_DEM_APPLICATION=OFF -DMIXED_ELEMENT_APPLICATION=OFF " +configopts += "-DSHAPE_OPTIMIZATION_APPLICATION=OFF -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF " +# -DMETIS_APPLICATION=OFF -DPARMETIS_ROOT_DIR=$EBROOTPARMETIS # still requires ParMETIS 3.x ?! +# -DTRILINOS_APPLICATION=OFF -DTRILINOS_ROOT=$EBROOTTRILINOS + +sanity_check_paths = { + 'files': ['libs/libKratosCore.so', 'runkratos'], + 'dirs': ['applications', 'kratos'], +} + +sanity_check_commands = [ + "python -c 'import Kratos'", + "python -c 'import KratosMultiphysics'", +] + +modextrapaths = { + 'LD_LIBRARY_PATH': 'libs', + 'PATH': '', + 'PYTHONPATH': ['', 'libs'], +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0_fix-install.patch b/easybuild/easyconfigs/k/Kratos/Kratos-6.0_fix-install.patch new file mode 100644 index 00000000000..d51bfb875b2 --- /dev/null +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0_fix-install.patch @@ -0,0 +1,48 @@ +* don't determine absolute path for '-lm' in ${LAPACK_LIBRARIES} +* don't copy BLAS/LAPACK & Python libraries in Kratos installation directory +author: Kenneth Hoste (HPC-UGent) +--- Kratos-6.0/CMakeLists.txt.orig 2018-06-03 01:01:18.000000000 +0200 ++++ Kratos-6.0/CMakeLists.txt 2018-11-05 13:24:15.910188812 +0100 +@@ -289,7 +289,12 @@ + find_package(LAPACK REQUIRED) + message("LAPACK = " ${LAPACK_LIBRARIES}) + foreach( l ${LAPACK_LIBRARIES}) +- GET_FILENAME_COMPONENT(aux ${l} REALPATH) ++ string(SUBSTRING "${l}" 0 1 lstart) ++ if(${lstart} STREQUAL "-") ++ set(aux "${l}") ++ else() ++ GET_FILENAME_COMPONENT(aux ${l} REALPATH) ++ endif() + set(LAPACK_LIBRARIES_REALPATH ${LAPACK_LIBRARIES_REALPATH} ${aux}) + endforeach(l) + +@@ -413,12 +421,12 @@ + install(FILES ${EXTRA_INSTALL_LIBS} DESTINATION libs) + + # Install blas and lapack +-if(${BLAS_INCLUDE_NEEDED} MATCHES ON ) +- message("installed blas = " ${BLAS_LIBRARIES}) +- install(FILES ${BLAS_LIBRARIES} DESTINATION libs) +- message("installed lapack = " ${LAPACK_LIBRARIES}) +- install(FILES ${LAPACK_LIBRARIES} DESTINATION libs) +-endif(${BLAS_INCLUDE_NEEDED} MATCHES ON ) ++#if(${BLAS_INCLUDE_NEEDED} MATCHES ON ) ++# message("installed blas = " ${BLAS_LIBRARIES}) ++# install(FILES ${BLAS_LIBRARIES} DESTINATION libs) ++# message("installed lapack = " ${LAPACK_LIBRARIES}) ++# install(FILES ${LAPACK_LIBRARIES} DESTINATION libs) ++#endif(${BLAS_INCLUDE_NEEDED} MATCHES ON ) + + # Kratos Testing. Install everything except sources + if(${INSTALL_TESTING_FILES} MATCHES ON ) +--- Kratos-6.0/embedded_python/CMakeLists.txt.orig 2018-11-06 11:06:53.182171930 +0100 ++++ Kratos-6.0/embedded_python/CMakeLists.txt 2018-11-06 11:06:59.232153624 +0100 +@@ -21,5 +21,5 @@ + endif(USE_COTIRE MATCHES ON) + install(TARGETS runkratos DESTINATION . ) + +-message("python libraries to be installed are: " ${PYTHON_LIBRARIES} ) +-install(FILES ${PYTHON_LIBRARIES} DESTINATION .) ++#message("python libraries to be installed are: " ${PYTHON_LIBRARIES} ) ++#install(FILES ${PYTHON_LIBRARIES} DESTINATION .) From 8c82a26ee196d6ee3287c888c3ac89544365371c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Nov 2018 17:30:13 +0100 Subject: [PATCH 072/698] build Kratos with MPI supports by also including METIS & Trilinos as dependencies --- .../k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb index 6d4886cb21e..577f3f30d35 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -24,6 +24,8 @@ dependencies = [ ('Python', '3.6.4'), ('Boost', '1.66.0'), ('zlib', '1.2.11'), + ('METIS', '5.1.0'), + ('Trilinos', '12.12.1', versionsuffix), ] separate_build_dir = True @@ -34,13 +36,13 @@ configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DINSTALL_EMBEDDED_P configopts += "-DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSTRUCTURAL_MECHANICS_APPLICATION=ON " configopts += "-DCONVECTION_DIFFUSION_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DFSI_APPLICATION=ON " configopts += "-DCONSTITUTIVE_MODELS_APPLICATION=ON -DFLUID_DYNAMICS_APPLICATION=ON -DMESH_MOVING_APPLICATION=ON " +configopts += "-DMETIS_APPLICATION=ON -DUSE_METIS_5=ON " +configopts += "-DTRILINOS_APPLICATION=ON -DTRILINOS_ROOT=$EBROOTTRILINOS " configopts += "-DDEM_APPLICATION=OFF -DSWIMMING_DEM_APPLICATION=OFF -DMIXED_ELEMENT_APPLICATION=OFF " configopts += "-DSHAPE_OPTIMIZATION_APPLICATION=OFF -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF " -# -DMETIS_APPLICATION=OFF -DPARMETIS_ROOT_DIR=$EBROOTPARMETIS # still requires ParMETIS 3.x ?! -# -DTRILINOS_APPLICATION=OFF -DTRILINOS_ROOT=$EBROOTTRILINOS sanity_check_paths = { - 'files': ['libs/libKratosCore.so', 'runkratos'], + 'files': ['libs/libKratosCore.%s' % SHLIB_EXT, 'runkratos'], 'dirs': ['applications', 'kratos'], } From 91d0281fe2c19e81f7c1d1c6935f2439e8952097 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Nov 2018 12:09:01 +0100 Subject: [PATCH 073/698] enhance sanity check for Kratos to verify MPI support --- .../easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb index 577f3f30d35..71438dd0e92 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -42,7 +42,7 @@ configopts += "-DDEM_APPLICATION=OFF -DSWIMMING_DEM_APPLICATION=OFF -DMIXED_ELEM configopts += "-DSHAPE_OPTIMIZATION_APPLICATION=OFF -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF " sanity_check_paths = { - 'files': ['libs/libKratosCore.%s' % SHLIB_EXT, 'runkratos'], + 'files': ['libs/libKratosCore.%s' % SHLIB_EXT, 'runkratos', 'KratosMultiphysics/mpi.py'], 'dirs': ['applications', 'kratos'], } From 0e1424b8a8c9d26a6fac7669fdbe8ed8566e17ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Nov 2018 15:08:33 +0100 Subject: [PATCH 074/698] make sure system Boost does not get picked up by Kratos build --- .../k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb index 71438dd0e92..807582f81ac 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -31,7 +31,8 @@ dependencies = [ separate_build_dir = True # see configure.sh script for default set of configuration options -configopts = "-DCMAKE_BUILD_TYPE=Release -DKRATOS_INSTALL_PREFIX=%(installdir)s -DBOOST_ROOT=$EBROOTBOOST " +configopts = "-DCMAKE_BUILD_TYPE=Release -DKRATOS_INSTALL_PREFIX=%(installdir)s " +configopts += "-DBOOST_ROOT=$EBROOTBOOST -DBoost_NO_SYSTEM_PATHS=ON -DBoost_NO_BOOST_CMAKE=ON " configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python -DINSTALL_EMBEDDED_PYTHON=ON -DINSTALL_PYTHON_FILES=ON " configopts += "-DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSTRUCTURAL_MECHANICS_APPLICATION=ON " configopts += "-DCONVECTION_DIFFUSION_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DFSI_APPLICATION=ON " From 612e2780f77280c87ff4d718ff92c6956a5f8e4b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Jan 2019 21:30:14 +0100 Subject: [PATCH 075/698] use patch for OpenFOAM 2.2.2 to fix compilation errors for 'isnan' --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb index 2dd736009f9..b321f796822 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb @@ -18,6 +18,7 @@ patches = [ 'cleanup-OpenFOAM-%(version)s.patch', 'OpenFOAM-2.2.0_libreadline.patch', ('cleanup-ThirdParty-%(version)s.patch', ".."), # patch should not be applied in OpenFOAM subdir + 'OpenFOAM-3.0.1_fix_isnan.patch', ] checksums = [ '097adf813e035d04c9be19ee244632cd76971fde107682d50983f8d5cdcf0210', # OpenFOAM-2.2.2.tgz @@ -25,6 +26,7 @@ checksums = [ '17e7ef6fa04020316e60bf286942f3d30d33e9dfe57f744839131d0511a4e885', # cleanup-OpenFOAM-2.2.2.patch 'f1c94764fe07a43877d85497d5c7958a3f162d1b5f1370232084912a6d606181', # OpenFOAM-2.2.0_libreadline.patch 'acae6d27ab8d5197d1df167f986a03188e6404aa58d710f41a693008a11e2583', # cleanup-ThirdParty-2.2.2.patch + 'fb545ccd2a81a8d405382bcfe11996ef6790aede1b553426283680c2cb9b39de', # OpenFOAM-3.0.1_fix_isnan.patch ] dependencies = [ From 8c3398c3948c655b5129b5fa52808cd8ec44e11d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Jan 2019 23:18:00 +0100 Subject: [PATCH 076/698] fix SCOTCH dep in OpenFOAM 2.2.2 easyconfig to use v6.0.6 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb index b321f796822..60aeb624364 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.2.2-intel-2018a.eb @@ -33,7 +33,7 @@ dependencies = [ ('libreadline', '7.0'), ('METIS', '5.1.0'), ('ncurses', '6.0'), - ('SCOTCH', '6.0.5'), + ('SCOTCH', '6.0.6'), ('Boost', '1.66.0'), ] From 962adbcd14e91067b56e8d2122634ea5ee62b69a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Feb 2019 15:48:19 +0100 Subject: [PATCH 077/698] Added openmp and -i8 suffix --- ...alton-2016-intel-2017b.eb => Dalton-2016-intel-2017b-i8.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/d/Dalton/{Dalton-2016-intel-2017b.eb => Dalton-2016-intel-2017b-i8.eb} (96%) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb similarity index 96% rename from easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb rename to easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb index 0d553826562..a10c9e730f7 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb @@ -2,6 +2,7 @@ easyblock = 'CMakeMake' name = 'Dalton' version = '2016' +versionsuffix = '-i8' homepage = 'http://daltonprogram.org/' description = """The Dalton code is a powerful tool for a wide range of molecular properties @@ -11,7 +12,7 @@ description = """The Dalton code is a powerful tool for a wide range of molecula http://www.daltonprogram.org/www/citation.html.""" toolchain = {'name': 'intel', 'version': '2017b'} -toolchainopts = {'i8': True, 'usempi': True} +toolchainopts = {'i8': True, 'usempi': True, 'openmp': True} # use git clone --recurse-submodules -b release/2016 git@gitlab.com:dalton/dalton.git # to fetch source, then make the bizpped tarball From 84ee261ab811f9ffbb05e2942df14ec99c023c30 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 8 Mar 2019 11:03:47 +0100 Subject: [PATCH 078/698] FRUIT v3.4.3 for foss/2018a and Ruby/2.5.0 --- .../FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb | 39 +++++++++++++++++++ .../FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb | 7 ++-- .../f/FRUIT/fruit_3.4.3-ifort-external.patch | 26 +------------ .../f/FRUIT/fruit_3.4.3-mpi-tests.patch | 26 +++++++++++++ ...T_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb | 36 +++++++++++++++++ ..._processor-3.4.3-intel-2018a-Ruby-2.5.1.eb | 5 ++- .../Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb | 30 ++++++++++++++ .../Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb | 2 +- 8 files changed, 141 insertions(+), 30 deletions(-) create mode 100644 easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb create mode 100644 easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-mpi-tests.patch create mode 100644 easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb create mode 100644 easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb new file mode 100644 index 00000000000..60ea89d39c3 --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'FRUIT' +version = '3.4.3' + +rubyver = '2.5.0' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://fortranxunit.sourceforge.io' +description = "FORTRAN Unit Test Framework (FRUIT)" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] +sources = ['fruit_%(version)s.zip'] +patches = ['fruit_%(version)s-mpi-tests.patch'] +checksums = [ + '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip + '6660820c26f647fecd397135d12c61b6ea7b3b2f1d2d7684455036ebc5ead0a4', # fruit_3.4.3-mpi-tests.patch +] + +builddependencies = [ + ('Ruby', rubyver), + ('FRUIT_processor', version, versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'rake || ' + +preinstallopts = 'mkdir -p %(installdir)s/include && cp src/*.mod %(installdir)s/include && ' +preinstallopts += 'mkdir -p %(installdir)s/lib && cp src/*.a %(installdir)s/lib || ' + +sanity_check_paths = { + 'files': ['include/fruit.mod', 'include/fruit_util.mod', 'lib/libfruit.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb index a8d3620bf05..fb3ee63850c 100644 --- a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -13,15 +13,16 @@ toolchain = {'name': 'intel', 'version': '2018a'} source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] sources = ['fruit_%(version)s.zip'] -patches = ['fruit_3.4.3-ifort-external.patch'] +patches = ['fruit_%(version)s-ifort-external.patch', 'fruit_%(version)s-mpi-tests.patch'] checksums = [ '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip - 'a77e1315d41da1f767536252f3afce77dbb58eda7aea138055f03b11c9836bf8', # fruit_3.4.3-ifort-external.patch + '6f608988078d079ef73f30f47208d2b7d5645b6fc55526790b826f82f8d85b85', # fruit_3.4.3-ifort-external.patch + '6660820c26f647fecd397135d12c61b6ea7b3b2f1d2d7684455036ebc5ead0a4', # fruit_3.4.3-mpi-tests.patch ] builddependencies = [ ('Ruby', rubyver), - ('FRUIT_processor', '3.4.3', versionsuffix), + ('FRUIT_processor', version, versionsuffix), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch index 67626086533..d8ec2684ddd 100644 --- a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch +++ b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-ifort-external.patch @@ -1,3 +1,5 @@ +# Patch to build with Intel Fortran +# S.D. Pinches diff -Nru fruit_3.4.3-orig/rake_base.rb fruit_3.4.3/rake_base.rb --- fruit_3.4.3-orig/rake_base.rb 2018-07-20 17:34:13.506622790 +0200 +++ fruit_3.4.3/rake_base.rb 2018-07-20 18:04:32.166241482 +0200 @@ -15,27 +17,3 @@ diff -Nru fruit_3.4.3-orig/rake_base.rb fruit_3.4.3/rake_base.rb $mpiexec = nil else # Intel FORTRAN on Windows -diff -Nru fruit_3.4.3-orig/sample_mpi/rakefile fruit_3.4.3/sample_mpi/rakefile ---- fruit_3.4.3-orig/sample_mpi/rakefile 2018-07-20 17:34:13.507622832 +0200 -+++ fruit_3.4.3/sample_mpi/rakefile 2018-07-23 11:38:34.669769977 +0200 -@@ -46,7 +46,7 @@ - - task :run => [ $goal, "mpi_machine_file" ] do - sleep 3 -- sh "mpiexec -np 2 -machinefile mpi_machine_file #{$goal}" -+ sh "mpiexec -np 2 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal}" - end - - -diff -Nru fruit_3.4.3-orig/self_test_mpi/rakefile fruit_3.4.3/self_test_mpi/rakefile ---- fruit_3.4.3-orig/self_test_mpi/rakefile 2018-07-20 17:34:13.506622790 +0200 -+++ fruit_3.4.3/self_test_mpi/rakefile 2018-07-20 18:50:42.630311001 +0200 -@@ -31,7 +31,7 @@ - - task :run => [ $goal, "mpi_machine_file" ] do - sleep 3 -- sh "mpiexec -np 3 -machinefile mpi_machine_file #{$goal} > stdout" -+ sh "mpiexec -np 3 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal} > stdout" - end - - task :verify => [ :run ] do diff --git a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-mpi-tests.patch b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-mpi-tests.patch new file mode 100644 index 00000000000..2d6295278ee --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-mpi-tests.patch @@ -0,0 +1,26 @@ +# Patch to fix MPI tests +# S.D. Pinches +diff -Nru fruit_3.4.3-orig/sample_mpi/rakefile fruit_3.4.3/sample_mpi/rakefile +--- fruit_3.4.3-orig/sample_mpi/rakefile 2018-07-20 17:34:13.507622832 +0200 ++++ fruit_3.4.3/sample_mpi/rakefile 2018-07-23 11:38:34.669769977 +0200 +@@ -46,7 +46,7 @@ + + task :run => [ $goal, "mpi_machine_file" ] do + sleep 3 +- sh "mpiexec -np 2 -machinefile mpi_machine_file #{$goal}" ++ sh "mpiexec -np 2 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal}" + end + + +diff -Nru fruit_3.4.3-orig/self_test_mpi/rakefile fruit_3.4.3/self_test_mpi/rakefile +--- fruit_3.4.3-orig/self_test_mpi/rakefile 2018-07-20 17:34:13.506622790 +0200 ++++ fruit_3.4.3/self_test_mpi/rakefile 2018-07-20 18:50:42.630311001 +0200 +@@ -31,7 +31,7 @@ + + task :run => [ $goal, "mpi_machine_file" ] do + sleep 3 +- sh "mpiexec -np 3 -machinefile mpi_machine_file #{$goal} > stdout" ++ sh "mpiexec -np 3 -machinefile mpi_machine_file "+Dir.pwd+"/#{$goal} > stdout" + end + + task :verify => [ :run ] do diff --git a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb new file mode 100644 index 00000000000..d27f9fbda09 --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'FRUIT_processor' +version = '3.4.3' + +rubyver = '2.5.0' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://fortranxunit.sourceforge.io' +description = "FORTRAN Unit Test Framework (FRUIT)" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] + +sources = ['fruit_%(version)s.zip'] +checksums = ['01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862'] + +builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix, toolchain)] + +dependencies = [('Ruby', rubyver)] + +skipsteps = ['configure', 'build'] + +preinstallopts = 'GEM_HOME=%(installdir)s ' +preinstallopts += 'gem install --bindir %(installdir)s/bin --local ' +preinstallopts += '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem ||' + +modextrapaths = {'GEM_PATH': ''} + +sanity_check_paths = { + 'files': ['gems/%(namelower)s-%(version)s/lib/%(namelower)s.rb'], + 'dirs': ['gems/%(namelower)s-%(version)s/lib'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb index 6a67ed476fb..e17932740e6 100644 --- a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -23,12 +23,13 @@ dependencies = [('Ruby', rubyver)] skipsteps = ['configure', 'build'] preinstallopts = 'GEM_HOME=%(installdir)s ' -preinstallopts += 'gem install --bindir %(installdir)s/bin --local fruit_processor_gem/pkg/fruit_processor-3.4.3.gem ||' +preinstallopts += 'gem install --bindir %(installdir)s/bin --local ' +preinstallopts += '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem ||' modextrapaths = {'GEM_PATH': ''} sanity_check_paths = { - 'files': ['gems/fruit_processor-3.4.3/lib/%(namelower)s.rb'], + 'files': ['gems/%(namelower)s-%(version)s/lib/%(namelower)s.rb'], 'dirs': ['gems/%(namelower)s-%(version)s/lib'], } diff --git a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb new file mode 100644 index 00000000000..fb1d6461252 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RubyGem' + +name = 'Ruby-Tk' +version = '0.2.0' + +rubyver = '2.5.0' +versionsuffix = '-Ruby-%s' % rubyver + +homepage = 'https://github.com/ruby/tk' +description = "Ruby Tk interface module using tcltklib" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://rubygems.org/downloads/'] +sources = ['tk-%(version)s.gem'] +checksums = ['0d324ae915c20020bea946b1d0b0b35244f16fd2dacc35cf9647b9ac1ea1fc3f'] + +dependencies = [ + ('Ruby', rubyver), + ('Tk', '8.6.8'), +] + +sanity_check_paths = { + 'files': ['gems/tk-%(version)s/bin/console', + 'gems/tk-%(version)s/bin/setup', + 'gems/tk-%s/lib/tkutil.%s' % (version, SHLIB_EXT)], + 'dirs': ['gems/tk-%(version)s/bin', 'gems/tk-%(version)s/lib/tk'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb index cc104d58c06..b0f9098d833 100644 --- a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb @@ -7,7 +7,7 @@ rubyver = '2.5.1' versionsuffix = '-Ruby-%s' % rubyver homepage = 'https://github.com/ruby/tk' -description = "Ruby/Tk" +description = "Ruby Tk interface module using tcltklib" toolchain = {'name': 'intel', 'version': '2018a'} From be8f14e508314de304cec0277f79d8f1e3acbfcb Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 13 Mar 2019 17:21:43 +0100 Subject: [PATCH 079/698] Patch to compile FRUIT v3.4.3 using foss/2018a with -fPIC --- .../f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb | 6 +++++- .../f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch | 12 ++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb index 60ea89d39c3..d72c08bb902 100644 --- a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb @@ -13,9 +13,13 @@ toolchain = {'name': 'foss', 'version': '2018a'} source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] sources = ['fruit_%(version)s.zip'] -patches = ['fruit_%(version)s-mpi-tests.patch'] +patches = [ + 'fruit_%(version)s-gfortran-fPIC.patch', + 'fruit_%(version)s-mpi-tests.patch' +] checksums = [ '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip + '72f94f3238a8c9d2155147aa19381d745cf533a0f3399484e979b06771217b7b', # fruit_3.4.3-gfortran-fPIC.patch '6660820c26f647fecd397135d12c61b6ea7b3b2f1d2d7684455036ebc5ead0a4', # fruit_3.4.3-mpi-tests.patch ] diff --git a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch new file mode 100644 index 00000000000..3d5139b51f2 --- /dev/null +++ b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch @@ -0,0 +1,12 @@ +diff -Nru fruit_3.4.3-orig/rake_base.rb fruit_3.4.3/rake_base.rb +--- fruit_3.4.3-orig/rake_base.rb 2017-09-18 10:59:23.000000000 +0200 ++++ fruit_3.4.3/rake_base.rb 2019-03-13 16:12:19.000000000 +0100 +@@ -71,7 +71,7 @@ + puts "Fortran compiler " + $compiler + " not exists. Trying gfortran." + $compiler = "gfortran" + $option = "-Wall -Wextra -pedantic -fbounds-check " + +- "-Wuninitialized -O -g -Wno-unused-parameter -cpp " ++ "-Wuninitialized -O -g -Wno-unused-parameter -cpp -fPIC" + $ext_obj = "o" + $dosish_path = false + $gcov = "-coverage" From ce152bfb384c9096e8e13875919816c1c43c6a16 Mon Sep 17 00:00:00 2001 From: Shahzeb Siddiqui Date: Wed, 8 May 2019 12:30:54 -0400 Subject: [PATCH 080/698] adding version suffix to indicate this is commercial version --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb index 3b43211a37d..fcec1426753 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb @@ -1,5 +1,6 @@ name = 'FLUENT' version = '18.2' +versionsuffix = 'com' homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed From 04af765abc9367a5adbc41a7ef0685d14a9583ab Mon Sep 17 00:00:00 2001 From: vsc43020 vscuser Date: Tue, 14 May 2019 15:52:13 +0200 Subject: [PATCH 081/698] Fix debian --- .../n/Nek5000/Nek5000-17.0-intel-2018a.eb | 6 +++++- .../n/Nek5000/Nek5000-17.0_sundials.patch | 13 +++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_sundials.patch diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index 81d4b4d8e29..fc6523bb558 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -15,11 +15,15 @@ patches = ['%(name)s-%(version)s_hypre_blas.patch'] checksums = [ '4d8d4793ce3c926c54e09a5a5968fa959fe0ba46bd2e6b8043e099528ee35a60', # v17.0.tar.gz '55d66818151b63826b55545051145a0b0d806d4df7fcf5cf57cf2c75f461f441', # Nek5000-17.0_hypre_blas.patch + 'af9e3771483d9a1732135ca1fd25f902706bf6e8f9c8552bc4bdf24d9a1c0244', # Nek5000-17.0_sundials.patch ] builddependencies = [('CMake', '3.10.2')] -dependencies = [('X11', '20180131')] +dependencies = [ + ('X11', '20180131'), + ('SUNDIALS', '2.7.0'), +] buildininstalldir = True diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_sundials.patch b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_sundials.patch new file mode 100644 index 00000000000..a07135dad6f --- /dev/null +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_sundials.patch @@ -0,0 +1,13 @@ +# REHL does not complain if cd command has multiple arguments but the first is a directory, Debian does. +# May 14th 2019 by B. Hajgato (Ghent University) +--- Nek5000-17.0/3rd_party/cvode/install.orig 2017-12-17 10:08:30.000000000 +0100 ++++ Nek5000-17.0/3rd_party/cvode/install 2019-05-14 15:40:38.398947000 +0200 +@@ -17,7 +17,7 @@ + + tar -zxf *.tar.gz + +-cd sundials* ++cd sundials-2.7.0 + mkdir -p build + cd build + From 458cc8b3cd60145b04c2109e00fc4acf29b3735b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Tue, 14 May 2019 15:59:34 +0200 Subject: [PATCH 082/698] Update Nek5000-17.0-intel-2018a.eb remove accidental sundials dep. --- easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index fc6523bb558..3b1cc0ae762 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -20,10 +20,7 @@ checksums = [ builddependencies = [('CMake', '3.10.2')] -dependencies = [ - ('X11', '20180131'), - ('SUNDIALS', '2.7.0'), -] +dependencies = [('X11', '20180131')] buildininstalldir = True From c8187920def8f32c176141c7a93f04ad126e9481 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bal=C3=A1zs=20Hajgat=C3=B3?= Date: Wed, 15 May 2019 07:34:22 +0200 Subject: [PATCH 083/698] add patch to ebconfig --- .../easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb | 8 ++++++-- .../easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index 3b1cc0ae762..721d55040e3 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -11,10 +11,14 @@ toolchainopts = {'pic': True, 'usempi': True} source_urls = ['https://github.com/Nek5000/Nek5000/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_hypre_blas.patch'] +patches = [ + '%(name)s-%(version)s_hypre_blas.patch', + '%(name)s-%(version)s_sundials.patch', +] + checksums = [ '4d8d4793ce3c926c54e09a5a5968fa959fe0ba46bd2e6b8043e099528ee35a60', # v17.0.tar.gz - '55d66818151b63826b55545051145a0b0d806d4df7fcf5cf57cf2c75f461f441', # Nek5000-17.0_hypre_blas.patch + '62ef4277156ddad2520b9107df8329039a0e4d427a7717c58aa948f3e8c385f3', # Nek5000-17.0_hypre_blas.patch 'af9e3771483d9a1732135ca1fd25f902706bf6e8f9c8552bc4bdf24d9a1c0244', # Nek5000-17.0_sundials.patch ] diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch index 76400c683a3..6b8700c8738 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch @@ -1,4 +1,4 @@ -# Make hyopre to use optimized BLAS/LAPACK and use EB provided compiler flags. Delete LIB as interferes with build in EB +# Make hypre to use optimized BLAS/LAPACK and use EB provided compiler flags. Delete LIB as interferes with build in EB # 01 June 2018 by B. Hajgato (Free University Brussel - VUB) diff -ru Nek5000-17.0.org/tools/amg_hypre/hypre/install Nek5000-17.0/tools/amg_hypre/hypre/install --- Nek5000-17.0.org/tools/amg_hypre/hypre/install 2017-12-17 10:08:30.000000000 +0100 From b25b3fcc7328a95f93104a2bab35bd430b92f2ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 19:24:52 +0200 Subject: [PATCH 084/698] adding easyconfigs: PSI4-1.3.1-foss-2019a-Python-3.7.2.eb --- .../PSI4-1.3.1-foss-2019a-Python-3.7.2.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..5e1a69511ae --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,53 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/psi4/psi4/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['PSI4-%(version)s_fix_cmake_release.patch'] +checksums = [ + 'f6798f323d10fe700c205f714230705049ea74fe8673c4abcf081666608f7cc0', # v1.3.1.tar.gz + '9e202d000fcace884cc62876cd6a384c2cd208f7c4e973c2a788f8f2e9249dec', # PSI4-1.3.1_fix_cmake_release.patch +] + +dependencies = [ + ('Python', '3.7.2'), + ('libxc', '4.3.4'), + ('PCMSolver', '1.2.3', versionsuffix), + ('CheMPS2', '1.8.9'), + ('networkx', '2.3', versionsuffix), + ('deepdiff', '4.0.6', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.13.3'), + # Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation + ('Perl', '5.28.1'), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python module to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' + +# runtest uses ctest, and some of the tests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From d84a0955a8caf887aa7e8ec209a799f0a98fbe7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 21 May 2019 20:44:08 +0200 Subject: [PATCH 085/698] add missing patch file for PSI4 1.3.1 --- .../p/PSI4/PSI4-1.3.1_fix_cmake_release.patch | 95 +++++++++++++++++++ 1 file changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch new file mode 100644 index 00000000000..a2b29c2ce68 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch @@ -0,0 +1,95 @@ +diff -ru psi4-1.3.1.orig/cmake/autocmake_safeguards.cmake psi4-1.3.1/cmake/autocmake_safeguards.cmake +--- psi4-1.3.1.orig/cmake/autocmake_safeguards.cmake 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/cmake/autocmake_safeguards.cmake 2019-05-17 19:51:47.000000000 +0200 +@@ -19,8 +19,8 @@ + string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower) + string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper) + +-if(NOT cmake_build_type_tolower STREQUAL "debug" AND +- NOT cmake_build_type_tolower STREQUAL "release" AND +- NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") +- message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") +-endif() ++#if(NOT cmake_build_type_tolower STREQUAL "debug" AND ++# NOT cmake_build_type_tolower STREQUAL "release" AND ++# NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") ++# message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") ++#endif() +diff -ru psi4-1.3.1.orig/external/upstream/dkh/CMakeLists.txt psi4-1.3.1/external/upstream/dkh/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/dkh/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/dkh/CMakeLists.txt 2019-05-17 19:55:10.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/dkh + GIT_TAG v1.2 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/dkh: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/dkh: CMakeLists.txt.rej +diff -ru psi4-1.3.1.orig/external/upstream/gau2grid/CMakeLists.txt psi4-1.3.1/external/upstream/gau2grid/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/gau2grid/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/gau2grid/CMakeLists.txt 2019-05-17 19:53:08.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/dgasmith/gau2grid + GIT_TAG v1.3.1 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/gau2grid: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/gau2grid: CMakeLists.txt.rej +diff -ru psi4-1.3.1.orig/external/upstream/gdma/CMakeLists.txt psi4-1.3.1/external/upstream/gdma/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/gdma/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/gdma/CMakeLists.txt 2019-05-17 19:55:48.000000000 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/gdma + GIT_TAG 9d607d7 # v2.2.6-2-g9d607d7 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/gdma: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/gdma: CMakeLists.txt.rej +diff -ru psi4-1.3.1.orig/external/upstream/libefp/CMakeLists.txt psi4-1.3.1/external/upstream/libefp/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/libefp/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/libefp/CMakeLists.txt 2019-05-17 19:55:38.000000000 +0200 +@@ -17,6 +17,7 @@ + GIT_REPOSITORY https://github.com/ilyak/libefp + GIT_TAG 15cd7ce # v1.5.0 + 10 (docs and a cmake lapack patch) + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/libefp: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/libefp: CMakeLists.txt.rej +diff -ru psi4-1.3.1.orig/external/upstream/libint/CMakeLists.txt psi4-1.3.1/external/upstream/libint/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/libint/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/libint/CMakeLists.txt 2019-05-17 19:54:22.000000000 +0200 +@@ -14,6 +14,7 @@ + ExternalProject_Add(libint_external + # "git checkout" fails on Windows, because of "*" in filenames (e.g. basis set files) + URL https://github.com/evaleev/libint/archive/b13e71d3cf9960460c4019e5ecf2546a5f361c71.zip ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/libint: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/libint: CMakeLists.txt.rej +diff -ru psi4-1.3.1.orig/external/upstream/libxc/CMakeLists.txt psi4-1.3.1/external/upstream/libxc/CMakeLists.txt +--- psi4-1.3.1.orig/external/upstream/libxc/CMakeLists.txt 2019-04-12 19:25:25.000000000 +0200 ++++ psi4-1.3.1/external/upstream/libxc/CMakeLists.txt 2019-05-17 19:56:11.000000000 +0200 +@@ -15,6 +15,7 @@ + GIT_REPOSITORY https://gitlab.com/libxc/libxc.git + GIT_TAG 4.3.3 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +Only in psi4-1.3.1/external/upstream/libxc: CMakeLists.txt.orig +Only in psi4-1.3.1/external/upstream/libxc: CMakeLists.txt.rej From f8c529360216147030938c927836ea9056e46543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 May 2019 12:16:57 +0200 Subject: [PATCH 086/698] add missing 'Pint' and 'pydantic' extensiosn to PSI 1.3.1 easyconfig + add 'import psi4' sanity check command --- .../p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb index 5e1a69511ae..01fc7e48033 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb @@ -48,6 +48,21 @@ configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2 # runtest = '-L smoke' runtest = False +exts_defaultclass = 'PythonPackage' +exts_filter = ("python -c 'import %(ext_name)s'", '') +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('pydantic', '0.26'), + ('Pint', '0.9'), +] + modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +sanity_check_commands = ["python -c 'import psi4'"] + moduleclass = 'chem' From fe24ff77461f780f70256c620fff3da4151ac200 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 May 2019 12:35:10 +0200 Subject: [PATCH 087/698] add checksums for extensions in PSI4 1.3.1 easyconfig --- .../p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb index 01fc7e48033..cd96b130e9e 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb @@ -57,8 +57,12 @@ exts_default_options = { } exts_list = [ - ('pydantic', '0.26'), - ('Pint', '0.9'), + ('pydantic', '0.26', { + 'checksums': ['dab99d3070e040b8b2e987dfbe237350ab92d5d57a22d4e0e268ede2d85c7964'], + }), + ('Pint', '0.9', { + 'checksums': ['32d8a9a9d63f4f81194c0014b3b742679dce81a26d45127d9810a68a561fe4e2'], + }), ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From d6987c19d80716f09b851a69c0d25eae3d3360c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 28 May 2019 20:01:09 +0200 Subject: [PATCH 088/698] add comment to patch for PSI4 1.3.1 --- .../easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch | 3 +++ 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb index cd96b130e9e..405769bd638 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1-foss-2019a-Python-3.7.2.eb @@ -17,7 +17,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['PSI4-%(version)s_fix_cmake_release.patch'] checksums = [ 'f6798f323d10fe700c205f714230705049ea74fe8673c4abcf081666608f7cc0', # v1.3.1.tar.gz - '9e202d000fcace884cc62876cd6a384c2cd208f7c4e973c2a788f8f2e9249dec', # PSI4-1.3.1_fix_cmake_release.patch + 'e7459050671935ffbcc9f6b23fbd0a581f8cbdc49dbdb282cd4a455f64e15d82', # PSI4-1.3.1_fix_cmake_release.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch index a2b29c2ce68..82ddf331e3c 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.1_fix_cmake_release.patch @@ -1,3 +1,6 @@ +remove CMAKE_BUILD_TYPE check (beacuse it is set to EasyBuildRelease to avoid -O3 optimization flag) +original patch by B. Hajgato - (Free University Brussels - VUB) +ported to PSI4 1.3.1 by Kenneth Hoste (HPC-UGent) diff -ru psi4-1.3.1.orig/cmake/autocmake_safeguards.cmake psi4-1.3.1/cmake/autocmake_safeguards.cmake --- psi4-1.3.1.orig/cmake/autocmake_safeguards.cmake 2019-04-12 19:25:25.000000000 +0200 +++ psi4-1.3.1/cmake/autocmake_safeguards.cmake 2019-05-17 19:51:47.000000000 +0200 From 675c2e98bf3d54cf911f97287210f2b226676275 Mon Sep 17 00:00:00 2001 From: Davide Vanzo Date: Fri, 19 Jul 2019 14:23:28 -0500 Subject: [PATCH 089/698] adding easyconfigs: V8-2.3-foss-2019a-R-3.6.0.eb, V8-2.3-intel-2019a-R-3.6.0.eb --- .../v/V8/V8-2.3-foss-2019a-R-3.6.0.eb | 30 +++++++++++++++++++ .../v/V8/V8-2.3-intel-2019a-R-3.6.0.eb | 30 +++++++++++++++++++ 2 files changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb create mode 100644 easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb diff --git a/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb new file mode 100644 index 00000000000..7003dbc6917 --- /dev/null +++ b/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'V8' +version = '2.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/V8/' +description = """R interface to Google's open source JavaScript engine""" + +toolchain = {'name': 'foss', 'version': '2019a'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f720d772c1d66cac0320230f2e6189e0b8a59af6e589e421e3d2423099d505b3'] + +dependencies = [ + ('R', '3.6.0'), + ('nodejs', '10.15.3'), +] + +installopts = '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"' + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': ['%(name)s'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb b/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb new file mode 100644 index 00000000000..d90249673fc --- /dev/null +++ b/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'V8' +version = '2.3' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/V8/' +description = """R interface to Google's open source JavaScript engine""" + +toolchain = {'name': 'intel', 'version': '2019a'} + +source_urls = [ + 'http://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f720d772c1d66cac0320230f2e6189e0b8a59af6e589e421e3d2423099d505b3'] + +dependencies = [ + ('R', '3.6.0'), + ('nodejs', '10.15.3'), +] + +installopts = '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"' + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': ['%(name)s'], +} + +moduleclass = 'lang' From 3a11bd10d0ee0acf32c70d1163f71fc770449689 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Sep 2019 19:34:46 +0200 Subject: [PATCH 090/698] remove useless 'full_sanity_check' line in BDBag easyconfig --- .../b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb index c0955788c59..6d142adb022 100644 --- a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb @@ -36,10 +36,6 @@ exts_list = [ }), ] - -# specify that Bundle easyblock should run a full sanity check, rather than just trying to load the module -full_sanity_check = True - sanity_check_paths = { 'files': [], 'dirs': ['lib/python%(pyshortver)s/site-packages'], From 2ff0ac3849631ab714fae24eae3219996ba81b15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 28 Sep 2019 19:37:49 +0200 Subject: [PATCH 091/698] switch to PythonBundle + enable use_pip in BDBag easyconfig file --- .../BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb | 15 +++------------ 1 file changed, 3 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb index 6d142adb022..3da7954f320 100644 --- a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'BDBag' version = '1.4.1' @@ -10,14 +10,12 @@ working with BagIt packages that conform to the Bagit and Bagit/RO profiles.""" toolchain = {'name': 'intel', 'version': '2018a'} -# this is a bundle of Python packages -exts_defaultclass = 'PythonPackage' -exts_download_dep_fail = True - dependencies = [ ('Python', '3.6.4'), ] +use_pip = True + exts_list = [ ('tzlocal', '2.0.0b1', { 'source_urls': ['https://pypi.python.org/packages/source/t/tzlocal'], @@ -36,11 +34,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} - moduleclass = 'data' From d03601a0f3f211f055ff4a32e48409c146252abd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 29 Sep 2019 09:55:23 +0200 Subject: [PATCH 092/698] use https in homepage/source_urls for lavaan --- .../l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb index 3de0a5f8bb0..bdddde13f4c 100644 --- a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb +++ b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb @@ -4,15 +4,15 @@ name = 'lavaan' version = '0.6-2' versionsuffix = '-R-%(rver)s' -homepage = 'http://cran.r-project.org/web/packages/%(name)s' +homepage = 'https://cran.r-project.org/web/packages/%(name)s' description = """Fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.""" toolchain = {'name': 'intel', 'version': '2018a'} source_urls = [ - 'http://cran.r-project.org/src/contrib/', - 'http://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['91d5aea1468394f9e2bda773ab51f8a16a198bfc1d8474c1c48bcaba87f9c0be'] From 134d2f8ab0b137531f1fa96517688b0d4e0a2780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Feb 2020 20:57:01 +0100 Subject: [PATCH 093/698] adding easyconfigs: MMseqs2-11-e1a1c-iimpi-2019b.eb --- .../m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb new file mode 100644 index 00000000000..ebaf2980bc1 --- /dev/null +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'MMseqs2' +version = '11-e1a1c' + +homepage = 'https://mmseqs.com' +description = "MMseqs2: ultra fast and sensitive search and clustering suite" + +toolchain = {'name': 'iimpi', 'version': '2019b'} + +source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ffe1ae300dbe1a0e3d72fc9e947356a4807f07951cb56316f36974d8d5875cbb'] + +builddependencies = [('CMake', '3.15.3')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE' + +sanity_check_paths = { + 'files': ['bin/mmseqs'], + 'dirs': [], +} + +moduleclass = 'bio' From 0bb45e4501835c93309bbec8ba46a013724e1408 Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 4 Mar 2020 16:00:02 +0200 Subject: [PATCH 094/698] adding easyconfigs: SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb --- ...bundle-2019.10-intel-2019a-Python-3.7.2.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..3c05789ed80 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2019.10' +versionsuffix = '-Python-3.7.2' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'intel', 'version': '2019a'} +toolchainopts = {'pic': True, 'lowopt': True} + +dependencies = [ + ('Python', '3.7.2'), +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.17.3', { + 'source_urls': ['https://pypi.python.org/packages/source/n/numpy/'], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'patches': ['numpy-1.12.0-mkl.patch'], + 'checksums': [ + 'a0678793096205a4d784bd99f32803ba8100f639cf3b932dc63b21621390ea7e', + 'f212296ed289eb1b4e3f703997499dee8a2cdd0af78b55e017477487b6377ca4', # numpy-1.12.0-mkl.patch + ], + }), + ('scipy', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'], + 'checksums': ['2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5'], + }), + ('mpi4py', '3.0.2', { + 'source_urls': ['https://bitbucket.org/mpi4py/mpi4py/downloads/'], + 'checksums': ['f8d629d1e3e3b7b89cb99d0e3bc5505e76cc42089829807950d5c56606ed48e0'], + }), + ('pandas', '0.25.3', { + 'source_urls': ['https://pypi.python.org/packages/source/p/pandas/'], + 'checksums': ['52da74df8a9c9a103af0a72c9d5fdc8e0183a90884278db7f386b5692a2220a4'], + }), + ('mpmath', '1.1.0', { + 'source_urls': ['https://pypi.python.org/packages/source/m/mpmath/'], + 'checksums': ['fc17abe05fbab3382b61a123c398508183406fa132e0223874578e20946499f6'], + }), +] + +moduleclass = 'lang' From 1883fb3559aee26948b68262235de17e4ddf68ea Mon Sep 17 00:00:00 2001 From: guacke Date: Wed, 4 Mar 2020 16:45:41 +0200 Subject: [PATCH 095/698] Bugfix: enable sanity_pip_check. --- .../SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb index 3c05789ed80..ead229b0905 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2019.10-intel-2019a-Python-3.7.2.eb @@ -15,6 +15,7 @@ dependencies = [ ] use_pip = True +sanity_pip_check = True # order is important! exts_list = [ From 91e90aeed0e80978e2b6ad162ec62afb10b69b64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Apr 2020 16:18:55 +0200 Subject: [PATCH 096/698] adding easyconfigs: Longshot-0.4.1-GCCcore-8.3.0.eb, Rust-1.42.0-GCCcore-8.3.0.eb --- .../Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb | 38 +++++++++++++++++++ .../r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb | 28 ++++++++++++++ 2 files changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..2b4d5e3f087 --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCCcore-8.3.0.eb @@ -0,0 +1,38 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.1' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['062529eb47fafc2ef4a1a12ea30a565a0df922b310b6fc5705a1605ce4f495f3'] + +builddependencies = [ + ('binutils', '2.32'), + ('Rust', '1.42.0'), + ('Clang', '9.0.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +extract_sources = True + +install_cmd = "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..11b48f9f188 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-8.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.42.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] + +builddependencies = [ + ('binutils', '2.32'), + ('CMake', '3.15.3'), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +moduleclass = 'lang' From b9ffcd2554fd015c46c5338b37ee8541f4c8a4cd Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 27 May 2020 19:47:47 +0200 Subject: [PATCH 097/698] adding easyconfigs: MDSplus-7.96.12-GCCcore-9.3.0.eb, MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb, MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb --- ...plus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 43 ++++++++++++++++ ...-Python-7.96.12-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ .../MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb | 45 +++++++++++++++++ 3 files changed, 138 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb create mode 100644 easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb new file mode 100644 index 00000000000..86db577926a --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus-Java' +version = '7.96.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/MDSplus/mdsplus/archive'] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] +checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] + +# patches = ['MDSplus-Java-%(version)s_classpath.patch'] + +builddependencies = [ + ('binutils', '2.34') +] + +dependencies = [ + ('Java', '13', '', True), + ('MDSplus', version), +] + +preconfigopts = 'find . -type f -regex .*Makefile.* -maxdepth 12 -exec sed -i "s/JAVASOURCE = 6/JAVASOURCE = 8/g" {} \; && ' +preconfigopts += 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +configopts = '--with-jdk=$JAVA_HOME --enable-java_only --disable-doxygen-doc --disable-valgrind' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/jTraverser', 'bin/jScope', 'bin/jServer'], + 'dirs': ['bin', 'include', 'java/classes'], +} + +modextrapaths = {'CLASSPATH': 'java/classes/*'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d5d26c65de0 --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus-Python' +version = '7.96.12' +local_pyver = '3.8.2' + +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/MDSplus/mdsplus/archive'] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] +checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] + +dependencies = [ + ('Python', local_pyver), + ('SciPy-bundle', '2020.03', versionsuffix), + ('MDSplus', version), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +local_moddir = modextrapaths['PYTHONPATH'] + '/MDSplus' + +skipsteps = ['build', 'test'] + +configopts = '--disable-doxygen-doc --disable-java' +# hardcode version via configure script (git is unavailable) +configopts += ' RELEASE_VERSION=%(version)s BRANCH=stable' + +# install by simply copying into a subdir because +# running setup.py will try to make an egg link instead of installing. +install_cmd = 'mkdir -p %(installdir)s/' + local_moddir +install_cmd += ' && pwd && cp -a python/MDSplus/* %(installdir)s/' + local_moddir + '/' + +sanity_check_paths = { + 'files': [], + 'dirs': [local_moddir], +} + +# MDSplus.__version__ shows an ugly non-fatal warning, +# the logic in the mdsplus package seems broken and may need patching. +sanity_check_commands = [ + ('python', "-c 'import MDSplus ; print(MDSplus.__version__)'"), +] +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2608ca19209 --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'MDSplus' +version = '7.96.12' + +homepage = 'http://mdsplus.org/' +description = """MDSplus is a set of software tools for data acquisition and storage and a methodology + for management of complex scientific data.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(namelower)s/archive'] +sources = ['stable_release-%s.zip' % version.replace('.', '-')] +checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] + +builddependencies = [ + ('binutils', '2.34') +] + +dependencies = [ + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), + ('ncurses', '6.2'), + ('libreadline', '8.0') +] + +configopts = '--disable-doxygen-doc --disable-java --disable-hdf5' +# hardcode version via configure script (git is unavailable) +configopts += ' RELEASE_VERSION=%(version)s BRANCH=stable' + +preconfigopts = 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' + +parallel = 1 + +modextravars = { + 'MDSPLUS_DIR': '%(installdir)s', + 'MDS_PATH': '%(installdir)s/tdi', +} + +modextrapaths = { + 'IDL_PATH': 'idl', +} + +moduleclass = 'data' From a135b2f2a4fd3bc92edfb2521f4e7d154f61edf9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2020 10:56:57 +0200 Subject: [PATCH 098/698] add Python 3 as build dep for Xvfb --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index f14e6802026..fb0ffdd7656 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} builddependencies = [ ('binutils', '2.31.1'), ('pkg-config', '0.29.2'), + ('Python', '3.7.2'), ] dependencies = [ diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index dda838ba39f..c0a7733f09b 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -12,6 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} builddependencies = [ ('binutils', '2.32'), ('pkg-config', '0.29.2'), + ('Python', '3.7.2'), ] dependencies = [ From 50e1b4f084e1006e2c515467309b2ca54ad6cdd4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jun 2020 11:05:15 +0200 Subject: [PATCH 099/698] use correct Python 3 version for Xvfb build dep --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index c0a7733f09b..f4c5a46fc86 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} builddependencies = [ ('binutils', '2.32'), ('pkg-config', '0.29.2'), - ('Python', '3.7.2'), + ('Python', '3.7.4'), ] dependencies = [ From d98fee3aa492a1a34a2c827236a89eb5cfe17868 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 8 Jun 2020 10:59:21 +0200 Subject: [PATCH 100/698] Use EB variables during MDSplus-Java build --- ...plus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 2 +- .../MDSplus-Java-7.96.12_classpath.patch | 394 ++++++++++++++++++ 2 files changed, 395 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb index 86db577926a..7578d8a42fe 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -15,7 +15,7 @@ source_urls = ['https://github.com/MDSplus/mdsplus/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] -# patches = ['MDSplus-Java-%(version)s_classpath.patch'] +patches = ['MDSplus-Java-%(version)s_classpath.patch'] builddependencies = [ ('binutils', '2.34') diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch new file mode 100644 index 00000000000..bf67f6ecf00 --- /dev/null +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch @@ -0,0 +1,394 @@ +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template +--- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template 2019-09-26 16:26:07.000000000 +0200 +@@ -2,7 +2,7 @@ + #! + # + exec env \ +-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/lib \ +-SHLIB_PATH=$MDSPLUS_DIR/lib \ +-CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ ++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/lib \ ++SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ ++CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ + java jDispatcherIp $1 $2 $3 $4 $5 +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatchMonitor.template mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatchMonitor.template +--- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatchMonitor.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatchMonitor.template 2019-09-26 16:26:08.000000000 +0200 +@@ -2,7 +2,7 @@ + #! + # + exec env \ +-LD_LIBRARY_PATH=$MDSPLUS_DIR/lib \ +-SHLIB_PATH=$MDSPLUS_DIR/lib \ +-CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ ++LD_LIBRARY_PATH=$EBROOTMDSPLUSMINJAVA/lib \ ++SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ ++CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ + java jDispatchMonitor $1 $2 $3 $4 $5 +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jServer.template mdsplus-stable_release-7-84-6/java/jdispatcher/jServer.template +--- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jServer.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jdispatcher/jServer.template 2019-09-26 16:26:08.000000000 +0200 +@@ -2,7 +2,7 @@ + #! + # + exec env \ +-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/lib \ +-SHLIB_PATH=$MDSPLUS_DIR/lib \ +-CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jDispatcher.jar:$MDSPLUS_DIR/java/classes: \ ++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/lib \ ++SHLIB_PATH=$EBROOTMDSPLUSMINJAVA/lib \ ++CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDispatcher.jar:$EBROOTMDSPLUSMINJAVA/java/classes: \ + java -Xss10M jServer $1 +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jscope/jScope.template mdsplus-stable_release-7-84-6/java/jscope/jScope.template +--- mdsplus-stable_release-7-84-6.orig/java/jscope/jScope.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jscope/jScope.template 2019-09-26 16:26:08.000000000 +0200 +@@ -4,17 +4,17 @@ + # + lib=lib + if java -d64 -version > /dev/null 2>&1; then +- if [ -r $MDSPLUS_DIR/lib64 ] ; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then + lib=/lib64 + fi + else +- if [ -r $MDSPLUS_DIR/lib32 ]; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then + lib=lib32 + fi + fi + exec env \ +-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ +-DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-CLASSPATH=$HOME:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes:$HOME:$MDSPLUS_DIR/java/classes/mdsobjects.jar \ +-java -Xmx512M -Djava.library.path=$MDSPLUS_DIR/${lib} jScope $1 $2 $3 $4 $5 $6 $7 ++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++CLASSPATH=$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes:$HOME:$EBROOTMDSPLUSMINJAVA/java/classes/mdsobjects.jar \ ++java -Xmx512M -Djava.library.path=$EBROOTMDSPLUSMINJAVA/${lib} jScope $1 $2 $3 $4 $5 $6 $7 +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jtraverser/jTraverser.template mdsplus-stable_release-7-84-6/java/jtraverser/jTraverser.template +--- mdsplus-stable_release-7-84-6.orig/java/jtraverser/jTraverser.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jtraverser/jTraverser.template 2019-09-26 16:26:08.000000000 +0200 +@@ -4,17 +4,17 @@ + # + lib=lib + if java -d64 -version > /dev/null 2>&1; then +- if [ -r $MDSPLUS_DIR/lib64 ] ; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then + lib=/lib64 + fi + else +- if [ -r $MDSPLUS_DIR/lib32 ]; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then + lib=lib32 + fi + fi + exec env \ +-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ +-DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-CLASSPATH=$MDSPLUS_DIR/java/classes/jTraverser.jar:$MDSPLUS_DIR/java/classes/jScope.jar:$MDSPLUS_DIR/java/classes/jDevices.jar \ +-java -Xss5M -Djava.library.path=$MDSPLUS_DIR/${lib} jTraverser $1 $2 $3 $4 $5 $6 $7 ++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++CLASSPATH=$EBROOTMDSPLUSMINJAVA/java/classes/jTraverser.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jScope.jar:$EBROOTMDSPLUSMINJAVA/java/classes/jDevices.jar \ ++java -Xss5M -Djava.library.path=$EBROOTMDSPLUSMINJAVA/${lib} jTraverser $1 $2 $3 $4 $5 $6 $7 +diff -Nru mdsplus-stable_release-7-84-6.orig/java/jtraverser2/jTraverser2.template mdsplus-stable_release-7-84-6/java/jtraverser2/jTraverser2.template +--- mdsplus-stable_release-7-84-6.orig/java/jtraverser2/jTraverser2.template 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/java/jtraverser2/jTraverser2.template 2019-09-26 16:26:08.000000000 +0200 +@@ -1,16 +1,16 @@ + #!/bin/sh + lib=lib + if java -d64 -version > /dev/null 2>&1; then +- if [ -r $MDSPLUS_DIR/lib64 ] ; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib64 ] ; then + lib=/lib64 + fi + else +- if [ -r $MDSPLUS_DIR/lib32 ]; then ++ if [ -r $EBROOTMDSPLUSMINJAVA/lib32 ]; then + lib=lib32 + fi + fi + exec env \ +-LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-SHLIB_PATH=$SHLIB_PATH:$MDSPLUS_DIR/${lib} \ +-DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$MDSPLUS_DIR/${lib} \ +-java -jar $MDSPLUS_DIR/java/classes/jTraverser2.jar "$@" ++LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++SHLIB_PATH=$SHLIB_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH:$EBROOTMDSPLUSMINJAVA/${lib} \ ++java -jar $EBROOTMDSPLUSMINJAVA/java/classes/jTraverser2.jar "$@" +diff -Nru mdsplus-stable_release-7-84-6.orig/Makefile.in mdsplus-stable_release-7-84-6/Makefile.in +--- mdsplus-stable_release-7-84-6.orig/Makefile.in 2019-09-02 18:02:07.000000000 +0200 ++++ mdsplus-stable_release-7-84-6/Makefile.in 2019-09-26 16:28:01.000000000 +0200 +@@ -40,8 +40,8 @@ + D3D_PACKAGE = d3dshr + + ifeq "@JAVA_ONLY@" "yes" +-NON_JAR = +-PARTS = $(JAVA_JAR) ++NON_JAR = @JAVA_APS@ ++PARTS = $(NON_JAR) $(JAVA_JAR) + else + NON_JAR = \ + mdsshr \ +diff -Nru mdsplus-stable_release-7-84-6.orig/Makefile.in~ mdsplus-stable_release-7-84-6/Makefile.in~ +--- mdsplus-stable_release-7-84-6.orig/Makefile.in~ 1970-01-01 01:00:00.000000000 +0100 ++++ mdsplus-stable_release-7-84-6/Makefile.in~ 2019-09-02 18:02:07.000000000 +0200 +@@ -0,0 +1,252 @@ ++#@(#)$RCSfile$ $Revision$ ++# @configure_input@ ++ ++include @top_builddir@/Makefile.inc ++ ++srcdir=@srcdir@ ++builddir=@builddir@ ++VPATH=@srcdir@ ++@AX_RECONFIGURE_TARGET@ ++ ++ ++ ++JAVA_JAR = \ ++ java/mdsplus-api \ ++ java/mdsplus-api/tests \ ++ java/jscope \ ++ java/jtraverser \ ++ java/jtraverser2 \ ++ java/jdispatcher \ ++ java/jdevices \ ++ java/mdsplus \ ++ java/mdsobjects ++ ++JAVA_APS = \ ++ javamds \ ++ java/mdsplus-api/src/main/jni/mds/mdslib ++ ++ifeq "@HAVE_MOTIF@" "yes" ++MOTIF_APS = xmdsshr \ ++ actions \ ++ dwscope \ ++ @IDLMDSWIDGETS@ \ ++ mitdevices \ ++ traverser ++else ++MOTIF_APS = actions ++endif ++HDF5_APS = hdf5 ++ ++D3D_PACKAGE = d3dshr ++ ++ifeq "@JAVA_ONLY@" "yes" ++NON_JAR = ++PARTS = $(JAVA_JAR) ++else ++NON_JAR = \ ++ mdsshr \ ++ treeshr \ ++ tdishr \ ++ tditest \ ++ xtreeshr \ ++ @MDSTCPIP@ \ ++ mdslibidl \ ++ mdsdcl \ ++ @CAMSHR@ \ ++ @REMCAM@ \ ++ ccl \ ++ servershr \ ++ tcl \ ++ @TDIC@ \ ++ mdslib \ ++ math \ ++ wfevent \ ++ setevent \ ++ mdsmisc \ ++ scripts \ ++ rpm \ ++ mdsobjects/cpp \ ++ manpages \ ++ @D3D_PACKAGE@ \ ++ @JAVA_APS@ \ ++ @MOTIF_APS@ \ ++ @MDSSQL@ \ ++ @IDLMDSEVENT@ \ ++ @HDF5_APS@ \ ++ @LV@ \ ++ LabView \ ++ @MACOSX@ ++ ++@ENABLE_TESTS_TRUE@ NON_JAR += testing ++ ++PARTS = $(NON_JAR) @JAVA_JAR@ ++endif ++ ++.PHONY: all $(PARTS) ++all: ##@build build all active submodules ++all: ChangeLog $(PARTS) ++ ++DIRECTORIES = $(sort @MAKEBINDIR@ @MAKELIBDIR@ @MAKESHLIBDIR@ @MAKEUIDDIR@) ++ ++$(NON_JAR): $(DIRECTORIES) ++@MINGW_FALSE@ $(MAKE) -C $@ @MAKEFLAG_J@ @MAKEFLAG_O@ ++@MINGW_TRUE@ $(MAKE) -C $@ ++# override parallel flags for java apps ++$(JAVA_JAR): $(DIRECTORIES) ++ $(MAKE) -C $@ ++ ++.PHONY: docs ++docs: ##@docs build documentation using doxygen (ref to docs directory) ++ $(MAKE) -C docs install ++ ++ ++ ++clean_DIRS = $(addprefix clean_, $(PARTS)) ++ ++ChangeLog: ++ if (! git --git-dir=@top_srcdir@/.git log --decorate=full --no-merges > ChangeLog 2>/dev/null); then touch ChangeLog; fi ++ ++.PHONY: clean ++clean: ##@build recusively clean all built objects in submodules ++clean: $(clean_DIRS) clean_TESTS clean_DOCS ++ ++.PHONY: $(clean_DIRS) ++$(clean_DIRS): ++ $(MAKE) -C $(@:clean_%=%) clean ++ ++clean_DOCS: ##@docs clean generated documentation ++ $(MAKE) -C docs clean ++ ++.PHONY: distclean ++ ++distclean: ##@build make source directory look like original sources ++ @cpwd=$$(pwd); \ ++ cd @top_srcdir@; \ ++ if [ -r .git ]; \ ++ then \ ++ git clean -x -f -d -q; \ ++ else \ ++ if [ "$$(pwd)" == "$$cpwd" ]; \ ++ then make full_clean > /dev/null; \ ++ fi; \ ++ rm -Rf ./python/MDSplus/build; \ ++ fi; \ ++ cd $$cpwd ++ ++# Testing ++ ++.PHONY: tests ++tests: ##@tests recursively perform tests in submodules ++@ENABLE_TESTS_TRUE@ $(MAKE) $(AM_MAKEFLAGS) -C testing all tests ++@ENABLE_TESTS_FALSE@ @echo "Tests disabled" ++ ++.PHONY: tests-valgrind rebuild-tests ++tests-valgrind: ##@tests perform tests using valgrind tool ++rebuild-tests: ##@tests rebuild all tests binaries ++tests-valgrind rebuild-tests: ++@ENABLE_TESTS_TRUE@ $(MAKE) $(AM_MAKEFLAGS) -C testing all $@ ++@ENABLE_TESTS_FALSE@ @echo "Tests disabled" ++ ++.PHONY: $(clean_TESTS) ++clean_TESTS: ##@tests clean all tests results and compiled tests objects ++@ENABLE_TESTS_TRUE@ $(MAKE) -C testing tests-clean ++ ++ ++.PHONY: full_clean ++full_clean: ##@build perform deep clean of build directories ++full_clean: clean ++ @rm -Rf bin bin64 bin32 bin_x86 bin_x86_64 etc \ ++ lib lib64 lib32 java uid uid64 uid32 \ ++ config.cache config.log config.status aclocal.m4 \ ++ include/stamp-h1 autom4te.cache \ ++ $$(find . -name '.deps') \ ++ `find . -name '*.in' | \ ++ $(AWK) '{print substr($$1,0,length($$1)-3)}'` ++ ++.PHONY: depend ++depend: ++ cdir=`pwd`;\ ++ set -e; for dir in $(PARTS) ; do\ ++ cd $${dir}; $${MAKE:=make} depend > /dev/null 2> /dev/null; cd $$cdir;\ ++ done ++ ++MISC_PARTS = tdi pydevices idl trees setup.sh setup.csh include desktop pixmaps matlab php epics xml nodejs python/MDSplus ++ ++install_DIRS = $(addprefix install_, $(PARTS)) ++$(install_DIRS): ++ $(MAKE) -C $(@:install_%=%) install ++ ++.PHONY: install ++install: ##@build build and install active modules to prefix directory ++install: $(install_DIRS) ++ $(INSTALL) ChangeLog $(prefix)/ ++ $(MKDIR_P) $(prefix)/local/tdi ++ $(MKDIR_P) $(prefix)/java ++ $(MKDIR_P) $(prefix)/python/MDSplus ++ - find $(prefix)/java -name '*.class' -delete #### No need to include class files ++ tar -C ${top_srcdir} \ ++ --exclude='.gitignore' \ ++ --exclude='*.pyc' \ ++ --exclude=__pycache__ \ ++ --exclude=python/MDSplus/build \ ++ --exclude=python/MDSplus/docs \ ++ --exclude=tdi/*Devices/build \ ++ --exclude='*egg-info' \ ++ --exclude='*\.in' \ ++ --exclude='Makefile\.*' \ ++ -cf - $(MISC_PARTS) | (cd $(exec_prefix); tar -xf -) ++ tar -C ${top_builddir} -cf - include/mdsplus/mdsconfig.h $$(find . -name _version.py) | (cd $(exec_prefix); tar -xf -) ## TODO: remove this and config.h from headers ... ++ if [ ! -z "$$MDSPLUS_VERSION" ]; then echo "mdsplus_version='$$MDSPLUS_VERSION'" > $(exec_prefix)/python/MDSplus/mdsplus_version.py; fi ++ $(INSTALL) ${top_srcdir}/MDSplus-License.txt ${top_srcdir}/MDSplus-License.rtf $(exec_prefix) ++ (cd $(exec_prefix); chmod -R 755 $(MISC_PARTS)) ++ ++.PHONY: tests-envdump ++tests-envdump: ++ cd python/MDSobjects/tests&&(\ ++ make test-envdump;\ ++ cd ../../..;) ++ ++test-env: ++ cd python/MDSplus/tests&&(\ ++ make test-env;\ ++ cd ../../..;) ++ ++@HAVE_WINE_TRUE@wineconsole: ++@HAVE_WINE_TRUE@ cd python/MDSplus/tests&&(\ ++@HAVE_WINE_TRUE@ make wineconsole;\ ++@HAVE_WINE_TRUE@ cd ../../..;) ++ ++# Interdependent directories: ++actions: mdsshr tdishr treeshr xmdsshr mdstcpip servershr ++camshr: mdsdcl ++ccl: camshr mdsshr mdsdcl ++tcl: mdsshr treeshr tdishr mdstcpip servershr mdsdcl ++dwscope: xmdsshr ++java/jdevices: java/jtraverser ++java/jdispatcher: java/jscope java/jtraverser ++javamds: mdstcpip ++java/jtraverser: java/jscope ++java/jtraverser2: java/mdsplus-api ++java/mdsplus-api/tests: java/mdsplus-api ++math: mdsshr ++mdsdcl: mdsshr ++mdslib: mdstcpip ++mdslibidl: tdishr ++mdsmisc: tdishr xtreeshr ++mdsobjects/cpp: mdstcpip ++java/mdsobjects: java/jscope ++mdstcpip: tdishr ++mitdevices: mdsshr tdishr treeshr xmdsshr ++remcam: mdstcpip ++servershr: mdsdcl tdishr treeshr mdsshr mdstcpip ++setevent: mdsshr ++tdic: mdstcpip ++tdishr: mdsshr treeshr ++tditest: tdishr ++traverser: xmdsshr ++treeshr: mdsshr ++wfevent: tdishr mdsshr ++xmdsshr: tdishr ++xtreeshr: tdishr ++ ++am--refresh: From dd0b3d2958600624e83da71d12dcfd6f6e45c3f5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 8 Jul 2020 16:07:53 +0200 Subject: [PATCH 101/698] adding easyconfigs: PyOpenGL-3.1.5-GCCcore-8.3.0.eb, PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb --- .../PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb | 44 +++++++++++++++++++ ...yQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb | 30 +++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..2b6326c9a17 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.5-GCCcore-8.3.0.eb @@ -0,0 +1,44 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: +# +# Notes:: +## + +easyblock = 'PythonPackage' + +name = 'PyOpenGL' +version = '3.1.5' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4107ba0d0390da5766a08c242cf0cf3404c377ed293c5f6d701e457c57ba3424'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +builddependencies = [ + ('binutils', '2.32'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Mesa', '19.1.7'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'OpenGL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..9e2c511e763 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQtGraph/PyQtGraph-0.11.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'PyQtGraph' +version = '0.11.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyqtgraph.org/' +description = """PyQtGraph is a pure-python graphics and GUI library built on PyQt5/PySide2 and numpy.""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'pic': True} + +github_account = 'pyqtgraph' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['082cdec1e559644e083cd8c5752fc06a18582fb2bebb83cdf6eb8ad33c735535'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # required for numpy + ('PyQt5', '5.13.2', versionsuffix), + ('PyOpenGL', '3.1.5'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'vis' From 0893b6332755e073b60242245397e3926a900bc5 Mon Sep 17 00:00:00 2001 From: Tom Strempel Date: Mon, 27 Jul 2020 11:39:52 +0200 Subject: [PATCH 102/698] adding easyconfigs: IDBA-UD-1.1.3-GCCcore-8.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..06136635834 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads + Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. + IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth + contigs are removed iteratively with cutoff threshold from low to high to reduce the errors + in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled + locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD + can iterate k value of de Bruijn graph to a very large value with less gaps and less branches + to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +builddependencies = [ + ('binutils', '2.32') +] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' From b2d59cbfa2d9a8fc95f087241c57af5f5dc15db2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 6 Aug 2020 21:44:23 +0200 Subject: [PATCH 103/698] adding easyconfigs: LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb --- ...19-intel-2019b-Python-3.7.4-kokkos-OCTP.eb | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb new file mode 100644 index 00000000000..408a24af2e8 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -0,0 +1,112 @@ +name = 'LAMMPS' +version = '7Aug2019' +local_python_versionsuffix = '-Python-%(pyver)s' +versionsuffix = local_python_versionsuffix +versionsuffix += '-kokkos-OCTP' + +homepage = 'https://lammps.sandia.gov/' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} + +source_urls = [ + # 'https://github.com/lammps/lammps/archive/' + GITHUB_LOWER_SOURCE, + 'https://github.com/omoultosEthTuDelft/OCTP/archive/', +] +sources = [ + 'stable_%(version)s.tar.gz', + {'download_filename': '553885e.tar.gz', 'filename': 'OCTP-20190520.tar.gz'}, + {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz + '6d0b40394b288e877071f203d3946525d7d2b335367d2ee89c4bad0d757c1435', # OCTP-20190520.tar.gz + '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py +] + +local_source_dir_name = '%(namelower)s-%(version)s' + +builddependencies = [ + ('CMake', '3.15.3'), + ('pkg-config', '0.29.2'), + ('archspec', '0.1.0', local_python_versionsuffix), +] + +dependencies = [ + ('Python', '3.7.4'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.3'), + ('netCDF', '4.7.1'), + ('GSL', '2.6'), + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('cURL', '7.66.0'), + ('HDF5', '1.10.5'), + ('tbb', '2019_U9'), + ('PCRE', '8.43'), + ('libxml2', '2.9.9'), + ('FFmpeg', '4.2.1'), + ('Voro++', '0.4.6'), + ('kim-api', '2.1.3'), + ('Eigen', '3.3.7', '', True), + ('yaff', '1.6.0', local_python_versionsuffix), + ('PLUMED', '2.5.3', local_python_versionsuffix), +] + +# copy OCTP sources into LAMMPS source directory +preconfigopts = "cp -av %(builddir)s/OCTP-*/{*.cpp,*.h} %(builddir)s/lammps-stable_%(version)s/src/ && " + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# having the USER-INTEL package (https://lammps.sandia.gov/doc/Speed_intel.html) enabled with intel/2019b +# results in a LAMMPS installation that yields incorrect results, +# so disable this particular package for now... +configopts = '-DPKG_USER-INTEL=off' + +# auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# +# not enabled (yet), needs more work/additional dependencies: +# 'LATTE', - https://lammps.sandia.gov/doc/Build_extras.html#latte-package +# 'MSCG', - https://lammps.sandia.gov/doc/Build_extras.html#mscg-package +general_packages = [ + 'ASPHERE', 'BODY', 'CLASS2', 'COLLOID', 'COMPRESS', 'CORESHELL', 'DIPOLE', + 'GRANULAR', 'KIM', 'KSPACE', 'MANYBODY', 'MC', 'MESSAGE', 'MISC', + 'MOLECULE', 'MPIIO', 'PERI', 'POEMS', 'PYTHON', 'QEQ', 'REPLICA', 'RIGID', + 'SHOCK', 'SNAP', 'SPIN', 'SRD', 'VORONOI', +] + +# not enabled (yet), needs more work/additional dependencies: +# ADIOS - https://lammps.sandia.gov/doc/Build_extras.html#user-adios-package +# AWPMD - https://lammps.sandia.gov/doc/Build_extras.html#user-awpmd-package +# QUIP - https://lammps.sandia.gov/doc/Build_extras.html#user-quip-package +# SCAFACOS - https://lammps.sandia.gov/doc/Build_extras.html#user-scafacos-package +# VTK - https://lammps.sandia.gov/doc/Build_extras.html#user-vtk-package +user_packages = [ + 'ATC', 'BOCS', 'CGDNA', 'CGSDK', 'COLVARS', 'DIFFRACTION', 'DPD', 'DRUDE', + 'EFF', 'FEP', 'H5MD', 'LB', 'MANIFOLD', 'MEAMC', 'MESO', 'MGPT', 'MISC', + 'MOFFF', 'MOLFILE', 'NETCDF', 'PHONON', 'PLUMED', 'PTM', 'QTB', 'REAXC', + 'SMD', 'SMTBQ', 'SPH', 'TALLY', 'UEF', 'YAFF', +] + +enhance_sanity_check = True + +# run short test case to make sure installation doesn't produce blatently incorrect results; +# this catches a problem where having the USER-INTEL package enabled causes trouble when installing with intel/2019b +sanity_check_commands = ["cd %(builddir)s && python lammps_vs_yaff_test_single_point_energy.py"] + +moduleclass = 'chem' From 1968f1117e5e3c50da147778adcfaa8606b026cf Mon Sep 17 00:00:00 2001 From: Tom Strempel <37880275+tstrempel@users.noreply.github.com> Date: Sun, 16 Aug 2020 10:03:51 +0200 Subject: [PATCH 104/698] Update IDBA-UD-1.1.3-GCCcore-8.3.0.eb --- .../easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb index 06136635834..797f8c33f16 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb @@ -22,16 +22,12 @@ description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for S can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.""" -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] sources = ['idba-%(version)s.tar.gz'] checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] -builddependencies = [ - ('binutils', '2.32') -] - prebuildopts = './configure && ' # we delete every .o and Makefile file which is left in bin folder From a83bb0af989d0524606d881875f3a058400a550c Mon Sep 17 00:00:00 2001 From: Tom Strempel <37880275+tstrempel@users.noreply.github.com> Date: Mon, 17 Aug 2020 09:11:37 +0200 Subject: [PATCH 105/698] Rename IDBA-UD-1.1.3-GCCcore-8.3.0.eb to IDBA-UD-1.1.3-GCC-8.3.0.eb --- ...{IDBA-UD-1.1.3-GCCcore-8.3.0.eb => IDBA-UD-1.1.3-GCC-8.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/i/IDBA-UD/{IDBA-UD-1.1.3-GCCcore-8.3.0.eb => IDBA-UD-1.1.3-GCC-8.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb similarity index 100% rename from easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-8.3.0.eb rename to easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb From c4cc52d78ed38d1fa5e7272d249b680330ae5ff9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 20 Aug 2020 19:04:56 +0200 Subject: [PATCH 106/698] adding easyconfigs: PSI4-1.3.2-intel-2019b-Python-3.7.4.eb --- .../c/CheMPS2/CheMPS2-1.8.9-intel-2019b.eb | 32 ++++++++++ ...epdiff-5.0.2-GCCcore-8.3.0-Python-3.7.4.eb | 32 ++++++++++ ...CMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb | 41 +++++++++++++ .../PSI4-1.3.2-intel-2019b-Python-3.7.4.eb | 59 ++++++++++++++++++ .../Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb | 29 +++++++++ ...dantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb | 26 ++++++++ ...pytest-6.0.1-GCCcore-8.3.0-Python-3.7.4.eb | 60 +++++++++++++++++++ 7 files changed, 279 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019b.eb create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-5.0.2-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pytest/pytest-6.0.1-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019b.eb new file mode 100644 index 00000000000..c060d1d8243 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.9-intel-2019b.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.9' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ccd4c0d9432759d97690bf37a0333440f93513960c62d1f75842f090406a224d'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('HDF5', '1.10.5') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-5.0.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.0.2-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..d14ae0e440d --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.0.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '5.0.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://deepdiff.readthedocs.io/en/latest/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] +dependencies = [('Python', '3.7.4')] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('jsonpickle', '1.4.1', { + 'checksums': ['e8d4b7cd0bd6826001a74377df1079a76ad8bae0f909282de2554164c837c8ba'], + }), + ('ordered-set', '4.0.2', { + 'checksums': ['ba93b2df055bca202116ec44b9bead3df33ea63a7d5827ff8e16738b97f33a95'], + }), + (name, version, { + 'checksums': ['e2b74af4da0ef9cd338bb6e8c97242c1ec9d81fcb28298d7bb24acdc19ea79d7'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..4862bbfa6aa --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'iimpi', 'version': '2019b'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +builddependencies = [ + ('CMake', '3.15.3'), + ('Eigen', '3.3.7', '', True), +] + +dependencies = [ + ('Python', '3.7.4'), + ('zlib', '1.2.11'), + ('Boost', '1.71.0'), +] + +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN ' + +# The spherical test fails regardless of how it is compiled. +# Instead of patching the tests to skip it just don't run the tests for now. +# runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..d9f6a04d2e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb @@ -0,0 +1,59 @@ +easyblock = 'EB_PSI' + +name = 'PSI4' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.psicode.org/' +description = """PSI4 is an open-source suite of ab initio quantum chemistry programs designed for + efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform + computations with more than 2500 basis functions running serially or in parallel.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'usempi': True} + +github_account = 'psi4' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['PSI4-%(version)s_fix_cmake_release.patch'] + +builddependencies = [ + ('CMake', '3.15.3'), + # Perl needed for the ctest test suite during the installation, not for the pytest test suite after the installation + # ('Perl', '5.30.0'), +] + +dependencies = [ + ('Python', '3.7.4'), + # PCMSolver recent versions fail with recent intel compilers. + # Tried with intel/201{7,8}b, and versions 1.1.12, and 1.2.1 + # See in more details: https://github.com/PCMSolver/pcmsolver/issues/159 + ('PCMSolver', '1.2.3', versionsuffix), + ('CheMPS2', '1.8.9'), + ('pytest', '6.0.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('deepdiff', '5.0.2', versionsuffix), + ('libxc', '4.3.4'), + ('pybind11', '2.4.3', versionsuffix), + ('pydantic', '1.6.1', versionsuffix), + ('Pint', '0.14', versionsuffix), +] + +configopts = '-DENABLE_MPI=ON -DENABLE_PLUGINS=ON -DENABLE_XHOST=OFF ' +# Install python mudule to the standard location instead of lib +configopts += '-DPYMOD_INSTALL_LIBDIR=/python%(pyshortver)s/site-packages ' +# Add bundled (downloaded) packages +# -DENABLE_simint=ON does not work with intel/2018, so have to make with GCCcore +configopts += '-DENABLE_dkh=ON -DENABLE_gdma=ON -DENABLE_resp=ON -DENABLE_snsmp2=ON ' + +# runtest uses ctest, and some of the thests have to be manually compared +# to the reference output (those tests are marked failed) +# After installing PSI4, you can test the package using psi4 --test command. (This uses pytest framework) +# runtest = '-L smoke' +runtest = False + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_commands = ["python -c 'import psi4'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..75a70ab4798 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.14-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.14' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9aa450ebb9d722ed03fa9a450104cfd16c479b49f862d547c6f77320de597f72'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..a223a1117bb --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.6.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydantic' +version = '1.6.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['54122a8ed6b75fe1dd80797f8251ad2063ea348a03b77218d73ea9fe19bd4e73'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytest/pytest-6.0.1-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pytest/pytest-6.0.1-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..fc2d55f600c --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-6.0.1-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '6.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] +dependencies = [('Python', '3.7.4')] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('py', '1.9.0', { + 'checksums': ['9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('more-itertools', '8.4.0', { + 'modulename': 'more_itertools', + 'checksums': ['68c70cc7167bdf5c7c9d8f6954a7837089c6a36bf565383919bb595efb8a17e5'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('iniconfig', '1.0.1', { + 'checksums': ['e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + (name, version, { + 'checksums': ['85228d75db9f45e06e57ef9bf4429267f81ac7c0d742cc9ed63d09886a9fe6f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From efd27ac773a88b3a1abc7fb72e9c71d6adb9e358 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 21 Aug 2020 08:08:22 +0200 Subject: [PATCH 107/698] Add missing patch to PSI4 --- .../p/PSI4/PSI4-1.3.2_fix_cmake_release.patch | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch new file mode 100644 index 00000000000..9562f74dfc3 --- /dev/null +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch @@ -0,0 +1,83 @@ +diff -ru psi4-1.3.2.orig/cmake/autocmake_safeguards.cmake psi4-1.3.2/cmake/autocmake_safeguards.cmake +--- psi4-1.3.2.orig/cmake/autocmake_safeguards.cmake 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/cmake/autocmake_safeguards.cmake 2020-08-18 17:43:52.917814910 +0200 +@@ -19,8 +19,8 @@ + string(TOLOWER "${CMAKE_BUILD_TYPE}" cmake_build_type_tolower) + string(TOUPPER "${CMAKE_BUILD_TYPE}" cmake_build_type_toupper) + +-if(NOT cmake_build_type_tolower STREQUAL "debug" AND +- NOT cmake_build_type_tolower STREQUAL "release" AND +- NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") +- message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") +-endif() ++#if(NOT cmake_build_type_tolower STREQUAL "debug" AND ++# NOT cmake_build_type_tolower STREQUAL "release" AND ++# NOT cmake_build_type_tolower STREQUAL "relwithdebinfo") ++# message(FATAL_ERROR "Unknown build type \"${CMAKE_BUILD_TYPE}\". Allowed values are Debug, Release, RelWithDebInfo (case-insensitive).") ++#endif() +diff -ru psi4-1.3.2.orig/external/upstream/dkh/CMakeLists.txt psi4-1.3.2/external/upstream/dkh/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/dkh/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/dkh/CMakeLists.txt 2020-08-18 17:45:44.236805119 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/dkh + GIT_TAG v1.2 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ru psi4-1.3.2.orig/external/upstream/gau2grid/CMakeLists.txt psi4-1.3.2/external/upstream/gau2grid/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/gau2grid/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/gau2grid/CMakeLists.txt 2020-08-18 17:44:18.733580688 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/dgasmith/gau2grid + GIT_TAG v1.3.1 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ru psi4-1.3.2.orig/external/upstream/gdma/CMakeLists.txt psi4-1.3.2/external/upstream/gdma/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/gdma/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/gdma/CMakeLists.txt 2020-08-18 17:46:18.372495573 +0200 +@@ -16,6 +16,7 @@ + GIT_REPOSITORY https://github.com/psi4/gdma + GIT_TAG 9d607d7 # v2.2.6-2-g9d607d7 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ru psi4-1.3.2.orig/external/upstream/libefp/CMakeLists.txt psi4-1.3.2/external/upstream/libefp/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/libefp/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/libefp/CMakeLists.txt 2020-08-18 17:45:54.284714000 +0200 +@@ -17,6 +17,7 @@ + GIT_REPOSITORY https://github.com/ilyak/libefp + GIT_TAG 15cd7ce # v1.5.0 + 10 (docs and a cmake lapack patch) + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ru psi4-1.3.2.orig/external/upstream/libint/CMakeLists.txt psi4-1.3.2/external/upstream/libint/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/libint/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/libint/CMakeLists.txt 2020-08-18 17:45:11.141105284 +0200 +@@ -14,6 +14,7 @@ + ExternalProject_Add(libint_external + # "git checkout" fails on Windows, because of "*" in filenames (e.g. basis set files) + URL https://github.com/evaleev/libint/archive/b13e71d3cf9960460c4019e5ecf2546a5f361c71.zip ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} +diff -ru psi4-1.3.2.orig/external/upstream/libxc/CMakeLists.txt psi4-1.3.2/external/upstream/libxc/CMakeLists.txt +--- psi4-1.3.2.orig/external/upstream/libxc/CMakeLists.txt 2019-05-15 17:05:49.000000000 +0200 ++++ psi4-1.3.2/external/upstream/libxc/CMakeLists.txt 2020-08-18 17:46:32.960363301 +0200 +@@ -15,6 +15,7 @@ + GIT_REPOSITORY https://gitlab.com/libxc/libxc.git + GIT_TAG 4.3.3 + UPDATE_COMMAND "" ++ PATCH_COMMAND sed -e "s/debug/easybuildrelease/" -i cmake/autocmake_safeguards.cmake + CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${STAGED_INSTALL_PREFIX} + -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} + -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} From 84e8ebc44a76aad7923a3041919927e9c7140884 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 21 Aug 2020 09:13:48 +0200 Subject: [PATCH 108/698] PSI4: Add missing checksums --- .../easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb index d9f6a04d2e7..5016618bef8 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb @@ -16,6 +16,10 @@ github_account = 'psi4' source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] patches = ['PSI4-%(version)s_fix_cmake_release.patch'] +checksums = [ + 'ed76c67803b6420f35f57a6dd31c47108b9145b8c9fced5c94cdc179f6b5fbf3', # v1.3.2.tar.gz + 'c399b6a90e587976f7ec98a3f05c3b62525d015639f8352004b5bd4bea696eda', # PSI4-1.3.2_fix_cmake_release.patch +] builddependencies = [ ('CMake', '3.15.3'), From d7c95305302f08930f9d8c802ed38833ef9f0732 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2020 09:53:47 +0000 Subject: [PATCH 109/698] adding easyconfigs: CAVIAR-20200820-foss-2019b.eb and patches: CAVIAR-20200820-openblas.patch --- .../c/CAVIAR/CAVIAR-20200820-foss-2019b.eb | 43 +++++++++++++++++++ .../c/CAVIAR/CAVIAR-20200820-openblas.patch | 11 +++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb create mode 100644 easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb new file mode 100644 index 00000000000..808853c04f0 --- /dev/null +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb @@ -0,0 +1,43 @@ +easyblock = 'MakeCp' + +name = 'CAVIAR' +version = '20200820' + +homepage = "https://github.com/fhormoz/caviar" +description = """CAusal Variants Identication in Associated Regions. A statistical framework + that quantifies the probability of each variant to be causal while allowing an arbitrary + number of causal variants.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [{ + 'filename': 'CAVIAR-20200820.tar.gz', + 'git_config': { + 'url': 'https://github.com/fhormoz', + 'repo_name': 'caviar', + 'commit': '135b58b', + }, +}] +patches = ['CAVIAR-20200820-openblas.patch'] +checksums = [ + '7b8dae8b963207b676b2750f142fc86063468750a4ea6ca8cec383511ea8f483', # CAVIAR-20200820.tar.gz + '5fb85a0822902485c5da35f48ae86796e9d13d00763baac98a3ad1c6f27b7332', # CAVIAR-20200820-openblas.patch +] + +dependencies = [ + ('GSL', '2.6'), +] + +start_dir = "%(name)s-C++" + +files_to_copy = [ + (['%(name)s-C++/%(name)s', '%(name)s-C++/e%(name)s', '%(name)s-C++/set%(name)s', + '%(name)s-C++/mup%(name)s'], "bin"), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(name)s', 'e%(name)s', 'set%(name)s', 'mup%(name)s']], + 'dirs': [''], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch new file mode 100644 index 00000000000..8fe29a391f5 --- /dev/null +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch @@ -0,0 +1,11 @@ +--- caviar.orig/CAVIAR-C++/Makefile 2020-08-24 09:21:32.000000000 +0000 ++++ caviar/CAVIAR-C++/Makefile 2020-08-24 09:36:11.868606878 +0000 +@@ -1,7 +1,7 @@ + CC=g++ + DIC=$(PWD) + CFLAGS=-c -Wall -g -I $(DIC) +-LDFLAGS= -I $(DIC)/armadillo/include/ -DARMA_DONT_USE_WRAPPER -llapack -lblas -lgslcblas -lgsl ++LDFLAGS= -I $(DIC)/armadillo/include/ -DARMA_DONT_USE_WRAPPER -lopenblas -lgslcblas -lgsl + SOURCES1=caviar.cpp PostCal.cpp Util.cpp TopKSNP.cpp + SOURCES2=ecaviar.cpp PostCal.cpp Util.cpp + SOURCES3=setcaviar.cpp PostCal.cpp Util.cpp From 3a183df578c40bd7b8947a3a8b4234ff55d3809d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2020 10:56:59 +0000 Subject: [PATCH 110/698] Add comment in patch --- easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch index 8fe29a391f5..b84b41f6a5d 100644 --- a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-openblas.patch @@ -1,3 +1,4 @@ +# Fix link error by hard-coding openblas --- caviar.orig/CAVIAR-C++/Makefile 2020-08-24 09:21:32.000000000 +0000 +++ caviar/CAVIAR-C++/Makefile 2020-08-24 09:36:11.868606878 +0000 @@ -1,7 +1,7 @@ From f4dc1d767789db9877d865b68fbbe3b7e848c20e Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2020 11:26:07 +0000 Subject: [PATCH 111/698] use Github tarball of specific commit --- .../c/CAVIAR/CAVIAR-20200820-foss-2019b.eb | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb index 808853c04f0..698df559fc6 100644 --- a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb @@ -10,18 +10,12 @@ description = """CAusal Variants Identication in Associated Regions. A statistic toolchain = {'name': 'foss', 'version': '2019b'} -sources = [{ - 'filename': 'CAVIAR-20200820.tar.gz', - 'git_config': { - 'url': 'https://github.com/fhormoz', - 'repo_name': 'caviar', - 'commit': '135b58b', - }, -}] +source_urls = ['https://github.com/fhormoz/caviar/archive/'] +sources = ['135b58b.tar.gz'] patches = ['CAVIAR-20200820-openblas.patch'] checksums = [ - '7b8dae8b963207b676b2750f142fc86063468750a4ea6ca8cec383511ea8f483', # CAVIAR-20200820.tar.gz - '5fb85a0822902485c5da35f48ae86796e9d13d00763baac98a3ad1c6f27b7332', # CAVIAR-20200820-openblas.patch + '1cd0dea53a07ce59475de9d47c9e8e9f165c52798976d144e476b4e28a02e357', # 135b58b.tar.gz + '3fdcb1633f6364410f9e38745a874a52906a14dbf36c0c3151a8d11e55cd8ba1', # CAVIAR-20200820-openblas.patch ] dependencies = [ From b7239b1195faea63498318c3f926923ef1aa4bd5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2020 11:35:53 +0000 Subject: [PATCH 112/698] Better approach for using commit-based tarball --- .../CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb new file mode 100644 index 00000000000..4fe96ac20b1 --- /dev/null +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'CAVIAR' +local_commit_id = '135b58b' +version = '2.2-20190419' + +homepage = "https://github.com/fhormoz/caviar" +description = """CAusal Variants Identication in Associated Regions. A statistical framework + that quantifies the probability of each variant to be causal while allowing an arbitrary + number of causal variants.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +sources = [{ + 'source_urls': ['https://github.com/fhormoz/caviar/archive/'], + 'download_filename': '%s.tar.gz' % local_commit_id, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['CAVIAR-20200820-openblas.patch'] +checksums = [ + '1cd0dea53a07ce59475de9d47c9e8e9f165c52798976d144e476b4e28a02e357', # CAVIAR-2.2-20190419.tar.gz + '3fdcb1633f6364410f9e38745a874a52906a14dbf36c0c3151a8d11e55cd8ba1', # CAVIAR-20200820-openblas.patch +] + +dependencies = [ + ('GSL', '2.6'), +] + +start_dir = "%(name)s-C++" + +files_to_copy = [ + (['%(name)s-C++/%(name)s', '%(name)s-C++/e%(name)s', '%(name)s-C++/set%(name)s', + '%(name)s-C++/mup%(name)s'], "bin"), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['%(name)s', 'e%(name)s', 'set%(name)s', 'mup%(name)s']], + 'dirs': [''], +} + +moduleclass = 'bio' From 7f696a43bb0efe5729ad57aeaeac8b3eb152af12 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 24 Aug 2020 12:37:10 +0100 Subject: [PATCH 113/698] Delete CAVIAR-20200820-foss-2019b.eb Removed in favour of improved version with a different name --- .../c/CAVIAR/CAVIAR-20200820-foss-2019b.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb deleted file mode 100644 index 698df559fc6..00000000000 --- a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-20200820-foss-2019b.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'MakeCp' - -name = 'CAVIAR' -version = '20200820' - -homepage = "https://github.com/fhormoz/caviar" -description = """CAusal Variants Identication in Associated Regions. A statistical framework - that quantifies the probability of each variant to be causal while allowing an arbitrary - number of causal variants.""" - -toolchain = {'name': 'foss', 'version': '2019b'} - -source_urls = ['https://github.com/fhormoz/caviar/archive/'] -sources = ['135b58b.tar.gz'] -patches = ['CAVIAR-20200820-openblas.patch'] -checksums = [ - '1cd0dea53a07ce59475de9d47c9e8e9f165c52798976d144e476b4e28a02e357', # 135b58b.tar.gz - '3fdcb1633f6364410f9e38745a874a52906a14dbf36c0c3151a8d11e55cd8ba1', # CAVIAR-20200820-openblas.patch -] - -dependencies = [ - ('GSL', '2.6'), -] - -start_dir = "%(name)s-C++" - -files_to_copy = [ - (['%(name)s-C++/%(name)s', '%(name)s-C++/e%(name)s', '%(name)s-C++/set%(name)s', - '%(name)s-C++/mup%(name)s'], "bin"), -] - -sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['%(name)s', 'e%(name)s', 'set%(name)s', 'mup%(name)s']], - 'dirs': [''], -} - -moduleclass = 'bio' From f3654d4745982b5c163ffc1ea3acba4c1e5507be Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Aug 2020 09:19:12 +0200 Subject: [PATCH 114/698] Add missing author/description to patch. --- .../easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb index 5016618bef8..2792ec72584 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2-intel-2019b-Python-3.7.4.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['PSI4-%(version)s_fix_cmake_release.patch'] checksums = [ 'ed76c67803b6420f35f57a6dd31c47108b9145b8c9fced5c94cdc179f6b5fbf3', # v1.3.2.tar.gz - 'c399b6a90e587976f7ec98a3f05c3b62525d015639f8352004b5bd4bea696eda', # PSI4-1.3.2_fix_cmake_release.patch + '62252bfc3e974fb62db9377246467af637f007e95b5889be472b8e7c2e7fd546', # PSI4-1.3.2_fix_cmake_release.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch index 9562f74dfc3..b5bd15e8842 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.3.2_fix_cmake_release.patch @@ -1,3 +1,7 @@ +# remove CMAKE_BUILD_TYPE check (beacuse it is set to EasyBuildRelease to avoid -O3 optimization flag) +# November 02nd 2018 by B. Hajgato - (Free University Brussels - VUB) + +# Adopted to v1.3.2 by Åke Sandgren, HPC2N diff -ru psi4-1.3.2.orig/cmake/autocmake_safeguards.cmake psi4-1.3.2/cmake/autocmake_safeguards.cmake --- psi4-1.3.2.orig/cmake/autocmake_safeguards.cmake 2019-05-15 17:05:49.000000000 +0200 +++ psi4-1.3.2/cmake/autocmake_safeguards.cmake 2020-08-18 17:43:52.917814910 +0200 From 584e28bc63c2f0ded148b3db8201d3d720c22b2b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 28 Aug 2020 16:12:46 +0200 Subject: [PATCH 115/698] [TensorFlow] Patch out bug in collective primitive --- ...0_fix-collective-all-reduce-strategy.patch | 22 +++++++++++++++++++ ...ensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb | 3 +++ ...rFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb | 3 +++ 3 files changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch new file mode 100644 index 00000000000..bc1b8a20f01 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch @@ -0,0 +1,22 @@ +Fix for AttributeError: 'CollectiveAllReduceExtended' object has no attribute '_cfer_fn_cache' +See https://github.com/tensorflow/tensorflow/issues/39417 + +Author: Alexander Grund +--- tensorflow-2.1.0-orig/tensorflow/python/distribute/collective_all_reduce_strategy.py 2020-05-11 18:14:03.682085572 +0200 ++++ tensorflow-2.1.0/tensorflow/python/distribute/collective_all_reduce_strategy.py 2020-05-11 18:15:41.623409641 +0200 +@@ -19,6 +19,7 @@ + from __future__ import print_function + + import copy ++import weakref + + from tensorflow.core.protobuf import config_pb2 + from tensorflow.core.protobuf import rewriter_config_pb2 +@@ -172,6 +173,7 @@ + cross_device_ops_lib.CollectiveCommunication) + self._communication = communication + self._initialize_strategy(cluster_resolver) ++ self._cfer_fn_cache = weakref.WeakKeyDictionary() + assert isinstance(self._get_cross_device_ops(), + cross_device_ops_lib.CollectiveAllReduce) + diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb index 7c4e03c0c7d..d40a0ab6902 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb @@ -129,6 +129,7 @@ exts_list = [ 'patches': [ 'TensorFlow-1.14.0_swig-env.patch', 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -137,6 +138,8 @@ exts_list = [ '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch + '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb index fe727062968..a84d2cebb1f 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -131,6 +131,7 @@ exts_list = [ 'patches': [ 'TensorFlow-1.14.0_swig-env.patch', 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -139,6 +140,8 @@ exts_list = [ '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch + '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', ], }), ] From a202e1ecf8cb8a3248fe8d6bd46af400a8de0720 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 28 Aug 2020 14:41:23 -0700 Subject: [PATCH 116/698] update bx-python --- ...bx-python-0.8.8-foss-2019b-Python-3.7.4.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..438e1ae5448 --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.8.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('LZO', '2.10'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('python-lzo', '1.12', { + 'modulename': 'lzo', + 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], + }), + (name, version, { + 'modulename': 'bx', + 'checksums': ['ad0808ab19c007e8beebadc31827e0d7560ac0e935f1100fb8cc93607400bb47'], + }), +] + +moduleclass = 'bio' From 5198527ca2719a3c276991dd96607f131523c6ed Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 2 Sep 2020 15:38:26 +0100 Subject: [PATCH 117/698] adding easyconfigs: FHI-aims-200112_2-intel-2019b.eb --- .../FHI-aims/FHI-aims-200112_2-intel-2019b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb new file mode 100644 index 00000000000..4267a0b909f --- /dev/null +++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# +## +easyblock = 'CMakeMake' + +name = 'FHI-aims' +version = '200112_2' + +homepage = 'https://aimsclub.fhi-berlin.mpg.de/' +description = """FHI-aims is an efficient, accurate all-electron, +full-potential electronic structure code package for computational molecular +and materials science (non-periodic and periodic systems). The code supports +DFT (semilocal and hybrid) and many-body perturbation theory. FHI-aims is +particularly efficient for molecular systems and nanostructures, while +maintaining high numerical accuracy for all production tasks. Production +calculations handle up to several thousand atoms and can efficiently use (ten) +thousands of cores. +""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'opt': True, 'precise': True} + +# The source code must be downloaded manually from the FHI-aims club. +sources = ['%(namelower)s.%(version)s.tgz'] +checksums = ['b591b09c7cb2e0befe59067ae59a63f522a9b5200a4073018f616aea657704d6'] + +builddependencies = [('CMake', '3.15.3')] + +configopts = ' -DCMAKE_Fortran_COMPILER="$MPIF90" ' +configopts += ' -DLIBS="mkl_scalapack_lp64 mkl_blacs_intelmpi_lp64 mkl_intel_lp64 mkl_sequential mkl_core" ' +configopts += ' -DLIB_PATHS="$CMAKE_LIBRARY_PATH" ' +configopts += ' -DCMAKE_C_FLAGS="$CFLAGS -ip" ' +configopts += ' -DCMAKE_Fortran_FLAGS="$FFLAGS -ip" ' +configopts += ' -DFortran_MIN_FLAGS="-O0 -fp-model precise" ' +configopts += ' -DTARGET_NAME="aims.x" ' + +postinstallcmds = ["cp -ar %(builddir)s/%(namelower)s.%(version)s/{CHANGELOG.md,doc,external} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{regression_tests,species_defaults} %(installdir)s/", + "cp -ar %(builddir)s/%(namelower)s.%(version)s/{testcases,utilities} %(installdir)s/"] + +sanity_check_paths = { + 'files': ['bin/aims.x'], + 'dirs': [], +} + +moduleclass = 'math' From f7b3c5e182173c609f02bbd105ba968a45c940f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 2 Sep 2020 22:11:10 +0200 Subject: [PATCH 118/698] add missing groff build dependency for Perl (provides nroff tool requires to install man pages) --- .../g/groff/groff-1.22.4-GCCcore-9.3.0.eb | 26 +++++++++++++++++++ .../p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 5 +++- 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..35b9ec58681 --- /dev/null +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'groff' +version = '1.22.4' + +homepage = 'https://www.gnu.org/software/groff' +description = """Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands + and produces formatted output.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/groff'] +sources = [SOURCE_TAR_GZ] +checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] + +builddependencies = [ + ('binutils', '2.34'), + ('texinfo', '6.7'), # provides makeinfo +] + +sanity_check_paths = { + 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], + 'dirs': ['lib/groff', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 11dc18e301d..44d508b47b5 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -11,7 +11,10 @@ source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] -builddependencies = [('binutils', '2.34')] +builddependencies = [ + ('binutils', '2.34'), + ('groff', '1.22.4'), +] dependencies = [ ('zlib', '1.2.11'), # for Net::SSLeay From 0f257201d43f3d618d43d5c6e9ab7b9c17a1749e Mon Sep 17 00:00:00 2001 From: Tom Strempel <37880275+tstrempel@users.noreply.github.com> Date: Thu, 3 Sep 2020 14:15:19 +0200 Subject: [PATCH 119/698] Update attribution in IDBA-UD-1.1.3-GCC-8.3.0.eb --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb index 797f8c33f16..c1860655e56 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb @@ -2,6 +2,8 @@ # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 # "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock # to be sure everything is copied and we run ./configure in prebuildopts From b15d6a6bb832f8835f8e70bd56d9ffccbb087cfc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 15:09:15 +0200 Subject: [PATCH 120/698] {chem}[intel/2020a] phonopy v2.7.1 + spglib-python v1.16.0 w/ Python 3.8.2 --- .../phonopy-2.7.1-intel-2020a-Python-3.8.2.eb | 40 +++++++++++++++++++ ...-python-1.16.0-intel-2020a-Python-3.8.2.eb | 36 +++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..221af9c706f --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.7.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['482c6ff29c058d091ac885e561e28ba3e516ea9e91c44a951cad11f3ae19856c'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy + ('matplotlib', '3.2.1', versionsuffix), + ('PyYAML', '5.3'), + ('h5py', '2.10.0', versionsuffix), + ('spglib-python', '1.16.0', versionsuffix), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..22719ac82e8 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['94d056e48e7e6fe2e6fe4161471e774ac03221a6225fd83d551d3184220c1edf'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +# required because we're building a Python package using Intel compilers on top of Python built with GCC +check_ldshared = True + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'spglib'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_pip_check = True + +moduleclass = 'chem' From 7f5fb65718ffbef3dfefd89949e1e5c8180ef72a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 15:13:20 +0200 Subject: [PATCH 121/698] adding easyconfigs: ASE-3.20.1-intel-2020a-Python-3.8.2.eb --- .../ASE-3.20.1-intel-2020a-Python-3.8.2.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..99b1f725dda --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.20.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.20.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.2', { + 'checksums': ['4efa1ae2d7c9865af48986de8aeb8504bf32c7f3d6fdc9353d34b21f4b127060'], + }), + ('ase', version, { + 'checksums': ['72c81f21b6adb907595fce8d883c0231301cbd8e9f6e5ce8e98bab927054daca'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "ase --help", + # make sure Tkinter is available, otherwise 'ase gui' will not work + "python -c 'import tkinter' ", +] + +sanity_pip_check = True + +moduleclass = 'chem' From 119a36b10aaae048fd06cdc4937188f2f79c2c39 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Sep 2020 16:05:43 +0200 Subject: [PATCH 122/698] adding easyconfigs: nglview-2.7.7-intel-2020a-Python-3.8.2.eb, IPython-7.15.0-intel-2020a-Python-3.8.2.eb --- ...IPython-7.15.0-intel-2020a-Python-3.8.2.eb | 165 ++++++++++++++++++ .../nglview-2.7.7-intel-2020a-Python-3.8.2.eb | 38 ++++ 2 files changed, 203 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d8926b1dd07 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.15.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,165 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.15.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('ZeroMQ', '4.3.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('PyYAML', '5.3'), # required for jupyter_nbextensions_configurator +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['0ef1433879816a960cd3ae1ae1dc82c64732ca75cec8dab5a4e29783fb571d0e'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + }), + ('prompt_toolkit', '3.0.5', { + 'checksums': ['563d1a4140b63ff9dd587bda9557cffb2fe73650205ab6f4383092fb882e7dc8'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), + ('traitlets', '4.3.3', { + 'checksums': ['d023ee369ddd2763310e4c3eae1ff649689440d4ae59d7485eb4cfbbe3e359f7'], + }), + ('parso', '0.7.0', { + 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], + }), + ('jedi', '0.17.0', { + 'checksums': ['df40c97641cb943661d2db4c33c2e1ff75d491189423249e989bcea4464f3030'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('Send2Trash', '1.5.0', { + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.0.1', { + 'checksums': ['66cb0dcfdbbc4f9c3ba1a63fdb511ffdbd4f513b2b6d81b80cd26ce6b3fb3736'], + }), + ('bleach', '3.1.5', { + 'checksums': ['3c4c520fdb9db59ef139915a5db79f8b51bc2a7257ea0389f30c846883430a4b'], + }), + ('vcversioner', '2.16.0.0', { + 'checksums': ['dae60c17a479781f44a4010701833f1829140b1eeccd258762a74974aa06e19b'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('pandocfilters', '1.4.2', { + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '19.0.1', { + 'modulename': 'zmq', + 'checksums': ['13a5638ab24d628a6ade8f794195e1a1acd573496c3b85af2f1183603b7bf5e0'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('nbformat', '5.0.6', { + 'checksums': ['049af048ed76b95c3c44043620c17e56bc001329e07f83fec4f177f0e3d7b757'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('nbconvert', '5.6.1', { + 'checksums': ['21fb48e700b43e82ba0e3142421a659d7739b65568cc832a13976a77be16b523'], + }), + ('terminado', '0.8.3', { + 'use_pip': False, + 'checksums': ['4804a774f802306a7d9af7322193c5390f1da0abb429e082a10ef1d46e6fb2c2'], + }), + ('tornado', '6.0.4', { + 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], + }), + ('jupyter_client', '6.1.3', { + 'checksums': ['3a32fa4d0b16d1c626b30c3002a62dfd86d6863ed39eaba3f537fade197bb756'], + }), + ('backcall', '0.1.0', { + 'checksums': ['38ecd85be2c1e78f77fd91700c76e14667dc21e2713b63876c0eb901196e01e4'], + }), + ('ipykernel', '5.3.0', { + 'checksums': ['731adb3f2c4ebcaff52e10a855ddc87670359a89c9c784d711e62d66fccdafae'], + }), + ('prometheus_client', '0.8.0', { + 'checksums': ['c6e6b706833a6bd1fd51711299edee907857be10ece535126a158f911ee80915'], + }), + ('pyrsistent', '0.16.0', { + 'checksums': ['28669905fe725965daa16184933676547c5bb40a5153055a8dee2a4bd7933ad3'], + }), + ('ipywidgets', '7.5.1', { + 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], + }), + ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], + }), + ('jupyter_nbextensions_configurator', '0.4.1', { + 'checksums': ['e5e86b5d9d898e1ffb30ebb08e4ad8696999f798fef3ff3262d7b999076e4e83'], + }), + ('notebook', '6.0.3', { + 'checksums': ['47a9092975c9e7965ada00b9a20f0cf637d001db60d241d479f53c0be117ad48'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..5c095088b79 --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-2.7.7-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '2.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('IPython', '7.15.0', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), + (name, version, { + 'checksums': ['fd84e20f0c1e183f2c429509c4a64b226e8591253545358062f48f3ec7dafddb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nglview'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From fd4269abf68d2c44d20074bf41e60e8351189548 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Sep 2020 19:32:35 +0200 Subject: [PATCH 123/698] {tools}[gompi/2020a] phonemizer 2.2.1 /w Python-3.8.2 + deps --- .../e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb | 45 ++++++ .../eSpeak-NG-1.50_mbrola_location.patch | 13 ++ .../eSpeak-NG/eSpeak-NG-1.50_sonic_fftw.patch | 25 ++++ .../festival/festival-2.5.0-GCCcore-9.3.0.eb | 128 ++++++++++++++++++ .../festival-2.5.0_speech_tools.patch | 13 ++ ...BROLA-3.3-GCCcore-9.3.0-voices-20200330.eb | 52 +++++++ .../m/MBROLA/MBROLA-3.3_makefile.patch | 40 ++++++ ...onemizer-2.2.1-gompi-2020a-Python-3.8.2.eb | 44 ++++++ .../s/sonic/sonic-20180202-gompi-2020a.eb | 45 ++++++ .../easyconfigs/s/sonic/sonic-20180202.patch | 20 +++ .../speech_tools-2.5.0-GCCcore-9.3.0.eb | 59 ++++++++ .../speech_tools-2.5.0_easybuild.patch | 39 ++++++ 12 files changed, 523 insertions(+) create mode 100644 easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_mbrola_location.patch create mode 100644 easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_sonic_fftw.patch create mode 100644 easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/f/festival/festival-2.5.0_speech_tools.patch create mode 100644 easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb create mode 100644 easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch create mode 100644 easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/s/sonic/sonic-20180202.patch create mode 100644 easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_easybuild.patch diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb new file mode 100644 index 00000000000..58543a3d471 --- /dev/null +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'eSpeak-NG' +version = '1.50' + +homepage = 'https://github.com/espeak-ng/espeak-ng' +description = """ +The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +source_urls = ['https://github.com/espeak-ng/espeak-ng/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_sonic_fftw.patch', + '%(name)s-%(version)s_mbrola_location.patch', +] +checksums = [ + '5ce9f24ee662b5822a4acc45bed31425e70d7c50707b96b6c1603a335c7759fa', # 1.50.tar.gz + 'dc34e14ef4b8bc174c94ad220cbf35b80e6183298d24883cf252507154ef4ee4', # eSpeak-NG-1.50_sonic_fftw.patch + '1bf9bb98f1fd35ddbd373b504c3215641db532093fc5dd44099a820b80c76f83', # eSpeak-NG-1.50_mbrola_location.patch +] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('sonic', '20180202'), + ('MBROLA', '3.3', '-voices-20200330'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-dependency-tracking' + +maxparallel = 1 +sanity_check_paths = { + 'files': ['bin/%sspeak%s' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] + + ['include/espeak%s/speak_lib.h' % x for x in ['', '-ng']] + + ['include/espeak-ng/%s.h' % x for x in ['encoding', 'espeak_ng']] + + ['lib/libespeak%s' % x for x in ['.la', '-ng.a', '-ng.%s' % SHLIB_EXT]], + 'dirs': ['lib/pkgconfig'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_mbrola_location.patch b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_mbrola_location.patch new file mode 100644 index 00000000000..3c108cf7411 --- /dev/null +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_mbrola_location.patch @@ -0,0 +1,13 @@ +# Take MBROLA voices form MBROLA EasyBuild package +# SEP 8th 2020 by B. Hajgato (UGent) +--- src/libespeak-ng/synth_mbrola.c.orig 2019-11-29 17:50:54.000000000 +0100 ++++ src/libespeak-ng/synth_mbrola.c 2020-09-08 17:58:01.806240614 +0200 +@@ -90,7 +90,7 @@ + // if not found, then also look in + // usr/share/mbrola/xx, /usr/share/mbrola/xx/xx, /usr/share/mbrola/voices/xx + if (GetFileLength(path) <= 0) { +- sprintf(path, "/usr/share/mbrola/%s", mbrola_voice); ++ sprintf(path, "%s/share/mbrola/%s/%s", getenv("EBROOTMBROLA"), mbrola_voice, mbrola_voice); + + if (GetFileLength(path) <= 0) { + sprintf(path, "/usr/share/mbrola/%s/%s", mbrola_voice, mbrola_voice); diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_sonic_fftw.patch b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_sonic_fftw.patch new file mode 100644 index 00000000000..a2eddd48cea --- /dev/null +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50_sonic_fftw.patch @@ -0,0 +1,25 @@ +# sonic needs libfftw3 so add to the configure check +# and fixed missing separator in the Makefile +# SEP 3rd 2020 by B. Hajgato (UGent) +--- configure.ac.orig 2019-11-29 17:50:54.000000000 +0100 ++++ configure.ac 2020-09-03 11:29:21.961205274 +0200 +@@ -232,7 +232,7 @@ + else + AC_CHECK_HEADERS([sonic.h], + [ +- AC_CHECK_LIB([sonic], [sonicCreateStream]) ++ AC_CHECK_LIB([sonic -lfftw3], [sonicCreateStream]) + have_sonic=yes + ],[ + have_sonic=no +--- Makefile.am.orig 2020-09-03 12:02:45.023133962 +0200 ++++ Makefile.am 2020-09-03 12:04:48.778209845 +0200 +@@ -106,7 +106,7 @@ + src/speak-ng.1: src/speak-ng.1.ronn + ronn --roff $< + +-docs_MARKDOWN != ls docs/*.md docs/*/*.md docs/*/*/*.md ++ docs_MARKDOWN != ls docs/*.md docs/*/*.md docs/*/*/*.md + docs_HTML = ${docs_MARKDOWN:.md=.html} + + docs: $(docs_HTML) \ diff --git a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2525da9b956 --- /dev/null +++ b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb @@ -0,0 +1,128 @@ +easyblock = 'ConfigureMake' + +name = 'festival' +version = '2.5.0' + +homepage = ['http://festvox.org/festival/'] + +description = """ +University of Edinburgh's Festival Speech Synthesis Systems is a free software +multi-lingual speech synthesis workbench that runs on multiple-platforms +offering black box text to speech, as well as an open architecture for +research in speech synthesis. +It designed as a component of large speech technology systems. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'http://festvox.org/packed/festival/%(version_major_minor)s', + 'http://festvox.org/packed/festival/%(version_major_minor)s/voices', +] +sources = [] +local_sources = [ + '%(name)s-%(version)s-release.tar.gz', + 'festlex_CMU.tar.gz', + 'festlex_OALD.tar.gz', + 'festlex_POSLEX.tar.gz', + 'festvox_cmu_indic_ben_rm_cg.tar.gz', + 'festvox_cmu_indic_guj_ad_cg.tar.gz', + 'festvox_cmu_indic_guj_dp_cg.tar.gz', + 'festvox_cmu_indic_guj_kt_cg.tar.gz', + 'festvox_cmu_indic_hin_ab_cg.tar.gz', + 'festvox_cmu_indic_kan_plv_cg.tar.gz', + 'festvox_cmu_indic_mar_aup_cg.tar.gz', + 'festvox_cmu_indic_mar_slp_cg.tar.gz', + 'festvox_cmu_indic_pan_amp_cg.tar.gz', + 'festvox_cmu_indic_tam_sdr_cg.tar.gz', + 'festvox_cmu_indic_tel_kpn_cg.tar.gz', + 'festvox_cmu_indic_tel_sk_cg.tar.gz', + 'festvox_cmu_indic_tel_ss_cg.tar.gz', + 'festvox_cmu_us_aew_cg.tar.gz', + 'festvox_cmu_us_ahw_cg.tar.gz', + 'festvox_cmu_us_aup_cg.tar.gz', + 'festvox_cmu_us_awb_cg.tar.gz', + 'festvox_cmu_us_axb_cg.tar.gz', + 'festvox_cmu_us_bdl_cg.tar.gz', + 'festvox_cmu_us_clb_cg.tar.gz', + 'festvox_cmu_us_eey_cg.tar.gz', + 'festvox_cmu_us_fem_cg.tar.gz', + 'festvox_cmu_us_gka_cg.tar.gz', + 'festvox_cmu_us_jmk_cg.tar.gz', + 'festvox_cmu_us_ksp_cg.tar.gz', + 'festvox_cmu_us_ljm_cg.tar.gz', + 'festvox_cmu_us_lnh_cg.tar.gz', + 'festvox_cmu_us_rms_cg.tar.gz', + 'festvox_cmu_us_rxr_cg.tar.gz', + 'festvox_cmu_us_slp_cg.tar.gz', + 'festvox_cmu_us_slt_cg.tar.gz', + 'festvox_kallpc16k.tar.gz', + 'festvox_rablpc16k.tar.gz', +] +for local_x in local_sources: + sources.append({'filename': local_x, 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1'}) + +patches = ['%(name)s-%(version)s_speech_tools.patch'] +checksums = [ + '4c9007426b125290599d931df410e2def51e68a8aeebd89b4a61c7c96c09a4b4', # festival-2.5.0-release.tar.gz + 'c19430919bca45d5368cd4c82af6153fbcc96a487ebd30b78b5f3c08718b7c07', # festlex_CMU.tar.gz + 'e33a345390d4c76f8b987b06a5332bcdd0b168cf67c95ddc3270f9163cbe61f8', # festlex_OALD.tar.gz + 'e7c6e3642dbd5b0d64942bc015a986fdd6244a79e51ec2e8309e63d569e49ea3', # festlex_POSLEX.tar.gz + '56e2144d5eed6c89a451789ef7f37346dd351efdbb86a0fa650432a19b07367f', # festvox_cmu_indic_ben_rm_cg.tar.gz + '4a0ac2d1b15cd41108be803e23f11911be953b50733848a8e67428c642e02ba9', # festvox_cmu_indic_guj_ad_cg.tar.gz + '1a4e17d67db50a6d81f7860b64acc8d41245f6f763ccff4c9386ab9ae9923910', # festvox_cmu_indic_guj_dp_cg.tar.gz + '666017d8d64737c4fd70b72ab6cf846fd8e13de290a5ba494bd1697249a16e9d', # festvox_cmu_indic_guj_kt_cg.tar.gz + '60318e160d994d5174168cc94467c776de81426f91c4f8003206cff953cb79bd', # festvox_cmu_indic_hin_ab_cg.tar.gz + 'd87f4ea342e7cb37e90ddf49dde37f19c1470b3c5a09d00cef3212108107cb31', # festvox_cmu_indic_kan_plv_cg.tar.gz + '0c7509203483fc97c04b670127b20c2d51723b3a16517124e22d095f379cca7f', # festvox_cmu_indic_mar_aup_cg.tar.gz + 'f3be7241d35db1e18d652e2cfa4cb69bae038c3d21c59ed3ce365487894f0d46', # festvox_cmu_indic_mar_slp_cg.tar.gz + 'f1e9238c6b8646a2a252ab855f5773c8ebdf8b3df909e0bbe4a99d7b830a4f3e', # festvox_cmu_indic_pan_amp_cg.tar.gz + '9a4c088ce3bdbf17867d5df918fc3868597061380ae8daf896ce99d33723e570', # festvox_cmu_indic_tam_sdr_cg.tar.gz + '43ad700a82a270530dda44fd4a89b34429c37723cdde130faece4811723ff72b', # festvox_cmu_indic_tel_kpn_cg.tar.gz + '0ee102e8093a549171f5e4ff826ebf3f9eaf84e7d43259777e38cafe4c4b6eea', # festvox_cmu_indic_tel_sk_cg.tar.gz + 'b2e56ca4722e3d025d831fd1eef679ffbf00fe165b68a44a5596321411ffa1f0', # festvox_cmu_indic_tel_ss_cg.tar.gz + '5d9555580b95324fa734b7771c95dced44e7903510358481d24e4fe5c961111c', # festvox_cmu_us_aew_cg.tar.gz + '906492478bd86b5201f72ffe701279b98b3ba94ae74816a0d7f2ba20bc2b5bf7', # festvox_cmu_us_ahw_cg.tar.gz + '455476e1c5246d90aac090a06afa5a4e90c801aebace6fe357900c8e095be826', # festvox_cmu_us_aup_cg.tar.gz + 'b2adbdfeda0cba289bb4da68dd14114d3eb3e7f72049cc8d2cbdfb2df39f6934', # festvox_cmu_us_awb_cg.tar.gz + '172c826df9c8f49ecb03f997749b207a23de8678dcf13706709104c2c597ebfb', # festvox_cmu_us_axb_cg.tar.gz + '1dc6792af9e2c1660a46fe499aa67af4affa665a0bdc08207cc11719baa62f6d', # festvox_cmu_us_bdl_cg.tar.gz + '11c82d1c18ce3db6fb11ca788cc5d84f69f9346aff77c7495f50005d6b042148', # festvox_cmu_us_clb_cg.tar.gz + 'af8590f7c1ba7d5dba22ff52c30a7bb3f55592eabca9615cd712fa4da8f83e13', # festvox_cmu_us_eey_cg.tar.gz + 'f8788c2af4838bb90e0a859f38da66c95961bdff2572001d5a019a2127c74306', # festvox_cmu_us_fem_cg.tar.gz + '47cf21a96adfcad398bd28b4d2548493a2055f75e53cf71344eef3aebc03ab59', # festvox_cmu_us_gka_cg.tar.gz + '711db388bc500331cfda86a46a72193ca1e2c9dc7d5ef16dfc86827e499946f2', # festvox_cmu_us_jmk_cg.tar.gz + '3b8098ac30995ce245d518c5b8fee825917428cb3ebe0409a0b415c919bdd35f', # festvox_cmu_us_ksp_cg.tar.gz + 'aec062c3d0c30719dd7e3e9ee4c427cbaad5e47550e28af2e9f151a41dcad852', # festvox_cmu_us_ljm_cg.tar.gz + 'ece81f42379feba4c392ad723fb68374aff9cd78f57cf629f624b0bd0c928d08', # festvox_cmu_us_lnh_cg.tar.gz + '3167afa3a6ffb5bbc305c94a1e6b671e40783a87a49372fce04c54942872c421', # festvox_cmu_us_rms_cg.tar.gz + 'bf362b6f270b1a4c76be981c3e8bd862fbb17a64e971e5b4a84d970ed5ecec42', # festvox_cmu_us_rxr_cg.tar.gz + 'f1d8e601c9631dfb7f8bd05c341d9fce8899dc9547ed9a652c8ded6ab854de9a', # festvox_cmu_us_slp_cg.tar.gz + '78cb93e361ab016fd23833c56853ddf21e2f1356310f54eed1c09a9755ce9f43', # festvox_cmu_us_slt_cg.tar.gz + '809c4ab5ed9e4df4a658b58d5c56fe35055723f00d81a238168f5a1ebdaed08c', # festvox_kallpc16k.tar.gz + 'ecd14b77c528e94dfb076e44050102fe8fba57e5fe813acf78a66629317f52a5', # festvox_rablpc16k.tar.gz + '0716ea33c8eccee435ab08464657af2ec2b64cf02409cddb868f8ad869e7e172', # festival-2.5.0_speech_tools.patch +] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('speech_tools', '2.5.0'), +] + +# LIBS environmental variable interfers $EBROOTSPEECH_TOOLS/libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) +prebuildopts = 'unset LIBS &&' + +buildininstalldir = True + +maxparallel = 1 + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/festival%s' % x for x in ['', '_client']] + + ['lib/%s.scm' % x for x in ['siod', 'web', 'cstr', 'fringe']], + 'dirs': ['lib/voices', 'lib/dicts/cmu', 'lib/dicts/oald'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/festival/festival-2.5.0_speech_tools.patch b/easybuild/easyconfigs/f/festival/festival-2.5.0_speech_tools.patch new file mode 100644 index 00000000000..321da5bc8d7 --- /dev/null +++ b/easybuild/easyconfigs/f/festival/festival-2.5.0_speech_tools.patch @@ -0,0 +1,13 @@ +# Pick up easybuild build speech_tools config +# SEP 9th 2020 by B. Hajgato (UGent) +--- config/config.in.org 2017-09-04 17:54:08.000000000 +0200 ++++ config/config.in 2020-09-08 11:27:08.819754926 +0200 +@@ -10,7 +10,7 @@ + ########################################################################### + ## Which speech tools to use + +-EST=$(TOP)/../speech_tools ++EST=${EBROOTSPEECH_TOOLS} + + ########################################################################### + ## Where the festival tree will be installed. diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb new file mode 100644 index 00000000000..a96588cee8a --- /dev/null +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'MBROLA' +version = '3.3' +local_commit_voices = 'fe05a0c' +local_version_voices = '20200330' +versionsuffix = '-voices-%s' % local_version_voices + +homepage = ['https://github.com/numediart/MBROLA%s' % x for x in ['', '-voices']] + +description = """ +MBROLA is a speech synthesizer based on the concatenation of diphones. +It takes a list of phonemes as input, together with prosodic information +(duration of phonemes and a piecewise linear description of pitch), +and produces speech samples on 16 bits (linear), +at the sampling frequency of the diphone database. + +MBROLA voices project provides list of MBROLA speech synthesizer voices. +It is intended to provide easier collaboration and +automatic updates for individual users and packagers. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/numediart/MBROLA%s/archive' % x for x in ['', '-voices']] +sources = [{ + 'download_filename': '%s.tar.gz' % version, + 'filename': SOURCE_TAR_GZ + }, { + 'download_filename': '%s.tar.gz' % local_commit_voices, + 'filename': '%%(name)s-voices-%s.tar.gz' % local_version_voices, +}] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + 'c01ded2c0a05667e6df2439c1c02b011a5df2bfdf49e24a524630686aea2b558', # MBROLA-3.3.tar.gz + '0dee14739f82fa247204791248b2d98a87e3f86f8cbb3a5844950103a41d33ba', # MBROLA-voices-20200330.tar.gz + '3a87cab3ca4cb72ea661d7351cf74f8c1641e4cfa756d2e686699402ca1f6c7d', # MBROLA-3.3_makefile.patch +] + +builddependencies = [('binutils', '2.34')] + +files_to_copy = [ + (['Bin/mbrola'], 'bin'), + (['../MBROLA-voices*/data/*'], 'share/mbrola'), +] + +sanity_check_paths = { + 'files': ['bin/mbrola'], + 'dirs': ['share/mbrola'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch new file mode 100644 index 00000000000..13d7ada2382 --- /dev/null +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch @@ -0,0 +1,40 @@ +# Use EasyBuilds CC and CFLAGS +# SEP 4th 2020 by B. Hajgato (UGent) +--- Makefile.org 2019-12-17 17:05:14.000000000 +0100 ++++ Makefile 2020-09-04 11:06:23.399740263 +0200 +@@ -4,7 +4,8 @@ + VERSION=3.3 + + # To test strict C ANSI compliance +-CC = gcc -ansi -pedantic ++CC ?= gcc -ansi -pedantic ++CCFLAGS += ${CFLAGS} -ansi -pedantic + LIB= -lm + + # This allow you to write commands like "make PURE=purify demo1" +@@ -26,14 +27,14 @@ + + # If endianess of your machine is not automatically detected in Misc/common.h + # you should manually specify here +-CFLAGS += -DLITTLE_ENDIAN ++# CFLAGS += -DLITTLE_ENDIAN + #CFLAGS += -DBIG_ENDIAN + + ####################### + # GENERAL FLAGS FOR GCC + + # Optimized code +-CFLAGS += -O6 ++#CFLAGS += -O6 + + # Debug mode with gdb + #CFLAGS += -g +@@ -48,7 +49,7 @@ + CFLAGS += -IParser -IStandalone -IMisc -ILibOneChannel -ILibMultiChannel -IEngine -IDatabase + + # Flags for GCC +-CFLAGS += -Wall ++#CFLAGS += -Wall + # CFLAGS += -fhandle-exceptions + + # Flags for OS/2 diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..9149ce107ea --- /dev/null +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'phonemizer' +version = '2.2.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/bootphon/phonemizer" +description = """ +The phonemizer allows simple phonemization of words and texts in many languages. +Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. +It is using four backends: espeak, espeak-mbrola, festival and segments. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('eSpeak-NG', '1.50'), + ('festival', '2.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('regex', '2020.7.14'), + ('csvw', '1.8.0'), + ('uritemplate', '3.0.1'), + ('isodate', '0.6.0'), + ('rfc3986', '1.4.0'), + ('colorlog', '4.2.1'), + ('clldutils', '3.5.2'), + ('segments', '2.1.3'), + (name, version), +] + +sanity_check_commands = [ + 'phonemize --version', + 'echo "hello world" | phonemize' +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb b/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb new file mode 100644 index 00000000000..0006836d5da --- /dev/null +++ b/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'sonic' +local_commit = '134074f' +version = '20180202' + +homepage = 'https://github.com/espeak-ng/sonic' +description = """ +Sonic is a simple algorithm for speeding up or slowing down speech. However, +it's optimized for speed ups of over 2X, unlike previous algorithms for changing +speech rate. The Sonic library is a very simple ANSI C library that is designed +to easily be integrated into streaming voice applications, like TTS back ends. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/espeak-ng/sonic/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['%(name)s-%(version)s.patch'] +checksums = [ + 'ace1ef03ab095cb73066e57b2467faddef0356579099ba64e917bf9dab072709', # sonic-20180202.tar.gz + '1e767c98286e13231d01ec7ae2ec2ea9b9c0ce074d4f8034b9d92ee2854d1be9', # sonic-20180202.patch +] + +dependencies = [('FFTW', '3.3.8')] + +keepsymlinks = True + +files_to_copy = [ + (['sonic'], 'bin'), + (['sonic.h'], 'include'), + (['libsonic*'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/sonic', 'include/sonic.h'] + + ['lib/libsonic.%s' % x for x in ['a'] + [ SHLIB_EXT + '%s' % y for y in ['', '.0', '.0.3.0']]], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sonic/sonic-20180202.patch b/easybuild/easyconfigs/s/sonic/sonic-20180202.patch new file mode 100644 index 00000000000..c506d6aab3f --- /dev/null +++ b/easybuild/easyconfigs/s/sonic/sonic-20180202.patch @@ -0,0 +1,20 @@ +# Make use of EasyBuild environmental variables +# SEP 1st 2020 by B. Hajgato (UGent) +--- Makefile.org 2018-02-02 02:41:30.000000000 +0100 ++++ Makefile 2020-09-01 13:12:05.438782738 +0200 +@@ -13,11 +13,11 @@ + SONAME=install_name + endif + #CFLAGS=-Wall -Wno-unused-function -g -ansi -fPIC -pthread +-CFLAGS=-Wall -Wno-unused-function -O3 -ansi -fPIC -pthread ++CFLAGS?=-Wall -Wno-unused-function -O3 -ansi -fPIC -pthread + LIB_TAG=0.3.0 +-CC=gcc +-PREFIX=/usr +-LIBDIR=$(PREFIX)/lib ++CC?=gcc ++#PREFIX=/usr ++#LIBDIR=$(PREFIX)/lib + SRC=sonic.c + FFTLIB= + ifeq ($(USE_SPECTROGRAM), 1) diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..090cf5653a6 --- /dev/null +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'speech_tools' +version = '2.5.0' + +homepage = ['http://festvox.org/festival/'] + +description = """ +The Edinburgh Speech Tools Library is a collection of C++ class, +functions and related programs for manipulating the sorts of objects +used in speech processing. It includes support for reading and writing +waveforms, parameter files (LPC, Ceptra, F0) in various formats +and converting between them. +It also includes support for linguistic type objects and support +for various label files and ngrams (with smoothing). +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://festvox.org/packed/festival/%(version_major_minor)s'] +sources = ['%(name)s-%(version)s-release.tar.gz'] +patches = ['%(name)s-%(version)s_easybuild.patch'] +checksums = [ + 'e4fd97ed78f14464358d09f36dfe91bc1721b7c0fa6503e04364fb5847805dcc', # speech_tools-2.5.0-release.tar.gz + '192012d97a671b151f084e0423042e03446a6031a8d7718354f2a56022210921', # speech_tools-2.5.0_easybuild.patch +] + +unpack_options = '--strip-components=1' + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('ncurses', '6.2'), + ('Perl', '5.30.2'), +] + +# LIBS environmental variable interfers with libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) +prebuildopts = 'unset LIBS &&' + +# If g++ used for compiling c++ files, then some extra link-time libraries detrmined wrongly +# and the binary creation fails +buildopts = 'CXX="${CC}"' + +buildininstalldir = True + +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['align', 'bcat', 'ch_lab', 'ch_track', 'ch_utt', 'ch_wave', 'design_filter', + 'est_program', 'Makefile', 'na_play', 'na_record', 'ngram_build', 'ols', 'pda', + 'pitchmark', 'pm', 'raw_to_xgraph', 'resynth', 'scfg_make', 'scfg_parse', + 'scfg_train', 'sig2fv', 'sigfilter', 'siod', 'spectgen', 'tex_to_images', + 'tilt_analysis', 'tilt_synthesis', 'viterbi', 'wagon', 'wfst_build', 'wfst_run', + 'wfst_train', 'xml_parser']] + + ['lib/lib%s.a' % x for x in ['estbase', 'estools', 'eststring']], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_easybuild.patch b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_easybuild.patch new file mode 100644 index 00000000000..f0c146340b3 --- /dev/null +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_easybuild.patch @@ -0,0 +1,39 @@ +# Make sure that we use EasyBuild compiler flags +# SEP 4th 2020 by B. Hajgato (UGent) +--- config/compilers/gcc_defaults.mak.orig 2017-09-04 17:54:03.000000000 +0200 ++++ config/compilers/gcc_defaults.mak 2020-09-04 14:51:15.343251060 +0200 +@@ -38,8 +38,8 @@ + ## ## + ########################################################################### + +-CC=gcc +-CXX=gcc ++CC?=gcc ++CXX?=gcc + ifeq ($(OSTYPE),Darwin) + CXX=g++ + endif +@@ -47,8 +47,8 @@ + COMPILER_DESC=FSF gcc + COMPILER_VERSION_COMMAND=$(CXX) -v 2>&1 | tail -1 | sed -e 's/^....//' + +-CFLAGS = $(GCC_SYSTEM_OPTIONS) $(CC_OTHER_FLAGS) +-CXXFLAGS = $(GCC_SYSTEM_OPTIONS) -fno-implicit-templates $(CC_OTHER_FLAGS) $(OMP_OPTS) $(OMP_DEFS) ++CFLAGS = $(GCC_SYSTEM_OPTIONS) $(CC_OTHER_FLAGS) ${EBVARCFLAGS} ++CXXFLAGS = $(GCC_SYSTEM_OPTIONS) -fno-implicit-templates $(CC_OTHER_FLAGS) $(OMP_OPTS) $(OMP_DEFS) ${EBVARCXXFAGS} + + DEBUG_CCFLAGS = -g + DEBUG_CXXFLAGS = -g +@@ -62,9 +62,9 @@ + VERBOSE_CXXFLAGS = + VERBOSE_LINKFLAGS = + +-OPTIMISE_CCFLAGS = -O$(OPTIMISE) +-OPTIMISE_CXXFLAGS = -O$(OPTIMISE) +-OPTIMISE_LINKFLAGS = -O$(OPTIMISE) ++OPTIMISE_CCFLAGS = ++OPTIMISE_CXXFLAGS = ++OPTIMISE_LINKFLAGS = + + PROFILE_DEFAULT = gprof + From 5630ae3c1812766eaaed93b1d34081254d1b4ce9 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Sep 2020 19:40:06 +0200 Subject: [PATCH 124/698] add checksum --- ...onemizer-2.2.1-gompi-2020a-Python-3.8.2.eb | 36 ++++++++++++++----- 1 file changed, 27 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb index 9149ce107ea..efdd61fa5bf 100644 --- a/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-2.2.1-gompi-2020a-Python-3.8.2.eb @@ -25,15 +25,33 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ - ('regex', '2020.7.14'), - ('csvw', '1.8.0'), - ('uritemplate', '3.0.1'), - ('isodate', '0.6.0'), - ('rfc3986', '1.4.0'), - ('colorlog', '4.2.1'), - ('clldutils', '3.5.2'), - ('segments', '2.1.3'), - (name, version), + ('regex', '2020.7.14', { + 'checksums': ['3a3af27a8d23143c49a3420efe5b3f8cf1a48c6fc8bc6856b03f638abc1833bb'], + }), + ('csvw', '1.8.0', { + 'checksums': ['1cfc8d05b6db59a0f4004c8f9c96aefbbc4888f702404ee93d12e63b874c7c47'], + }), + ('uritemplate', '3.0.1', { + 'checksums': ['5af8ad10cec94f215e3f48112de2022e1d5a37ed427fbd88652fa908f2ab7cae'], + }), + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rfc3986', '1.4.0', { + 'checksums': ['112398da31a3344dc25dbf477d8df6cb34f9278a94fee2625d89e4514be8bb9d'], + }), + ('colorlog', '4.2.1', { + 'checksums': ['75e55822c3a3387d721579241e776de2cf089c9ef9528b1f09e8b04d403ad118'], + }), + ('clldutils', '3.5.2', { + 'checksums': ['4ceb6c50eafce44a83901df0de6ed5ec9de9c6c7c8514338f0f1db78f55b7ddd'], + }), + ('segments', '2.1.3', { + 'checksums': ['fb24845f8826444054dfb1605e6aa8a300fd6114420d6106faeec1a8823085af'], + }), + (name, version, { + 'checksums': ['4bf1b7a70967b69f8bb82e83b4307c8b9328ab0a8cee8e1a0606f70f8223f688'], + }), ] sanity_check_commands = [ From 1f812a62ff07bdc38dfcbc2690b21eea634a8628 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Sep 2020 20:53:06 +0200 Subject: [PATCH 125/698] style fix --- .../easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb | 5 ++++- .../easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb | 3 ++- .../m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb | 4 ++-- easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb | 2 +- .../s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb | 2 +- 5 files changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb index 58543a3d471..3f0ac409613 100644 --- a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb @@ -5,7 +5,10 @@ version = '1.50' homepage = 'https://github.com/espeak-ng/espeak-ng' description = """ -The eSpeak NG is a compact open source software text-to-speech synthesizer for Linux, Windows, Android and other operating systems. It supports more than 100 languages and accents. It is based on the eSpeak engine created by Jonathan Duddington. +The eSpeak NG is a compact open source software text-to-speech synthesizer +for Linux, Windows, Android and other operating systems. +It supports more than 100 languages and accents. +It is based on the eSpeak engine created by Jonathan Duddington. """ toolchain = {'name': 'gompi', 'version': '2020a'} diff --git a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb index 2525da9b956..4c93a96ff12 100644 --- a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb @@ -110,7 +110,8 @@ dependencies = [ ('speech_tools', '2.5.0'), ] -# LIBS environmental variable interfers $EBROOTSPEECH_TOOLS/libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) +# LIBS environmental variable interfers $EBROOTSPEECH_TOOLS/libs/Makefile +# line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) prebuildopts = 'unset LIBS &&' buildininstalldir = True diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb index a96588cee8a..fe79770a1b7 100644 --- a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb @@ -26,7 +26,7 @@ source_urls = ['https://github.com/numediart/MBROLA%s/archive' % x for x in ['', sources = [{ 'download_filename': '%s.tar.gz' % version, 'filename': SOURCE_TAR_GZ - }, { +}, { 'download_filename': '%s.tar.gz' % local_commit_voices, 'filename': '%%(name)s-voices-%s.tar.gz' % local_version_voices, }] @@ -45,7 +45,7 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': ['bin/mbrola'], + 'files': ['bin/mbrola'], 'dirs': ['share/mbrola'] } diff --git a/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb b/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb index 0006836d5da..1cbaef14976 100644 --- a/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb +++ b/easybuild/easyconfigs/s/sonic/sonic-20180202-gompi-2020a.eb @@ -38,7 +38,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/sonic', 'include/sonic.h'] + - ['lib/libsonic.%s' % x for x in ['a'] + [ SHLIB_EXT + '%s' % y for y in ['', '.0', '.0.3.0']]], + ['lib/libsonic.%s' % x for x in ['a'] + [SHLIB_EXT + '%s' % y for y in ['', '.0', '.0.3.0']]], 'dirs': [] } diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb index 090cf5653a6..b0dd36dd5f0 100644 --- a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb @@ -41,7 +41,7 @@ prebuildopts = 'unset LIBS &&' # and the binary creation fails buildopts = 'CXX="${CC}"' -buildininstalldir = True +buildininstalldir = True maxparallel = 1 From 3f3f2da22efe8158732fe5d1604b6f4ff8ff9dc4 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 8 Sep 2020 21:34:17 +0200 Subject: [PATCH 126/698] fix mbrola patch --- .../m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb | 2 +- easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb index fe79770a1b7..0b4d4106cdc 100644 --- a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb @@ -34,7 +34,7 @@ patches = ['%(name)s-%(version)s_makefile.patch'] checksums = [ 'c01ded2c0a05667e6df2439c1c02b011a5df2bfdf49e24a524630686aea2b558', # MBROLA-3.3.tar.gz '0dee14739f82fa247204791248b2d98a87e3f86f8cbb3a5844950103a41d33ba', # MBROLA-voices-20200330.tar.gz - '3a87cab3ca4cb72ea661d7351cf74f8c1641e4cfa756d2e686699402ca1f6c7d', # MBROLA-3.3_makefile.patch + '3f06bffdf900c51b531f473a760c50842ccf92a9d0598bd17fd556d049593a9e', # MBROLA-3.3_makefile.patch ] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch index 13d7ada2382..da04ee381f3 100644 --- a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3_makefile.patch @@ -8,7 +8,7 @@ # To test strict C ANSI compliance -CC = gcc -ansi -pedantic +CC ?= gcc -ansi -pedantic -+CCFLAGS += ${CFLAGS} -ansi -pedantic ++CFLAGS = ${EBVARCFLAGS} -ansi -pedantic LIB= -lm # This allow you to write commands like "make PURE=purify demo1" From ccbc9b228b18dcd8f82ae886082d7bb5661059f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 11:05:00 +0200 Subject: [PATCH 127/698] adding easyconfigs: GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb, HMMER-3.3.1-iimpi-2020a.eb, FastANI-1.31-iccifort-2020.1.217.eb, DendroPy-4.4.0-GCCcore-9.3.0.eb, prodigal-2.6.3-GCCcore-9.3.0.eb --- .../DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb | 40 ++++++++++++ .../FastANI-1.31-iccifort-2020.1.217.eb | 43 +++++++++++++ .../GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb | 44 +++++++++++++ .../h/HMMER/HMMER-3.3.1-iimpi-2020a.eb | 62 +++++++++++++++++++ .../prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb | 44 +++++++++++++ 5 files changed, 233 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b47fb0db506 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb @@ -0,0 +1,40 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.4.0' + +homepage = 'https://pypi.python.org/pypi/DendroPy/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f0a0e2ce78b3ed213d6c1791332d57778b7f63d602430c1548a5d822acf2799c'] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +builddependencies = [('binutils', '2.34')] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..a687114fdd0 --- /dev/null +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb @@ -0,0 +1,43 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'ConfigureMake' + +name = 'FastANI' +version = '1.31' + +homepage = "https://github.com/ParBLiSS/FastANI" +description = """FastANI is developed for fast alignment-free computation of + whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean + nucleotide identity of orthologous gene pairs shared between two microbial + genomes. FastANI supports pairwise comparison of both complete and draft + genome assemblies.""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +source_urls = ['https://github.com/ParBLiSS/FastANI/archive'] +sources = ['v%(version)s.zip'] +patches = ['FastANI-1.2-memcpy.patch'] +checksums = [ + '05104b153f30259eb465d46621056cd670a637e0bf911ff3bf5aa032dcbc1e8b', # v1.31.zip + 'eebcf0b64c31ee360ca79136f644157064ac69747ed13cff70f5c9932c6bb0d5', # FastANI-1.2-memcpy.patch +] + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('GSL', '2.6'), + ('zlib', '1.2.11'), +] + +preconfigopts = 'autoconf && ' + +sanity_check_paths = { + 'files': ['bin/fastANI'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..54dc20a75fc --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-1.3.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,44 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'GTDB-Tk' +version = '1.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://pypi.python.org/packages/source/g/gtdbtk'] +sources = ['gtdbtk-%(version)s.tar.gz'] +checksums = ['50f83378ae4d1116f9f98fc75088a851f39904772b91f41dab782c2d97dba00f'] + +dependencies = [ + ('Python', '3.8.2'), + ('DendroPy', '4.4.0'), + ('matplotlib', '3.2.1', versionsuffix), + ('prodigal', '2.6.3'), + ('HMMER', '3.3.1'), + ('pplacer', '1.1.alpha19', '', True), + ('FastANI', '1.31'), + ('FastTree', '2.1.11'), + ('tqdm', '4.47.0'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'gtdbtk'} + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb new file mode 100644 index 00000000000..d4210f0b1e1 --- /dev/null +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb @@ -0,0 +1,62 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Nils Christian , +# Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a +# component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'HMMER' +version = '3.3.1' + +homepage = 'http://hmmer.org/' +description = """HMMER is used for searching sequence databases for homologs + of protein sequences, and for making protein sequence alignments. It + implements methods using probabilistic models called profile hidden Markov + models (profile HMMs). Compared to BLAST, FASTA, and other sequence + alignment and database search tools based on older scoring methodology, + HMMER aims to be significantly more accurate and more able to detect remote + homologs because of the strength of its underlying mathematical models. In the + past, this strength came at significant computational expense, but in the new + HMMER3 project, HMMER is now essentially as fast as BLAST.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = [ + 'http://eddylab.org/software/hmmer/', + 'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/', +] +sources = ['hmmer-%(version)s.tar.gz'] +checksums = ['8ce66a6930869534ad84bc7c9a5a566fd57188d6726c74c12fcd39c3c9c99bd5'] + +configopts = '--enable-mpi' + +runtest = 'check' + +installopts = ' && cd easel && make install' + +local_bin_files = ['alimask', 'esl-alirev', 'esl-reformat', 'esl-translate', + 'hmmlogo', 'jackhmmer', 'esl-afetch', 'esl-alistat', + 'esl-selectn', 'esl-weight', 'hmmpgmd', 'makehmmerdb', + 'esl-alimanip', 'esl-compalign', 'esl-seqrange', 'hmmalign', + 'hmmpress', 'nhmmer', 'esl-alimap', 'esl-compstruct', + 'esl-seqstat', 'hmmbuild', 'hmmscan', 'nhmmscan', 'esl-alimask', + 'esl-construct', 'esl-sfetch', 'hmmconvert', 'hmmsearch', + 'phmmer', 'esl-alimerge', 'esl-histplot', 'esl-shuffle', + 'hmmemit', 'hmmsim', 'esl-alipid', 'esl-mask', 'esl-ssdraw', + 'hmmfetch', 'hmmstat'] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in local_bin_files], + 'dirs': ['bin', 'share'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..00e68db0785 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.34')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +moduleclass = 'bio' From 5df4973bcd11674af529c4e05ec2b9dbedf4c31f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 13:50:46 +0200 Subject: [PATCH 128/698] enhance sanity check for recent DendroPy, FastANI, HMMER, prodigal easyconfigs --- .../DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb | 4 ++++ .../FastANI-1.31-iccifort-2020.1.217.eb | 2 ++ .../h/HMMER/HMMER-3.3.1-iimpi-2020a.eb | 24 +++++++++++-------- .../prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb | 2 ++ 4 files changed, 22 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb index b47fb0db506..08ba82d0a53 100644 --- a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.4.0-GCCcore-9.3.0.eb @@ -30,11 +30,15 @@ builddependencies = [('binutils', '2.34')] download_dep_fail = True use_pip = True +fix_python_shebang_for = ['bin/*.py'] + sanity_check_paths = { 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ["sumtrees.py --help"] + sanity_pip_check = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb b/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb index a687114fdd0..8eaac990bbf 100644 --- a/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/f/FastANI/FastANI-1.31-iccifort-2020.1.217.eb @@ -40,4 +40,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["fastANI --help"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb index d4210f0b1e1..eaf2531a9b6 100644 --- a/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb +++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.3.1-iimpi-2020a.eb @@ -43,20 +43,24 @@ runtest = 'check' installopts = ' && cd easel && make install' -local_bin_files = ['alimask', 'esl-alirev', 'esl-reformat', 'esl-translate', - 'hmmlogo', 'jackhmmer', 'esl-afetch', 'esl-alistat', - 'esl-selectn', 'esl-weight', 'hmmpgmd', 'makehmmerdb', - 'esl-alimanip', 'esl-compalign', 'esl-seqrange', 'hmmalign', - 'hmmpress', 'nhmmer', 'esl-alimap', 'esl-compstruct', - 'esl-seqstat', 'hmmbuild', 'hmmscan', 'nhmmscan', 'esl-alimask', - 'esl-construct', 'esl-sfetch', 'hmmconvert', 'hmmsearch', - 'phmmer', 'esl-alimerge', 'esl-histplot', 'esl-shuffle', - 'hmmemit', 'hmmsim', 'esl-alipid', 'esl-mask', 'esl-ssdraw', - 'hmmfetch', 'hmmstat'] +local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask', + 'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign', + 'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat', + 'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle', + 'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild', + 'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress', + 'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb', + 'nhmmer', 'nhmmscan', 'phmmer'] sanity_check_paths = { 'files': ["bin/%s" % x for x in local_bin_files], 'dirs': ['bin', 'share'], } +sanity_check_commands = [ + "esl-construct -h", + "hmmsearch -h", + "nhmmer -h", +] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb index 00e68db0785..8b65726786a 100644 --- a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-9.3.0.eb @@ -41,4 +41,6 @@ sanity_check_paths = { 'dirs': ['include', 'license'], } +sanity_check_commands = ["prodigal -h"] + moduleclass = 'bio' From 29277f85415fcf9ade958e7d0fd642993f769557 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 14:10:50 +0200 Subject: [PATCH 129/698] adding easyconfigs: QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb --- .../QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..15ea9746de0 --- /dev/null +++ b/easybuild/easyconfigs/q/QuickFF/QuickFF-2.2.4-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'QuickFF' +version = '2.2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/QuickFF/' +description = """QuickFF is a Python package developed at the Center for +Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio +calculations.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/QuickFF/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9c916eab890eec865985bc3e11249b0b5fee28a049206b9755081adeaf13ff60'] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('molmod', '1.4.5', versionsuffix), + ('yaff', '1.6.0', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From ca1a27591f9b206f59a90d997e19a87eae6705fc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 15:30:16 +0200 Subject: [PATCH 130/698] adding easyconfigs: TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb and patches: TAMkin-1.2.6_fix-python38.patch --- .../TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb | 42 ++ .../t/TAMkin/TAMkin-1.2.6_fix-python38.patch | 392 ++++++++++++++++++ 2 files changed, 434 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-python38.patch diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1180c29afb4 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd', # TAMkin-1.2.6.tar.gz + '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b', # TAMkin-1.2.6_fix-python38.patch +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-python38.patch b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-python38.patch new file mode 100644 index 00000000000..b64ab380480 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-python38.patch @@ -0,0 +1,392 @@ +fix compatiblity with Python 3.8 +see https://github.com/molmod/tamkin/pull/31 + +From cda6a121392c4d3d58aed6cff1754c7574835e4c Mon Sep 17 00:00:00 2001 +From: Toon Verstraelen +Date: Tue, 16 Jun 2020 10:29:23 +0200 +Subject: [PATCH] Drop timer module + +--- + tamkin/__init__.py | 1 - + tamkin/examples/010_adk/analyse-adk.py | 81 ++++----------------- + tamkin/test/test_timer.py | 62 ---------------- + tamkin/timer.py | 98 -------------------------- + 4 files changed, 12 insertions(+), 230 deletions(-) + delete mode 100644 tamkin/test/test_timer.py + delete mode 100644 tamkin/timer.py + +diff --git a/tamkin/__init__.py b/tamkin/__init__.py +index dcdc533..5110aa5 100644 +--- a/tamkin/__init__.py ++++ b/tamkin/__init__.py +@@ -44,6 +44,5 @@ + from tamkin.nmatools import * + from tamkin.partf import * + from tamkin.rotor import * +-from tamkin.timer import * + from tamkin.pftools import * + from tamkin.tunneling import * +diff --git a/tamkin/examples/010_adk/analyse-adk.py b/tamkin/examples/010_adk/analyse-adk.py +index aaf6f53..61d20df 100644 +--- a/tamkin/examples/010_adk/analyse-adk.py ++++ b/tamkin/examples/010_adk/analyse-adk.py +@@ -37,121 +37,68 @@ + from tamkin import * + + +-def do_NMA(filecor, filehess, filechk, jobtimer): ++def do_NMA(filecor, filehess, filechk): + # Load the data. +- jobtimer.sample("start loading") +- jobtimer.dump() + molecule = load_molecule_charmm(filecor,filehess) + + # Perform the normal mode analysis +- jobtimer.sample("nma") +- jobtimer.dump() + nma = NMA(molecule) + + # Write to file +- jobtimer.sample("start writing") +- jobtimer.dump() + nma.write_to_file(filechk) + +- jobtimer.sample("done") +- jobtimer.dump() + +- +-def do_MBH(filecor, filehess, filefixed, filechk, jobtimer): ++def do_MBH(filecor, filehess, filefixed, filechk): + # Load the data. +- jobtimer.sample("start loading") +- jobtimer.dump() + molecule = load_molecule_charmm(filecor,filehess) +- jobtimer.sample("start loading fixed") + fixed = load_blocks_txt(filefixed) + + # Perform the normal mode analysis +- jobtimer.sample("mbh") +- jobtimer.dump() + nma = NMA(molecule, MBH(fixed)) + + # Write to file +- jobtimer.sample("start writing") +- jobtimer.dump() + nma.write_to_file(filechk) + +- jobtimer.sample("done") +- jobtimer.dump() + +-def do_VSA(filecor, filehess, filefixed, filechk, jobtimer): ++def do_VSA(filecor, filehess, filefixed, filechk): + # Load the data. +- jobtimer.sample("start loading") +- jobtimer.dump() + molecule = load_molecule_charmm(filecor,filehess) +- jobtimer.sample("start loading fixed") + subs = load_subs_txt(filefixed) + + # Perform the normal mode analysis +- jobtimer.sample("vsa") +- jobtimer.dump() + nma = NMA(molecule, VSA(subs)) + + # Write to file +- jobtimer.sample("start writing") +- jobtimer.dump() + nma.write_to_file(filechk) + +- jobtimer.sample("done") +- jobtimer.dump() + +-def take_cut(filechk,jobtimer): ++def take_cut(filechk): + # Read the NMA object +- jobtimer.sample("start reading") +- jobtimer.dump() + nma = NMA.read_from_file(filechk) + +- jobtimer.sample("done") +- jobtimer.dump() +- + +-def do_gibbs(filechk, filethermo, jobtimer): +- jobtimer.sample("start reading") +- jobtimer.dump() ++def do_gibbs(filechk, filethermo): + nma = NMA.read_from_file(filechk) + +- jobtimer.sample("gibbs") +- jobtimer.dump() + pf = PartFun(nma, [Vibrations(), ExtTrans(), ExtRot(1)] ) + +- jobtimer.sample("thermo analysis") +- jobtimer.dump() + ta = ThermoAnalysis(pf, [300.0]) + ta.write_to_file(filethermo) + +- jobtimer.sample("done") +- jobtimer.dump() + +- +-def overlap(filecor1, filecor2, filechk, fileoverlap, jobtimer): ++def overlap(filecor1, filecor2, filechk, fileoverlap): + + # Get delta vector +- jobtimer.sample("delta") +- jobtimer.dump() + delta = get_delta_vector_charmmcor(filecor1, filecor2, normalize=True) + + # Read the NMA object +- jobtimer.sample("start reading") +- jobtimer.dump() + nma = NMA.read_from_file(filechk) + + # Calculate overlap +- jobtimer.sample("start overlap") +- jobtimer.dump() + calculate_overlap(nma.modes,nma.freqs, delta,[0.0],filename=fileoverlap) + +- jobtimer.sample("done") +- jobtimer.dump() +- +- + + def get_delta(filecor1,filecor2,filedelta): +- jobtimer.sample("start delta") +- jobtimer.dump() + get_delta_vector_charmmcor(filecor1, filecor2, normalize=True) + + +@@ -225,38 +172,34 @@ def get_delta(filecor1,filecor2,filedelta): + + options, args = parser.parse_args() + +- jobtimer = Timer() +- jobtimer.sample("start") +- +- + + if options.job == "nma": + if None in [options.filecor, options.filehess, options.filechk]: + print("at least one of the variables filecor, filehess or filechk is empty") + print("Doing nothing...") + else: +- do_NMA(options.filecor, options.filehess, options.filechk, jobtimer) ++ do_NMA(options.filecor, options.filehess, options.filechk) + + if options.job == "mbh": + if None in [options.filecor, options.filehess, options.filefixed, options.filechk]: + print("at least one of the variables filecor, filehess, filefixed or filechk is empty") + print("Doing nothing...") + else: +- do_MBH(options.filecor, options.filehess, options.filefixed, options.filechk, jobtimer) ++ do_MBH(options.filecor, options.filehess, options.filefixed, options.filechk) + + if options.job == "vsa": + if None in [options.filecor, options.filehess, options.filefixed, options.filechk]: + print("at least one of the variables filecor, filehess, filefixed or filechk is empty") + print("Doing nothing...") + else: +- do_VSA(options.filecor, options.filehess, options.filefixed, options.filechk, jobtimer) ++ do_VSA(options.filecor, options.filehess, options.filefixed, options.filechk) + + elif options.job == "cut": + if options.filechk is None: + print("variable filechk is empty") + print("Doing nothing...") + else: +- take_cut(options.filechk, jobtimer) ++ take_cut(options.filechk) + + elif options.job == "delta": + if None in [options.filecor, options.filecor2, options.filedelta]: +@@ -272,14 +215,14 @@ def get_delta(filecor1,filecor2,filedelta): + print("Doing nothing...") + else: + overlap(options.filecor, options.filecor2, +- options.filechk, options.fileoverlap, jobtimer) ++ options.filechk, options.fileoverlap) + + elif options.job == "gibbs": + if None in [options.filechk, options.filethermo]: + print("at least one of the variables filechk or filethermo is empty") + print("Doing nothing...") + else: +- do_gibbs(options.filechk, options.filethermo, jobtimer) ++ do_gibbs(options.filechk, options.filethermo) + + elif options.job is None: + print("no job specified") +diff --git a/tamkin/test/test_timer.py b/tamkin/test/test_timer.py +deleted file mode 100644 +index c0f2ad2..0000000 +--- a/tamkin/test/test_timer.py ++++ /dev/null +@@ -1,62 +0,0 @@ +-# -*- coding: utf-8 -*- +-# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry +-# and reaction kinetics. +-# Copyright (C) 2008-2012 Toon Verstraelen , An Ghysels +-# and Matthias Vandichel +-# Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all +-# rights reserved unless otherwise stated. +-# +-# This file is part of TAMkin. +-# +-# TAMkin is free software; you can redistribute it and/or +-# modify it under the terms of the GNU General Public License +-# as published by the Free Software Foundation; either version 3 +-# of the License, or (at your option) any later version. +-# +-# In addition to the regulations of the GNU General Public License, +-# publications and communications based in parts on this program or on +-# parts of this program are required to cite the following article: +-# +-# "TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics", +-# An Ghysels, Toon Verstraelen, Karen Hemelsoet, Michel Waroquier and Veronique +-# Van Speybroeck, Journal of Chemical Information and Modeling, 2010, 50, +-# 1736-1750W +-# http://dx.doi.org/10.1021/ci100099g +-# +-# TAMkin is distributed in the hope that it will be useful, +-# but WITHOUT ANY WARRANTY; without even the implied warranty of +-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +-# GNU General Public License for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with this program; if not, see +-# +-# -- +- +- +-from __future__ import print_function, division +- +-import os +-import unittest +- +-from molmod.test.common import tmpdir +- +-from tamkin import * +- +- +-__all__ = ["TimerTestCase"] +- +- +-class TimerTestCase(unittest.TestCase): +- def test_timer(self): +- timer = Timer() +- timer.sample("start") +- for i in range(100000): +- j = i**2 +- timer.sample("done") +- self.assertEqual(timer.labels[0], "start") +- self.assertEqual(timer.labels[1], "done") +- #timer.dump() # to write logfile to screen +- # just testing whether writing to file works +- with tmpdir(__name__, 'test_timer') as dn: +- timer.write_to_file(os.path.join(dn, "logfile-timings.txt")) +diff --git a/tamkin/timer.py b/tamkin/timer.py +deleted file mode 100644 +index 2799b63..0000000 +--- a/tamkin/timer.py ++++ /dev/null +@@ -1,98 +0,0 @@ +-# -*- coding: utf-8 -*- +-# TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry +-# and reaction kinetics. +-# Copyright (C) 2008-2012 Toon Verstraelen , An Ghysels +-# and Matthias Vandichel +-# Center for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all +-# rights reserved unless otherwise stated. +-# +-# This file is part of TAMkin. +-# +-# TAMkin is free software; you can redistribute it and/or +-# modify it under the terms of the GNU General Public License +-# as published by the Free Software Foundation; either version 3 +-# of the License, or (at your option) any later version. +-# +-# In addition to the regulations of the GNU General Public License, +-# publications and communications based in parts on this program or on +-# parts of this program are required to cite the following article: +-# +-# "TAMkin: A Versatile Package for Vibrational Analysis and Chemical Kinetics", +-# An Ghysels, Toon Verstraelen, Karen Hemelsoet, Michel Waroquier and Veronique +-# Van Speybroeck, Journal of Chemical Information and Modeling, 2010, 50, +-# 1736-1750W +-# http://dx.doi.org/10.1021/ci100099g +-# +-# TAMkin is distributed in the hope that it will be useful, +-# but WITHOUT ANY WARRANTY; without even the implied warranty of +-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +-# GNU General Public License for more details. +-# +-# You should have received a copy of the GNU General Public License +-# along with this program; if not, see +-# +-# -- +-"""Timer to keep track of wall and cpu time""" +- +-from __future__ import print_function, division +- +-import time +-import sys +- +- +-__all__ = ["Timer"] +- +- +-class Timer(object): +- """Timer object to keep track of the time spent in several parts of TAMKin. +- +- This timer works like a stopwatch. Each time the :meth:`sample` method is +- called the current cpu and wall times are recorded toghether with a label +- +- The methods :meth:`dump` and :meth:`write_to_file` can be used to +- generate a report. +- """ +- +- def __init__(self): +- self.cpu_times = [] +- self.wall_times = [] +- self.labels = [] +- +- def sample(self, label): +- """Record the current timings and associate them with the given label +- +- Argument: +- | label -- A string describing this point in the code. +- """ +- self.cpu_times.append(time.clock()) +- self.wall_times.append(time.time()) +- self.labels.append(label) +- +- def dump(self, f=sys.stdout): +- """Dump the logfile with timing information, to screen or to a file stream. +- +- Optional argument: +- | f -- the stream to write to. [default=sys.stdout] +- """ +- print("-------------------", file=f) +- print("Printing LOG jobtimer", file=f) +- print('%12s %12s %21s %16s %30s' %("cpu times [s]", "diff [s]", "wall times [s]", "diff [s]", "labels" ), file=f) +- for i,label in enumerate(self.labels[:-1]): +- print('%12.3f %12.3f %21.3f %16.3f %30s' %(self.cpu_times[i], +- self.cpu_times[i+1]-self.cpu_times[i], +- self.wall_times[i], +- self.wall_times[i+1]-self.wall_times[i], +- label), file=f) +- print('%12.3f %12s %21.3f %16s %30s' %(self.cpu_times[-1], "", +- self.wall_times[-1], "", +- self.labels[-1]), file=f) +- print("-------------------", file=f) +- +- def write_to_file(self, filename): +- """Write the logfile with timing information to filename. +- +- Argument: +- | filename -- the file to write to. +- """ +- with open(filename, 'w') as f: +- self.dump(f) From b37987c3e7d960e05bfae2b99dcad829b2a63eab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Sep 2020 15:57:55 +0200 Subject: [PATCH 131/698] use https for phonopy homepage --- .../p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb index 221af9c706f..8c8a26ebb86 100644 --- a/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.7.1-intel-2020a-Python-3.8.2.eb @@ -4,7 +4,7 @@ name = 'phonopy' version = '2.7.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://atztogo.github.io/phonopy/' +homepage = 'https://atztogo.github.io/phonopy/' description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" toolchain = {'name': 'intel', 'version': '2020a'} From 714682f34de67b928c9465e9a7fa5cb6d6f3b833 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 30 Jul 2020 10:06:44 +0200 Subject: [PATCH 132/698] adding easyconfigs: TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb and patches: TensorFlow-2.3.0-fix_protoc_build.patch --- ...rFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb | 169 ++++++++++++++++++ .../TensorFlow-2.3.0_fix-protoc-build.patch | 37 ++++ ...TensorFlow-2.3.0_fix-system-protobuf.patch | 100 +++++++++++ .../TensorFlow-2.3.0_fix-system_absl_py.patch | 55 ++++++ 4 files changed, 361 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0898ec5a460 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,169 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [ + ('Bazel', '3.4.1'), + ('protobuf', '3.10.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('cuDNN', '7.6.4.38'), + ('NCCL', '2.4.8'), + ('Python', '3.7.4'), + ('h5py', '2.10.0', versionsuffix), + ('cURL', '7.66.0'), + ('double-conversion', '3.1.4'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '64.2'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('protobuf-python', '3.10.0', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.7'), + ('SWIG', '4.0.1'), + ('zlib', '1.2.11'), + # TF 2.3 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle + ('scipy', '1.4.1', versionsuffix), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.2.2', { + 'checksums': ['1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.6', { + 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], + }), + ('cachetools', '4.1.1', { + 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], + }), + ('google-auth', '1.20.0', { + 'modulename': 'google.auth', + 'checksums': ['c6e9735a2ee829a75b546702e460489db5cc35567a27fabd70b7c459f11efd58'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.9.0', { + 'modulename': 'absl', + 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.30.0', { + 'modulename': 'grpc', + 'checksums': ['e8f2f5d16e0164c415f1b31a8d9a81f2e4645a43d1b261375d6bab7b0adf511f'], + }), + ('tensorboard-plugin-wit', '1.7.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], + }), + ('astor', '0.8.0', { + 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + }), + ('Keras-Applications', '1.0.8', { + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.3.0_fix-system_absl_py.patch', + 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.3.0_fix-system-protobuf.patch', + 'TensorFlow-2.3.0_fix-protoc-build.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + '2595a5c401521f20a2734c4e5d54120996f8391f00bb62a57267d930bce95350', # v2.3.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.3.0_fix-system_absl_py.patch + '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', + # TensorFlow-2.1.0_fix-system-jsoncpp.patch + 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.3.0_fix-system-protobuf.patch + '576a5f1de3039b6cecbc6ef67c9fcecc117b779f0d18f01e2af541f6030e9518', + # TensorFlow-2.3.0_fix-protoc-build.patch + '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch new file mode 100644 index 00000000000..d9c98c14dcb --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-protoc-build.patch @@ -0,0 +1,37 @@ +commit c8231eb55bdbff94c44e4b554321017fbd01bda9 +Author: Alexander Grund +Date: Wed Jul 29 16:57:39 2020 +0200 + + Fix environment for protobuf compilation + + Patch using upstream https://github.com/grpc/grpc/pull/23664 + +https://github.com/tensorflow/tensorflow/pull/41889 +diff --git a/tensorflow/workspace.bzl b/tensorflow/workspace.bzl +index 24446d846c..ee63c4a811 100755 +--- a/tensorflow/workspace.bzl ++++ b/tensorflow/workspace.bzl +@@ -687,6 +687,7 @@ def tf_repositories(path_prefix = "", tf_repo_name = ""): + sha256 = "b956598d8cbe168b5ee717b5dafa56563eb5201a947856a6688bbeac9cac4e1f", + strip_prefix = "grpc-b54a5b338637f92bfcf4b0bc05e0f57a5fd8fadd", + system_build_file = clean_dep("//third_party/systemlibs:grpc.BUILD"), ++ patch_file = clean_dep("//third_party/grpc:generate_cc_env_fix.patch"), + system_link_files = { + "//third_party/systemlibs:BUILD": "bazel/BUILD", + "//third_party/systemlibs:grpc.BUILD": "src/compiler/BUILD", +diff --git a/third_party/grpc/generate_cc_env_fix.patch b/third_party/grpc/generate_cc_env_fix.patch +new file mode 100644 +index 0000000000..51832fe962 +--- /dev/null ++++ b/third_party/grpc/generate_cc_env_fix.patch +@@ -0,0 +1,10 @@ ++--- a/bazel/generate_cc.bzl +++++ b/bazel/generate_cc.bzl ++@@ -141,6 +141,7 @@ def generate_cc_impl(ctx): ++ outputs = out_files, ++ executable = ctx.executable._protoc, ++ arguments = arguments, +++ use_default_shell_env = True, ++ ) ++ ++ return struct(files = depset(out_files)) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch new file mode 100644 index 00000000000..05fa8cd11b2 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch @@ -0,0 +1,100 @@ +Based on: https://github.com/tensorflow/tensorflow/pull/42591 +Modified by Alexander Grund (TU Dresden) + +From ab6c3bf9d98d7627509865e91913c25a1f8cc693 Mon Sep 17 00:00:00 2001 +From: Steven Clarkson +Date: Sat, 22 Aug 2020 16:57:25 -0700 +Subject: [PATCH] Add missing systemlib protobuf libraries + +--- + third_party/systemlibs/protobuf.BUILD | 83 +++++++++++++++++++++++++++ + 1 file changed, 83 insertions(+) + +diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD +index 118135d129005..ef3e0c93c6483 100644 +--- a/third_party/systemlibs/protobuf.BUILD ++++ b/third_party/systemlibs/protobuf.BUILD +@@ -31,6 +31,7 @@ HEADERS = [ + "google/protobuf/io/zero_copy_stream.h", + "google/protobuf/io/zero_copy_stream_impl_lite.h", + "google/protobuf/map.h", ++ "google/protobuf/port_def.inc", + "google/protobuf/repeated_field.h", + "google/protobuf/text_format.h", + "google/protobuf/timestamp.pb.h", +@@ -102,3 +99,75 @@ py_library( + srcs_version = "PY2AND3", + visibility = ["//visibility:public"], + ) ++ ++proto_library( ++ name = "any_proto", ++ srcs = ["google/protobuf/any.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "api_proto", ++ srcs = ["google/protobuf/api.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "compiler_plugin_proto", ++ srcs = ["google/protobuf/compiler/plugin.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "descriptor_proto", ++ srcs = ["google/protobuf/descriptor.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "duration_proto", ++ srcs = ["google/protobuf/duration.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "empty_proto", ++ srcs = ["google/protobuf/empty.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "field_mask_proto", ++ srcs = ["google/protobuf/field_mask.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "source_context_proto", ++ srcs = ["google/protobuf/source_context.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "struct_proto", ++ srcs = ["google/protobuf/struct.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "timestamp_proto", ++ srcs = ["google/protobuf/timestamp.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "type_proto", ++ srcs = ["google/protobuf/type.proto"], ++ visibility = ["//visibility:public"], ++) ++ ++proto_library( ++ name = "wrappers_proto", ++ srcs = ["google/protobuf/wrappers.proto"], ++ visibility = ["//visibility:public"], ++) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch new file mode 100644 index 00000000000..abe1835f0ba --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system_absl_py.patch @@ -0,0 +1,55 @@ +From fda56a4c619d093108cd2778e74073d65fb0e407 Mon Sep 17 00:00:00 2001 +From: Balint Cristian +Date: Wed, 24 Jun 2020 12:10:23 +0300 +Subject: [PATCH] [EXT-SYSLIB] Add absl_py logging submodule to build flow. + +From https://github.com/tensorflow/tensorflow/pull/40749 + +--- + tensorflow/opensource_only.files | 1 + + tensorflow/workspace.bzl | 1 + + third_party/systemlibs/absl_py.absl.logging.BUILD | 11 +++++++++++ + 3 files changed, 13 insertions(+) + create mode 100644 third_party/systemlibs/absl_py.absl.logging.BUILD + +diff --git a/tensorflow/opensource_only.files b/tensorflow/opensource_only.files +index 3d57e5f2089c5..cddf018bb21f7 100644 +--- a/tensorflow/opensource_only.files ++++ b/tensorflow/opensource_only.files +@@ -170,6 +170,7 @@ tensorflow/third_party/systemlibs/BUILD.tpl + tensorflow/third_party/systemlibs/absl_py.BUILD + tensorflow/third_party/systemlibs/absl_py.absl.flags.BUILD + tensorflow/third_party/systemlibs/absl_py.absl.testing.BUILD ++tensorflow/third_party/systemlibs/absl_py.absl.logging.BUILD + tensorflow/third_party/systemlibs/astor.BUILD + tensorflow/third_party/systemlibs/boringssl.BUILD + tensorflow/third_party/systemlibs/build_defs.bzl.tpl +diff --git a/tensorflow/workspace.bzl b/tensorflow/workspace.bzl +index f2d0c028c5fa7..d142910619c09 100755 +--- a/tensorflow/workspace.bzl ++++ b/tensorflow/workspace.bzl +@@ -535,6 +535,7 @@ def tf_repositories(path_prefix = "", tf_repo_name = ""): + "//third_party/systemlibs:absl_py.absl.BUILD": "absl/BUILD", + "//third_party/systemlibs:absl_py.absl.flags.BUILD": "absl/flags/BUILD", + "//third_party/systemlibs:absl_py.absl.testing.BUILD": "absl/testing/BUILD", ++ "//third_party/systemlibs:absl_py.absl.logging.BUILD": "absl/logging/BUILD", + }, + urls = [ + "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +diff --git a/third_party/systemlibs/absl_py.absl.logging.BUILD b/third_party/systemlibs/absl_py.absl.logging.BUILD +new file mode 100644 +index 0000000000000..71cfc7a247c8a +--- /dev/null ++++ b/third_party/systemlibs/absl_py.absl.logging.BUILD +@@ -0,0 +1,11 @@ ++licenses(["notice"]) # Apache 2.0 ++ ++package(default_visibility = ["//visibility:public"]) ++ ++filegroup( ++ name = "LICENSE", ++) ++ ++py_library( ++ name = "logging", ++) From 2239f72bbb11b67ae47c7f6af5701168ffd1623a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 9 Sep 2020 18:17:07 +0200 Subject: [PATCH 133/698] Fix system json and protobuf patches --- ...rFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb | 14 +- ...sorFlow-2.3.0_fix-json-include-style.patch | 137 ++++++++++++++++++ ...TensorFlow-2.3.0_fix-system-protobuf.patch | 28 +++- 3 files changed, 170 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb index 0898ec5a460..be14fd964c5 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb @@ -140,9 +140,9 @@ exts_list = [ (name, version, { 'patches': [ 'TensorFlow-2.1.0_fix-cuda-build.patch', - 'TensorFlow-2.3.0_fix-system_absl_py.patch', - 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.3.0_fix-json-include-style.patch', + 'TensorFlow-2.3.0_fix-system_absl_py.patch', 'TensorFlow-2.3.0_fix-system-protobuf.patch', 'TensorFlow-2.3.0_fix-protoc-build.patch', ], @@ -152,14 +152,14 @@ exts_list = [ 'checksums': [ '2595a5c401521f20a2734c4e5d54120996f8391f00bb62a57267d930bce95350', # v2.3.0.tar.gz '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch - # TensorFlow-2.3.0_fix-system_absl_py.patch - '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', - # TensorFlow-2.1.0_fix-system-jsoncpp.patch - 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', # TensorFlow-2.1.0_fix-system-nasm.patch '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.3.0_fix-json-include-style.patch + 'e04f5d9aa4c1222393b2cad4b84cd63128ef56eb5cc732d2afbc5d98dfa596a4', + # TensorFlow-2.3.0_fix-system_absl_py.patch + '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', # TensorFlow-2.3.0_fix-system-protobuf.patch - '576a5f1de3039b6cecbc6ef67c9fcecc117b779f0d18f01e2af541f6030e9518', + '35172b70be02e0b34963a7eabd108e96e9def005466d84f90737c57269c9b8bc', # TensorFlow-2.3.0_fix-protoc-build.patch '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch new file mode 100644 index 00000000000..8e2429a01fc --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-json-include-style.patch @@ -0,0 +1,137 @@ +From 20a00a0328fe1ad08ef51311b93d72d939c142e7 Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Thu, 20 Aug 2020 16:39:40 +0200 +Subject: [PATCH] Include jsonCPP headers via #include "json/json.h" + +Don't use #include "include/json/json.h" which is unusual and therefore confusing +This allows to remove the header symlinking done for the system lib version + +Closes #42303 +--- + .../core/platform/cloud/gcs_file_system.cc | 2 +- + .../platform/cloud/google_auth_provider.cc | 2 +- + tensorflow/core/platform/cloud/oauth_client.h | 2 +- + .../profiler/convert/trace_events_to_json.cc | 2 +- + .../convert/trace_events_to_json_test.cc | 2 +- + .../core/profiler/internal/tfprof_timeline.h | 2 +- + third_party/systemlibs/jsoncpp.BUILD | 27 ------------------- + 9 files changed, 8 insertions(+), 35 deletions(-) + +diff --git a/tensorflow/core/platform/cloud/gcs_file_system.cc b/tensorflow/core/platform/cloud/gcs_file_system.cc +index f0d2138b379ea..59eb610fc5377 100644 +--- a/tensorflow/core/platform/cloud/gcs_file_system.cc ++++ b/tensorflow/core/platform/cloud/gcs_file_system.cc +@@ -30,7 +30,7 @@ limitations under the License. + #include // for _mktemp + #endif + #include "absl/base/macros.h" +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/lib/gtl/map_util.h" + #include "tensorflow/core/platform/cloud/curl_http_request.h" + #include "tensorflow/core/platform/cloud/file_block_cache.h" +diff --git a/tensorflow/core/platform/cloud/google_auth_provider.cc b/tensorflow/core/platform/cloud/google_auth_provider.cc +index e8546ca022f22..57240fa2494b8 100644 +--- a/tensorflow/core/platform/cloud/google_auth_provider.cc ++++ b/tensorflow/core/platform/cloud/google_auth_provider.cc +@@ -24,7 +24,7 @@ limitations under the License. + #include + + #include "absl/strings/match.h" +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/platform/base64.h" + #include "tensorflow/core/platform/env.h" + #include "tensorflow/core/platform/errors.h" +diff --git a/tensorflow/core/platform/cloud/oauth_client.h b/tensorflow/core/platform/cloud/oauth_client.h +index ed8bf2572535e..97af3ecaf1785 100644 +--- a/tensorflow/core/platform/cloud/oauth_client.h ++++ b/tensorflow/core/platform/cloud/oauth_client.h +@@ -18,7 +18,7 @@ limitations under the License. + + #include + +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/platform/cloud/http_request.h" + #include "tensorflow/core/platform/env.h" + #include "tensorflow/core/platform/status.h" +diff --git a/tensorflow/core/profiler/convert/trace_events_to_json.cc b/tensorflow/core/profiler/convert/trace_events_to_json.cc +index ba3e4516c8cae..ad40292ceffb3 100644 +--- a/tensorflow/core/profiler/convert/trace_events_to_json.cc ++++ b/tensorflow/core/profiler/convert/trace_events_to_json.cc +@@ -21,7 +21,7 @@ limitations under the License. + + #include "absl/strings/str_cat.h" + #include "absl/strings/str_format.h" +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/platform/types.h" + #include "tensorflow/core/profiler/protobuf/trace_events.pb.h" + +diff --git a/tensorflow/core/profiler/convert/trace_events_to_json_test.cc b/tensorflow/core/profiler/convert/trace_events_to_json_test.cc +index dc985f2f76feb..bf08a19e0221e 100644 +--- a/tensorflow/core/profiler/convert/trace_events_to_json_test.cc ++++ b/tensorflow/core/profiler/convert/trace_events_to_json_test.cc +@@ -15,7 +15,7 @@ limitations under the License. + + #include "tensorflow/core/profiler/convert/trace_events_to_json.h" + +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/platform/protobuf.h" + #include "tensorflow/core/platform/test.h" + #include "tensorflow/core/profiler/protobuf/trace_events.pb.h" +diff --git a/tensorflow/core/profiler/internal/tfprof_timeline.h b/tensorflow/core/profiler/internal/tfprof_timeline.h +index 834e3c9be911e..fb9ff8012e06f 100644 +--- a/tensorflow/core/profiler/internal/tfprof_timeline.h ++++ b/tensorflow/core/profiler/internal/tfprof_timeline.h +@@ -17,7 +17,7 @@ limitations under the License. + #define TENSORFLOW_CORE_PROFILER_INTERNAL_TFPROF_TIMELINE_H_ + + #include "absl/strings/str_cat.h" +-#include "include/json/json.h" ++#include "json/json.h" + #include "tensorflow/core/framework/graph.pb.h" + #include "tensorflow/core/framework/step_stats.pb.h" + #include "tensorflow/core/profiler/internal/tfprof_node_show.h" +diff --git a/third_party/systemlibs/jsoncpp.BUILD b/third_party/systemlibs/jsoncpp.BUILD +index 7d54f9289bfc7..b5951e3a3404f 100644 +--- a/third_party/systemlibs/jsoncpp.BUILD ++++ b/third_party/systemlibs/jsoncpp.BUILD +@@ -5,35 +5,8 @@ filegroup( + visibility = ["//visibility:public"], + ) + +-HEADERS = [ +- "include/json/allocator.h", +- "include/json/assertions.h", +- "include/json/autolink.h", +- "include/json/config.h", +- "include/json/features.h", +- "include/json/forwards.h", +- "include/json/json.h", +- "include/json/reader.h", +- "include/json/value.h", +- "include/json/version.h", +- "include/json/writer.h", +-] +- +-genrule( +- name = "link_headers", +- outs = HEADERS, +- cmd = """ +- for i in $(OUTS); do +- i=$${i##*/} +- ln -sf $(INCLUDEDIR)/jsoncpp/json/$$i $(@D)/include/json/$$i +- done +- """, +-) +- + cc_library( + name = "jsoncpp", +- hdrs = HEADERS, +- includes = ["."], + linkopts = ["-ljsoncpp"], + visibility = ["//visibility:public"], + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch index 05fa8cd11b2..1f9944c4f5a 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch @@ -14,14 +14,38 @@ diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/prot index 118135d129005..ef3e0c93c6483 100644 --- a/third_party/systemlibs/protobuf.BUILD +++ b/third_party/systemlibs/protobuf.BUILD -@@ -31,6 +31,7 @@ HEADERS = [ - "google/protobuf/io/zero_copy_stream.h", +@@ -15,8 +15,13 @@ filegroup( + HEADERS = [ + "google/protobuf/any.pb.h", + "google/protobuf/any.proto", ++ "google/protobuf/api.pb.h", ++ "google/protobuf/api.proto", + "google/protobuf/arena.h", + "google/protobuf/compiler/importer.h", ++ "google/protobuf/compiler/plugin.h", ++ "google/protobuf/compiler/plugin.pb.h", ++ "google/protobuf/compiler/plugin.proto", + "google/protobuf/descriptor.h", + "google/protobuf/descriptor.pb.h", + "google/protobuf/descriptor.proto", +@@ -32,9 +37,17 @@ HEADERS = [ "google/protobuf/io/zero_copy_stream_impl_lite.h", "google/protobuf/map.h", + "google/protobuf/port_def.inc", ++ "google/protobuf/port_undef.inc", "google/protobuf/repeated_field.h", ++ "google/protobuf/source_context.pb.h", ++ "google/protobuf/source_context.proto", ++ "google/protobuf/struct.pb.h", ++ "google/protobuf/struct.proto", "google/protobuf/text_format.h", "google/protobuf/timestamp.pb.h", + "google/protobuf/timestamp.proto", ++ "google/protobuf/type.pb.h", ++ "google/protobuf/type.proto", + "google/protobuf/util/json_util.h", + "google/protobuf/util/type_resolver_util.h", + "google/protobuf/wrappers.pb.h", @@ -102,3 +99,75 @@ py_library( srcs_version = "PY2AND3", visibility = ["//visibility:public"], From 83533dc80446a5344fff0da70d70996684a9aa41 Mon Sep 17 00:00:00 2001 From: Tom Strempel <37880275+tstrempel@users.noreply.github.com> Date: Thu, 10 Sep 2020 14:03:47 +0200 Subject: [PATCH 134/698] Update IDBA-UD-1.1.3-GCC-8.3.0.eb with tests Co-authored-by: Alex Domingo --- easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb index c1860655e56..c457653f127 100644 --- a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-8.3.0.eb @@ -37,6 +37,9 @@ buildopts = ' && rm -fr bin/*.o bin/Makefile*' files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] +pretestopts = "cd test && " +runtest = "check" + sanity_check_paths = { 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", "idba_ud", "parallel_blat", "idba_tran_test"]], From 6aa125b0c380025044657481ffaf9cf853d75573 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Sep 2020 15:23:07 +0200 Subject: [PATCH 135/698] adding easyconfigs: PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb --- .../PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb | 307 ++++++++++++++++++ 1 file changed, 307 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..92bf5f42a63 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,307 @@ +name = 'PyTorch' +version = '1.6.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +local_pytorchthirdpartydir = 'pytorch-%(version)s/third_party' +local_extract_cmd_pattern = 'tar -C %s/%s --strip-components=1 -xf %%s' + +source_urls = ['https://github.com/pytorch/pytorch/archive'] + +# PyTorch pulls in a bunch of submodules that are not releases. We download the submodule revisions from their repos. +# determine commit of additional sources via https://github.com/pytorch/pytorch/tree/v1.6.0/third_party +sources = [ + 'v%(version)s.tar.gz', # PyTorch + { + 'source_urls': ['https://github.com/Maratyszcza/FP16/archive'], + 'download_filename': '4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz', + 'filename': 'FP16-20200514.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FP16'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/FXdiv/archive'], + 'download_filename': 'b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz', + 'filename': 'FXdiv-20200417.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'FXdiv'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/NNPACK/archive'], + 'download_filename': '24b55303f5cf65d75844714513a0d1b1409809bd.tar.gz', + 'filename': 'NNPACK-20191007.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'NNPACK'), + }, + { + 'source_urls': ['https://github.com/pytorch/QNNPACK/archive'], + 'download_filename': '7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz', + 'filename': 'QNNPACK-20190828.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'QNNPACK'), + }, + { + 'source_urls': ['https://github.com/google/XNNPACK/archive'], + 'download_filename': '1b354636b5942826547055252f3b359b54acff95.tar.gz', + 'filename': 'XNNPACK-20200323.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'XNNPACK'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': '505be96ab23056580a3a2315abba048f4428b04e.tar.gz', + 'filename': 'benchmark-20180606.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'benchmark'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': '63b254577ed77a8004a9be6ac707f3dccc4e1fd9.tar.gz', + 'filename': 'cpuinfo-20200611.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cpuinfo'), + }, + { + 'source_urls': ['https://github.com/NVlabs/cub/archive'], + 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', + 'filename': 'cub-20170829.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'cub'), + }, + { + 'source_urls': ['https://github.com/eigenteam/eigen-git-mirror/archive'], + 'download_filename': 'd41dc4dd74acce21fb210e7625d5d135751fa9e5.tar.gz', + 'filename': 'eigen-20190125.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'eigen'), + }, + { + 'source_urls': ['https://github.com/pytorch/fbgemm/archive'], + 'download_filename': '7d673046a6a3ad1fa0d15dfb189cd06ffa217041.tar.gz', + 'filename': 'fbgemm-20200531.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm'), + }, + { + 'source_urls': ['https://github.com/asmjit/asmjit/archive'], + 'download_filename': '9057aa30b620f0662ff51e2230c126a345063064.tar.gz', + 'filename': 'asmjit-20200429.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/asmjit'), + }, + { + 'source_urls': ['https://github.com/pytorch/cpuinfo/archive'], + 'download_filename': 'd5e37adf1406cf899d7d9ec1d317c47506ccb970.tar.gz', + 'filename': 'cpuinfo-20190201.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/cpuinfo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '0fc5466dbb9e623029b1ada539717d10bd45e99e.tar.gz', + 'filename': 'googletest-20180925.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fbgemm/third_party/googletest'), + }, + { + 'source_urls': ['https://github.com/fmtlib/fmt/archive'], + 'download_filename': '9bdd1596cef1b57b9556f8bef32dc4a32322ef3e.tar.gz', + 'filename': 'fmt-20200405.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'fmt'), + }, + { + 'source_urls': ['https://github.com/houseroad/foxi/archive'], + 'download_filename': '8015abb727dfc9e223bfd293730daa9138f1f9c4.tar.gz', + 'filename': 'foxi-20191220.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'foxi'), + }, + { + 'source_urls': ['https://github.com/google/gemmlowp/archive'], + 'download_filename': '3fb5c176c17c765a3492cd2f0321b0dab712f350.tar.gz', + 'filename': 'gemmlowp-20181126.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gemmlowp/gemmlowp'), + }, + { + 'source_urls': ['https://github.com/facebookincubator/gloo/archive'], + 'download_filename': '113bde13035594cafdca247be953610b53026553.tar.gz', + 'filename': 'gloo-20200317.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gloo'), + }, + { + 'source_urls': ['https://github.com/google/googletest/archive'], + 'download_filename': '2fe3bd994b3189899d93f1d5a881e725e046fdc2.tar.gz', + 'filename': 'googletest-20180831.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'googletest'), + }, + { + 'source_urls': ['https://github.com/intel/ideep/archive'], + 'download_filename': '938cc68897bb46b8d4b228966edd9e23e471cf3b.tar.gz', + 'filename': 'ideep-20200616.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep'), + }, + { + 'source_urls': ['https://github.com/intel/mkl-dnn/archive'], + 'download_filename': 'e2ac1fac44c5078ca927cb9b90e1b3066a0b2ed0.tar.gz', + 'filename': 'mkl-dnn-20200605.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'ideep/mkl-dnn'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx/archive'], + 'download_filename': 'a82c6a7010e2e332d8f74ad5b0c726fd47c85376.tar.gz', + 'filename': 'onnx-20200531.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx'), + }, + { + 'source_urls': ['https://github.com/google/benchmark/archive'], + 'download_filename': 'e776aa0275e293707b6a0901e0e8d8a8a3679508.tar.gz', + 'filename': 'benchmark-20180525.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx/third_party/benchmark'), + }, + { + 'source_urls': ['https://github.com/onnx/onnx-tensorrt/archive'], + 'download_filename': 'c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz', + 'filename': 'onnx-tensorrt-20190916.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx-tensorrt'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/psimd/archive'], + 'download_filename': '072586a71b55b7f8c584153d223e95687148a900.tar.gz', + 'filename': 'psimd-20200517.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'psimd'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], + 'download_filename': '029c88620802e1361ccf41d1970bd5b07fd6b7bb.tar.gz', + 'filename': 'pthreadpool-20200615.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'pthreadpool'), + }, + { + 'source_urls': ['https://github.com/Maratyszcza/PeachPy/archive'], + 'download_filename': '07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz', + 'filename': 'PeachPy-20180218.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'python-peachpy'), + }, + { + 'source_urls': ['https://github.com/shibatch/sleef/archive'], + 'download_filename': '7f523de651585fe25cade462efccca647dcc8d02.tar.gz', + 'filename': 'sleef-20190730.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'sleef'), + }, + { + 'source_urls': ['https://github.com/01org/tbb/archive'], + 'download_filename': 'a51a90bc609bb73db8ea13841b5cf7aa4344d4a9.tar.gz', + 'filename': 'tbb-20181009.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'tbb'), + }, + { + 'source_urls': ['https://github.com/pytorch/tensorpipe/archive'], + 'download_filename': '3b8089c9c6717038cff44b70b881d0ad6c93e679.tar.gz', + 'filename': 'tensorpipe-20200626.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'tensorpipe'), + }, + { + 'source_urls': ['https://github.com/libuv/libuv/archive'], + 'download_filename': '02a9e1be252b623ee032a3137c0b0c94afbe6809.tar.gz', + 'filename': 'libuv-20200419.tar.gz', + 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'tensorpipe/third_party/libuv'), + }, +] +patches = [ + '%(name)s-1.4.0_fix-system-pybind11.patch', + '%(name)s-1.6.0_fix-missing-source-dir.patch', + '%(name)s-1.6.0_fix-test-cuda.patch', + '%(name)s-1.6.0_fix-test-dataloader-fixed-affinity.patch', + '%(name)s-1.6.0_fix-test-tensorexpr.patch', + '%(name)s-1.6.0_fix-test-missing-rpc-shutdown.patch', + '%(name)s-1.6.0_fix-rpc-test-world-size.patch', + '%(name)s-1.6.0_fix-system-pybind11.patch', +] +checksums = [ + '7160e5bd291ad649d035f1c830dd064d1db42839b64b9a3502b5d47641233fb7', # v1.6.0.tar.gz + '90f20492621d5ed80b442aa682ff92d7ccf333ac8fac4a10e7e02afb159f3c13', # FP16-20200514.tar.gz + '9ccf554541666b5c089ad5dd465141d671c99971f36d72f313652f5c49ffce14', # FXdiv-20200417.tar.gz + '1f11dbbfad78d0a4c39fe94e52a28c0821cb25f9880420bb304f6302f73fe002', # NNPACK-20191007.tar.gz + '0d752bd75f46ce4d7c6f0a60b0d6c0e5918a7b4683c825284f8db3706dd24f76', # QNNPACK-20190828.tar.gz + 'b55a6ef3a0b4c0d3c39ad5578eb4fa9a7b2d7ee1ef06592b8a808a59a8e6589b', # XNNPACK-20200323.tar.gz + '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz + '18a99130ced1eaacab2ba8f75a1435f9955aab54fa0436b60468f020876ee902', # cpuinfo-20200611.tar.gz + '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz + '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190125.tar.gz + 'c2e122ea2c3a571207ef0ba9c495444bda4b83927d076ed04fbb6383ae428441', # fbgemm-20200531.tar.gz + '5c7ecb03ede09a38fa9bcf2527a0f1454cd67a34c0e6fd939ae4d93b276ce982', # asmjit-20200429.tar.gz + '3f2dc1970f397a0e59db72f9fca6ff144b216895c1d606f6c94a507c1e53a025', # cpuinfo-20190201.tar.gz + 'e99b904983d08ac8e9bddb5b0d21196b78ad9499e3c5d12192cee2ddd2b7515c', # googletest-20180925.tar.gz + '92b1ba081c55aca384d975bb2069e0ecc5f71a35f894a2047d9783ef6800b41e', # fmt-20200405.tar.gz + '982100f4a514b0678e3161e39c3660dc7be3c83bdc1e39617066dc49712d50ac', # foxi-20191220.tar.gz + 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181126.tar.gz + '5243b523dba4aa55090790c9836803c671daa58bff24411e52267e119f4a61e0', # gloo-20200317.tar.gz + 'd0d447b4feeedca837a0d46a289d4223089b32ac2f84545fa4982755cc8919be', # googletest-20180831.tar.gz + 'ab37b266702557b819a598d1bf89946cba281a8d49224ce105280eb657d0c733', # ideep-20200616.tar.gz + '4bc7dafaaaa55db55bb2654e043cc7f3fb35cd49d19c4efee2dbce1ab863c179', # mkl-dnn-20200605.tar.gz + 'c3bf8cc8091b24c43aa205a1f2037a518d249eb5997bea7f543b7fc880e80e21', # onnx-20200531.tar.gz + 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz + '314cde420a7cf692bdb6877bc6af6bc514805f6cdb8bee90f32566ed08d94b1c', # onnx-tensorrt-20190916.tar.gz + 'f6c4dab91ae9a03b3019e7cab0572743afd0e1b6e75b97fcca50259c737c924e', # psimd-20200517.tar.gz + 'd13818a10a645d557202aa005606337b2a0cdf690e5655253800ab11abb0c076', # pthreadpool-20200615.tar.gz + '13100c3deed300bbf16f87d8af3539f432462bfef9d38f0c7e3e387dc2e88676', # PeachPy-20180218.tar.gz + '8cb5fae822077ca9cbc14dcc7bba9a3a35ad519284fc5169f9a176672c63860a', # sleef-20190730.tar.gz + # checksum for original download of tbb-20181009.tar.gz from https://github.com/intel/tbb/archive + ('dc0a8d8d96cb8765782aa6ac1b509ad4db955d9bbb58fa5cc2265f0292756d72', + # checksum for download of tbb-20181009.tar.gz from https://github.com/01org/tbb/archive + 'be111cf161b587812fa3b106fe550efb6f129b8b0b702fef32fac23af9580e5e'), + '9d78a64a4456eb0caeba8742080c39e07019114c1f4914f0e1ffa8f0a507c40f', # tensorpipe-20200626.tar.gz + '5ca4e9091f3231d8ad8801862dc4e851c23af89c69141d27723157776f7291e7', # libuv-20200419.tar.gz + '1c9f36f959ea5d7cf0d4ca678ec6bf60ef9ed16c556f97197aa018c7b1e5e21d', # PyTorch-1.4.0_fix-system-pybind11.patch + 'f3725477d554800a19a8d7f4ab300ab7b70da76b62328081c0ed1f8517c6a61c', # PyTorch-1.6.0_fix-missing-source-dir.patch + 'adf21e77dbc5e60fd46fe21fceb908633b0da7d4fc9b6a3ea7f7cfb0c4a44678', # PyTorch-1.6.0_fix-test-cuda.patch + # PyTorch-1.6.0_fix-test-dataloader-fixed-affinity.patch + 'a4208a46cd2098744daaba96cebb96cd91166f8fc616924315e05974bad80c67', + '37c19e286f4090115bc67989e537241f2988041ef5c3ff6d02d8c736d8703090', # PyTorch-1.6.0_fix-test-tensorexpr.patch + # PyTorch-1.6.0_fix-test-missing-rpc-shutdown.patch + '9afd9b3a85a7b115e9535cf6a618d5dd137a69a5f36747d6290ac3bf123ab896', + '7d48c4ef7ae98a8a9e5eade3341ce18e41fa3fe4b868e9435efbfba849d1f977', # PyTorch-1.6.0_fix-rpc-test-world-size.patch + 'f0e09866e500a6ec96f7a0ad606d220960683901aa8dc491e245f9f8f4d89e45', # PyTorch-1.6.0_fix-system-pybind11.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.15.3'), + ('hypothesis', '4.44.2', versionsuffix), +] + +dependencies = [ + ('Ninja', '1.9.0'), # Required for JIT compilation of C++ extensions + ('protobuf', '3.10.0'), + ('Python', '3.7.4'), + ('pybind11', '2.4.3', versionsuffix), + ('SciPy-bundle', '2019.10', versionsuffix), + ('PyYAML', '5.1.2'), + ('MPFR', '4.0.2'), + ('GMP', '6.1.2'), + ('numactl', '2.0.12'), + ('FFmpeg', '4.2.1'), + ('gflags', '2.2.2'), + ('glog', '0.4.0'), + ('Pillow', '6.2.1'), +] + +excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/41186 + 'test_autograd', + # https://github.com/pytorch/pytorch/issues/41261 + 'test_cpp_extensions_aot_no_ninja', 'test_cpp_extensions_aot_ninja', + # https://github.com/pytorch/pytorch/issues/41400 + 'test_jit', + # https://github.com/pytorch/pytorch/issues/41469 + 'test_nn', + ], + '': [ + # This test fails everywhere: https://github.com/pytorch/pytorch/issues/41242 + 'test_cpp_extensions_jit', + # Throws illegal memory access due to float16: https://github.com/pytorch/pytorch/issues/41340 + 'test_torch', + # Potentially problematic save/load issue with test_lstm on only some machines. Tell users to verify save&load! + # https://github.com/pytorch/pytorch/issues/43209 + 'test_quantization', + ], +} + +runtest = 'cd test && %(python)s run_test.py --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'devel' From ffa2f0ef447318da4af01f8691cf1fc7b6145a6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Sep 2020 17:27:54 +0200 Subject: [PATCH 136/698] {devel}[GCCcore/10.2.0] Autotools v20200321 --- .../Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../Automake-1.16.2-GCCcore-10.2.0.eb | 44 +++++++++++++++++++ .../Autotools-20200321-GCCcore-10.2.0.eb | 24 ++++++++++ .../l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb | 32 ++++++++++++++ 4 files changed, 141 insertions(+) create mode 100644 easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c5f974ed99a --- /dev/null +++ b/easybuild/easyconfigs/a/Autoconf/Autoconf-2.69-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Autoconf' +version = '2.69' + +homepage = 'https://www.gnu.org/software/autoconf/' + +description = """ + Autoconf is an extensible package of M4 macros that produce shell scripts + to automatically configure software source code packages. These scripts can + adapt the packages to many kinds of UNIX-like systems without manual user + intervention. Autoconf creates a configuration script for a package from a + template file that lists the operating system features that the package can + use, in the form of M4 macro calls. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['954bd69b391edc12d6a4a51a2dd1476543da5c6bbf05a95b59dc0dd6fd4c2969'] + +builddependencies = [ + ('binutils', '2.35'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.32.0'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ["bin/%s" % x + for x in ["autoconf", "autoheader", "autom4te", "autoreconf", + "autoscan", "autoupdate", "ifnames"]], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..161cd23bf2f --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = '1.16.2' + +homepage = 'https://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] + +builddependencies = [ + ('binutils', '2.35'), + # non-standard Perl modules are required, + # see https://github.com/easybuilders/easybuild-easyconfigs/issues/1822 + ('Perl', '5.32.0'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..748c84f8d61 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20200321-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20200321' # date of the most recent change + +homepage = 'https://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.16.2'), # 20200321 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dd1e6e9fa2b --- /dev/null +++ b/easybuild/easyconfigs/l/libtool/libtool-2.4.6-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libtool' +version = '2.4.6' + +homepage = 'https://www.gnu.org/software/libtool' + +description = """ + GNU libtool is a generic library support script. Libtool hides the complexity + of using shared libraries behind a consistent, portable interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e3bd4d5d3d025a36c21dd6af7ea818a2afcd4dfc1ea5a17b39d7854bcd0c06e3'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('M4', '1.4.18'), +] + +sanity_check_paths = { + 'files': ['bin/libtool', 'bin/libtoolize', 'lib/libltdl.%s' % SHLIB_EXT], + 'dirs': ['include/libltdl', 'share/libtool/loaders', 'share/man/man1'], +} + +moduleclass = 'lib' From 87b5ff2013946e2abba101721bd5f743a4ece08d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 10 Sep 2020 17:38:08 +0200 Subject: [PATCH 137/698] Use GoPackage easyblock for building SeqKit from source --- .../easyconfigs/s/SeqKit/SeqKit-0.8.1.eb | 24 +- .../s/SeqKit/SeqKit-0.8.1_go-mod.patch | 222 ++++++++++++++++++ 2 files changed, 237 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1_go-mod.patch diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb index dfe91002e0f..27649f87dec 100644 --- a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PackedBinary' +easyblock = 'GoPackage' name = 'SeqKit' version = '0.8.1' @@ -6,15 +6,21 @@ version = '0.8.1' homepage = 'https://bioinf.shenwei.me/seqkit/' description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM -source_urls = ['https://github.com/shenwei356/%(namelower)s/releases/download/v%(version)s/'] -sources = ['%(namelower)s_linux_amd64.tar.gz'] -checksums = ['62dc2514d2f114146ff9377ce25abf7bd8159ac914d3ca2b9818828120b2097d'] +github_account = 'shenwei356' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [('SeqKit-0.8.1_go-mod.patch', 1)] +checksums = [ + 'c9558cee45a55e2f0f83375dc4991e85f9c2e30027099bb60dc0dae1590ecb49', # v0.8.1.tar.gz + '69cc35ba0eda60ffab8f3d61805867d04e8245a24b8ac2d81bbf3af2fe70b5da', # SeqKit-0.8.1_go-mod.patch +] -sanity_check_paths = { - 'files': ['%(namelower)s'], - 'dirs': [], -} +builddependencies = [ + ('Go', '1.14.1'), +] + +installopts = './%(namelower)s' moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1_go-mod.patch b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1_go-mod.patch new file mode 100644 index 00000000000..396dde26a25 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.8.1_go-mod.patch @@ -0,0 +1,222 @@ +Add go.mod and go.sum to have reproducible build. +# Generated by GoPackage Easyblock. +# modulename = 'github.com/shenwei356/seqkit' +# forced_deps = [ +# ('github.com/shenwei356/bio', 'f71378f731dfdfb1ef42de6d1f82dddc9c87fa57'), +# ] + + +author: Bob Dröge (University of Groningen) + +diff -ru --new-file seqkit-0.8.1.orig/go.mod seqkit-0.8.1/go.mod +--- seqkit-0.8.1.orig/go.mod 1970-01-01 01:00:00.000000000 +0100 ++++ seqkit-0.8.1/go.mod 2020-09-10 17:23:39.000000000 +0200 +@@ -0,0 +1,26 @@ ++module github.com/shenwei356/seqkit ++ ++go 1.14 ++ ++require ( ++ github.com/biogo/biogo v1.0.2 ++ github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 // indirect ++ github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 ++ github.com/dustin/go-humanize v1.0.0 ++ github.com/edsrzf/mmap-go v1.0.0 // indirect ++ github.com/klauspost/compress v1.11.0 // indirect ++ github.com/klauspost/pgzip v1.2.5 // indirect ++ github.com/mattn/go-colorable v0.1.7 ++ github.com/mattn/go-runewidth v0.0.9 // indirect ++ github.com/mitchellh/go-homedir v1.1.0 ++ github.com/remyoudompheng/bigfft v0.0.0-20200410134404-eec4a21b6bb0 // indirect ++ github.com/shenwei356/bio v0.0.0-20180629074701-f71378f731df ++ github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect ++ github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179 ++ github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba ++ github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect ++ github.com/shenwei356/util v0.0.0-20200809113039-4d78997fbf13 ++ github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992 ++ github.com/spf13/cobra v1.0.0 ++ github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 ++) + +diff -ru --new-file seqkit-0.8.1.orig/go.sum seqkit-0.8.1/go.sum +--- seqkit-0.8.1.orig/go.sum 1970-01-01 01:00:00.000000000 +0100 ++++ seqkit-0.8.1/go.sum 2020-09-10 17:24:39.000000000 +0200 +@@ -0,0 +1,177 @@ ++cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= ++github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= ++github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= ++github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc= ++github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= ++github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8= ++github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= ++github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= ++github.com/biogo/biogo v1.0.2 h1:PtMOoOb1ZrSjGMdwDa2VP3Y1QKC5uvWMrU4HThm1uys= ++github.com/biogo/biogo v1.0.2/go.mod h1:p+GFIiT20kY9/fPydaNTQW85a25lBqb0GzoDN5tEoPc= ++github.com/biogo/graph v0.0.0-20150317020928-057c1989faed/go.mod h1:UuyD2swDzTz1ChZTQld42mP5pyePLSDccmGycTpxRew= ++github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k= ++github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc= ++github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= ++github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk= ++github.com/coreos/etcd v3.3.10+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE= ++github.com/coreos/go-semver v0.2.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk= ++github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4= ++github.com/coreos/pkg v0.0.0-20180928190104-399ea9e2e55f/go.mod h1:E3G3o1h8I7cfcXa63jLwjI0eiQQMgzzUDFVpN/nH/eA= ++github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= ++github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 h1:iwZdTE0PVqJCos1vaoKsclOGD3ADKpshg3SRtYBbwso= ++github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548/go.mod h1:e6NPNENfs9mPDVNRekM7lKScauxd5kXTr1Mfyig6TDM= ++github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 h1:LpMLYGyy67BoAFGda1NeOBQwqlv7nUXpm+rIVHGxZZ4= ++github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8/go.mod h1:q2w6Bg5jeox1B+QkJ6Wp/+Vn0G/bo3f1uY7Fn3vivIQ= ++github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= ++github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ= ++github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no= ++github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4zYo= ++github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk= ++github.com/edsrzf/mmap-go v1.0.0 h1:CEBF7HpRnUCSJgGUb5h1Gm7e3VkmVDrR8lvWVLtrOFw= ++github.com/edsrzf/mmap-go v1.0.0/go.mod h1:YO35OhQPt3KJa3ryjFM5Bs14WD66h8eGKpfaBNrHW5M= ++github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo= ++github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04= ++github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as= ++github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE= ++github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk= ++github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY= ++github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ= ++github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4= ++github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= ++github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= ++github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= ++github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= ++github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= ++github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ= ++github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M= ++github.com/gorilla/websocket v1.4.0/go.mod h1:E7qHFY5m1UJ88s3WnNqhKjPHQ0heANvMoAMk2YaljkQ= ++github.com/grpc-ecosystem/go-grpc-middleware v1.0.0/go.mod h1:FiyG127CGDf3tlThmgyCl78X/SZQqEOJBCDaAfeWzPs= ++github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk= ++github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY= ++github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= ++github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= ++github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= ++github.com/jonboulle/clockwork v0.1.0/go.mod h1:Ii8DK3G1RaLaWxj9trq07+26W01tbo22gdxWY5EU2bo= ++github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w= ++github.com/kisielk/errcheck v1.1.0/go.mod h1:EZBBE59ingxPouuu3KfxchcWSUPOHkagtvWXihfKN4Q= ++github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck= ++github.com/klauspost/compress v1.11.0 h1:wJbzvpYMVGG9iTI9VxpnNZfd4DzMPoCWze3GgSqz8yg= ++github.com/klauspost/compress v1.11.0/go.mod h1:aoV0uJVorq1K+umq18yTdKaF57EivdYsUV+/s2qKfXs= ++github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE= ++github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= ++github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ= ++github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod 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h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo= ++github.com/spf13/pflag v1.0.3 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= ++github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4= ++github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= ++github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= ++github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= ++github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 h1:BhIUXV2ySTLrKgh/Hnts+QTQlIbWtomXt3LMdzME0A0= ++github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939/go.mod h1:omGxs4/6hNjxPKUTjmaNkPzehSnNJOJN6pMEbrlYIT4= ++github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= ++github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= ++github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= ++github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= ++go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= ++go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= ++go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= ++go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q= ++golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= ++golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= ++golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= ++golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc= 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++golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae h1:/WDfKMnPU+m5M4xB+6x4kaepxRw6jWvR5iDRdvjHgy8= ++golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= ++golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= ++golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= ++google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= ++google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= ++google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= ++google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= ++gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw= ++gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo= ++gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo= ++gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= ++gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= ++ From f7a868c65b58a56e05fada64f22c37fbb6ae513b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Sep 2020 19:05:20 +0200 Subject: [PATCH 138/698] fix SHA256 checksum for Automake 1.16.2 --- .../easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb index 161cd23bf2f..94d0fe00237 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.16.2-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['608a97523f97db32f1f5d5615c98ca69326ced2054c9f82e65bade7fc4c9dea8'] +checksums = ['b2f361094b410b4acbf4efba7337bdb786335ca09eb2518635a09fb7319ca5c1'] builddependencies = [ ('binutils', '2.35'), From d77b9aa16ae356ab864fd326d997b4021df9c95d Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 11 Sep 2020 15:30:56 +0200 Subject: [PATCH 139/698] adding easyconfigs: PAML-4.9j-GCCcore-9.3.0.eb --- .../p/PAML/PAML-4.9j-GCCcore-9.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..91df00b0204 --- /dev/null +++ b/easybuild/easyconfigs/p/PAML/PAML-4.9j-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'PAML' +version = '4.9j' + +homepage = 'http://abacus.gene.ucl.ac.uk/software/paml.html' +description = """PAML is a package of programs for phylogenetic + analyses of DNA or protein sequences using maximum likelihood.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://abacus.gene.ucl.ac.uk/software'] +sources = ['%(namelower)s%(version)s.tgz'] +checksums = ['9b00fbd37fe825129a160599372ba4c8e88b22d14c0388044a711fb281a0191d'] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +builddependencies = [('binutils', '2.34')] + +start_dir = 'src' +files_to_copy = [(["baseml", "basemlg", "codeml", "pamp", "evolver", "yn00", "chi2"], 'bin')] + +sanity_check_paths = { + 'files': ['bin/baseml'], + 'dirs': ['bin'] +} + +moduleclass = 'bio' From bea81bf265652e38181eecece27bc0151cdf9f9d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 11 Sep 2020 15:47:37 +0200 Subject: [PATCH 140/698] adding easyconfigs: Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb, pigz-2.4-GCCcore-9.3.0.eb --- .../p/pigz/pigz-2.4-GCCcore-9.3.0.eb | 55 +++++++++++++++++++ ...Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb | 52 ++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..66e5f58fc86 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-9.3.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.4' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + 'a4f816222a7b4269bd232680590b579ccc72591f1bb5adafcd7208ca77e14f73', # pigz-2.4.tar.gz + '8de19216a69b6402942f73177c566791f0c7fa4649376029d30d0c537d2195c1', # pigz-2.4_makefile.patch +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..e55fe4ccfae --- /dev/null +++ b/easybuild/easyconfigs/t/Trim_Galore/Trim_Galore-0.6.6-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,52 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# +# Updated to version 0.6.2: Pavel Grochal (INUITS) +# Updated to version 0.6.5: Alex Domingo (VUB) +# + +easyblock = 'Tarball' + +name = 'Trim_Galore' +version = '0.6.6' +versionsuffix = '-Python-%(pyver)s' + + +homepage = 'https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/' +description = """Trim Galore is a wrapper around Cutadapt and FastQC to +consistently apply adapter and quality trimming to FastQ files, with extra +functionality for RRBS data.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/FelixKrueger/TrimGalore/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b8db8ffd131d9d9e7c8532a5a1f1caee656c0c58d3eafd460fee3c39b9fcab5e'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', '3.8.2'), + ('Java', '11', '', True), + ('pigz', '2.4'), + ('Perl', '5.30.2'), + ('FastQC', '0.11.9', '-Java-%(javaver)s', True), + ('cutadapt', '2.10', '-Python-%(pyver)s'), +] + +postinstallcmds = [ + "chmod +x %(installdir)s/%(namelower)s", + "sed -i '1 i#!/usr/bin/env perl' %(installdir)s/%(namelower)s", + "mkdir %(installdir)s/bin && mv %(installdir)s/%(namelower)s %(installdir)s/bin/%(namelower)s", +] + +sanity_check_paths = { + 'files': ["bin/trim_galore"], + 'dirs': [], +} + +sanity_check_commands = [ + "trim_galore --help" +] + +moduleclass = 'bio' From 31cd09b56d573dbf56f46568c1c043ce66598421 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Sep 2020 17:40:36 +0200 Subject: [PATCH 141/698] Fix building with systemlibs, especially protobuf --- ...rFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb | 8 +- ...TensorFlow-2.3.0_fix-system-protobuf.patch | 9 +- ...ensorFlow-2.3.0_fix-system-protobuf2.patch | 103 ++++++++++++++++++ ...0_revert-tools-to-exectools-renaming.patch | 56 ++++++++++ 4 files changed, 168 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb index be14fd964c5..489d00b8d5e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb @@ -144,7 +144,9 @@ exts_list = [ 'TensorFlow-2.3.0_fix-json-include-style.patch', 'TensorFlow-2.3.0_fix-system_absl_py.patch', 'TensorFlow-2.3.0_fix-system-protobuf.patch', + 'TensorFlow-2.3.0_fix-system-protobuf2.patch', 'TensorFlow-2.3.0_fix-protoc-build.patch', + 'TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], @@ -159,9 +161,13 @@ exts_list = [ # TensorFlow-2.3.0_fix-system_absl_py.patch '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', # TensorFlow-2.3.0_fix-system-protobuf.patch - '35172b70be02e0b34963a7eabd108e96e9def005466d84f90737c57269c9b8bc', + '4407c3f126eb9d3c1658ef8d6ab3a26e7ed2a40ac869dd194d8a1282f6432c1d', + # TensorFlow-2.3.0_fix-system-protobuf2.patch + '74718e007acb7f5f016848218421895a33e9e894620154482deb75408225577d', # TensorFlow-2.3.0_fix-protoc-build.patch '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', + # TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch + '1a72f072a764bf66733445ce027c0bad7de7c88092363c0e2a7b91a422608d56', ], }), ] diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch index 1f9944c4f5a..f7447d6300e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf.patch @@ -1,6 +1,3 @@ -Based on: https://github.com/tensorflow/tensorflow/pull/42591 -Modified by Alexander Grund (TU Dresden) - From ab6c3bf9d98d7627509865e91913c25a1f8cc693 Mon Sep 17 00:00:00 2001 From: Steven Clarkson Date: Sat, 22 Aug 2020 16:57:25 -0700 @@ -28,11 +25,9 @@ index 118135d129005..ef3e0c93c6483 100644 "google/protobuf/descriptor.h", "google/protobuf/descriptor.pb.h", "google/protobuf/descriptor.proto", -@@ -32,9 +37,17 @@ HEADERS = [ +@@ -32,9 +37,15 @@ HEADERS = [ "google/protobuf/io/zero_copy_stream_impl_lite.h", "google/protobuf/map.h", -+ "google/protobuf/port_def.inc", -+ "google/protobuf/port_undef.inc", "google/protobuf/repeated_field.h", + "google/protobuf/source_context.pb.h", + "google/protobuf/source_context.proto", @@ -46,7 +41,7 @@ index 118135d129005..ef3e0c93c6483 100644 "google/protobuf/util/json_util.h", "google/protobuf/util/type_resolver_util.h", "google/protobuf/wrappers.pb.h", -@@ -102,3 +99,75 @@ py_library( +@@ -102,3 +113,75 @@ py_library( srcs_version = "PY2AND3", visibility = ["//visibility:public"], ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch new file mode 100644 index 00000000000..4eac729e655 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_fix-system-protobuf2.patch @@ -0,0 +1,103 @@ +From 32c2048560940dcc3c475eefdc857bb6202d18e0 Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 11 Sep 2020 17:14:34 +0200 +Subject: [PATCH] Do not symlink system protobuf headers but only required + .proto files + +Symlinking the system headers has proven to be problematic as newer +versions of protobuf add or remove headers which makes having a static +array of header files hard to impossible. Turns out the headers don't +need to be symlinked at all but only the .proto files used as inputs +need to be present. +--- + third_party/systemlibs/protobuf.BUILD | 35 +++------------------------ + 1 file changed, 3 insertions(+), 32 deletions(-) + +diff --git a/third_party/systemlibs/protobuf.BUILD b/third_party/systemlibs/protobuf.BUILD +index ef3e0c93c6483..ccf2ab4dc7d8b 100644 +--- a/third_party/systemlibs/protobuf.BUILD ++++ b/third_party/systemlibs/protobuf.BUILD +@@ -12,49 +12,24 @@ filegroup( + visibility = ["//visibility:public"], + ) + +-HEADERS = [ +- "google/protobuf/any.pb.h", ++PROTO_FILES = [ + "google/protobuf/any.proto", +- "google/protobuf/api.pb.h", + "google/protobuf/api.proto", +- "google/protobuf/arena.h", +- "google/protobuf/compiler/importer.h", +- "google/protobuf/compiler/plugin.h", +- "google/protobuf/compiler/plugin.pb.h", + "google/protobuf/compiler/plugin.proto", +- "google/protobuf/descriptor.h", +- "google/protobuf/descriptor.pb.h", + "google/protobuf/descriptor.proto", +- "google/protobuf/duration.pb.h", + "google/protobuf/duration.proto", +- "google/protobuf/dynamic_message.h", +- "google/protobuf/empty.pb.h", + "google/protobuf/empty.proto", +- "google/protobuf/field_mask.pb.h", + "google/protobuf/field_mask.proto", +- "google/protobuf/io/coded_stream.h", +- "google/protobuf/io/zero_copy_stream.h", +- "google/protobuf/io/zero_copy_stream_impl_lite.h", +- "google/protobuf/map.h", +- "google/protobuf/repeated_field.h", +- "google/protobuf/source_context.pb.h", + "google/protobuf/source_context.proto", +- "google/protobuf/struct.pb.h", + "google/protobuf/struct.proto", +- "google/protobuf/text_format.h", +- "google/protobuf/timestamp.pb.h", + "google/protobuf/timestamp.proto", +- "google/protobuf/type.pb.h", + "google/protobuf/type.proto", +- "google/protobuf/util/json_util.h", +- "google/protobuf/util/type_resolver_util.h", +- "google/protobuf/wrappers.pb.h", + "google/protobuf/wrappers.proto", + ] + + genrule( +- name = "link_headers", +- outs = HEADERS, ++ name = "link_proto_files", ++ outs = PROTO_FILES, + cmd = """ + for i in $(OUTS); do + f=$${i#$(@D)/} +@@ -66,14 +41,12 @@ genrule( + + cc_library( + name = "protobuf", +- hdrs = HEADERS, + linkopts = ["-lprotobuf"], + visibility = ["//visibility:public"], + ) + + cc_library( + name = "protobuf_headers", +- hdrs = HEADERS, + linkopts = ["-lprotobuf"], + visibility = ["//visibility:public"], + ) +@@ -94,7 +67,6 @@ genrule( + + cc_proto_library( + name = "cc_wkt_protos", +- hdrs = HEADERS, + internal_bootstrap_hack = 1, + protoc = ":protoc", + visibility = ["//visibility:public"], +@@ -109,7 +81,6 @@ proto_gen( + + py_library( + name = "protobuf_python", +- data = [":link_headers"], + srcs_version = "PY2AND3", + visibility = ["//visibility:public"], + ) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch new file mode 100644 index 00000000000..0791910e124 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch @@ -0,0 +1,56 @@ +This reverts the following commit. That change caused action_env variables to not be +passed through breaking build using system dependencies. +Author: Alexander Grund (TU Dresden) + +From f827c023906e7d30f0e5f2992b111ab34153310a Mon Sep 17 00:00:00 2001 +From: "A. Unique TensorFlower" +Date: Wed, 4 Mar 2020 22:27:03 -0800 +Subject: [PATCH] Use `exec_tools` rather than `tools` in tensorflow.bzl to + allow transitive dependencies to use python3 tools and deps in genrules + +PiperOrigin-RevId: 299023196 +Change-Id: I99981272330b060e9581c5c2a2f3992d524ae287 +--- + tensorflow/tensorflow.bzl | 12 ++++++------ + 1 file changed, 6 insertions(+), 6 deletions(-) + +diff --git a/tensorflow/tensorflow.bzl b/tensorflow/tensorflow.bzl +index b77b923cd4d4e..e4b3fa9ae90e5 100644 +--- a/tensorflow/tensorflow.bzl ++++ b/tensorflow/tensorflow.bzl +@@ -767,7 +767,7 @@ def tf_gen_op_wrapper_cc( + out_ops_file + "_internal.cc", + ], + srcs = srcs, +- exec_tools = [":" + tool] + tf_binary_additional_srcs(), ++ tools = [":" + tool] + tf_binary_additional_srcs(), + cmd = ("$(location :" + tool + ") $(location :" + out_ops_file + ".h) " + + "$(location :" + out_ops_file + ".cc) " + + str(include_internal_ops) + " " + api_def_args_str), +@@ -969,7 +969,7 @@ def tf_gen_op_wrapper_py( + name = name + "_pygenrule", + outs = [out], + srcs = api_def_srcs + [hidden_file], +- exec_tools = [tool_name] + tf_binary_additional_srcs(), ++ tools = [tool_name] + tf_binary_additional_srcs(), + cmd = ("$(location " + tool_name + ") " + api_def_args_str + + " @$(location " + hidden_file + ") > $@"), + ) +@@ -978,7 +978,7 @@ def tf_gen_op_wrapper_py( + name = name + "_pygenrule", + outs = [out], + srcs = api_def_srcs, +- exec_tools = [tool_name] + tf_binary_additional_srcs(), ++ tools = [tool_name] + tf_binary_additional_srcs(), + cmd = ("$(location " + tool_name + ") " + api_def_args_str + " " + + op_list_arg + " " + + ("1" if op_list_is_whitelist else "0") + " > $@"), +@@ -2430,7 +2430,7 @@ def tf_generate_proto_text_sources(name, srcs_relative_dir, srcs, protodeps = [] + cmd = + "$(location //tensorflow/tools/proto_text:gen_proto_text_functions) " + + "$(@D) " + srcs_relative_dir + " $(SRCS)", +- exec_tools = [ ++ tools = [ + clean_dep("//tensorflow/tools/proto_text:gen_proto_text_functions"), + ], + ) From 8b7342cb08b1e44f91241655ccd58cd3ec4f3687 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 11 Sep 2020 17:42:51 +0200 Subject: [PATCH 142/698] Add foss version --- ...ensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb | 173 ++++++++++++++++++ 1 file changed, 173 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..7127b094f76 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,173 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.3.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [ + ('Bazel', '3.4.1'), + ('protobuf', '3.10.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.7.4'), + ('h5py', '2.10.0', versionsuffix), + ('cURL', '7.66.0'), + ('double-conversion', '3.1.4'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '64.2'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('protobuf-python', '3.10.0', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.7'), + ('SWIG', '4.0.1'), + ('zlib', '1.2.11'), + # TF 2.3 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle + ('scipy', '1.4.1', versionsuffix), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.2.2', { + 'checksums': ['1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.6', { + 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], + }), + ('cachetools', '4.1.1', { + 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], + }), + ('google-auth', '1.20.0', { + 'modulename': 'google.auth', + 'checksums': ['c6e9735a2ee829a75b546702e460489db5cc35567a27fabd70b7c459f11efd58'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.9.0', { + 'modulename': 'absl', + 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.30.0', { + 'modulename': 'grpc', + 'checksums': ['e8f2f5d16e0164c415f1b31a8d9a81f2e4645a43d1b261375d6bab7b0adf511f'], + }), + ('tensorboard-plugin-wit', '1.7.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], + }), + ('tensorboard', version, { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', version, { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], + }), + ('astor', '0.8.0', { + 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + }), + ('Keras-Applications', '1.0.8', { + 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', + 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.3.0_fix-json-include-style.patch', + 'TensorFlow-2.3.0_fix-system_absl_py.patch', + 'TensorFlow-2.3.0_fix-system-protobuf.patch', + 'TensorFlow-2.3.0_fix-system-protobuf2.patch', + 'TensorFlow-2.3.0_fix-protoc-build.patch', + 'TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + '2595a5c401521f20a2734c4e5d54120996f8391f00bb62a57267d930bce95350', # v2.3.0.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.3.0_fix-json-include-style.patch + 'e04f5d9aa4c1222393b2cad4b84cd63128ef56eb5cc732d2afbc5d98dfa596a4', + # TensorFlow-2.3.0_fix-system_absl_py.patch + '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', + # TensorFlow-2.3.0_fix-system-protobuf.patch + '4407c3f126eb9d3c1658ef8d6ab3a26e7ed2a40ac869dd194d8a1282f6432c1d', + # TensorFlow-2.3.0_fix-system-protobuf2.patch + '74718e007acb7f5f016848218421895a33e9e894620154482deb75408225577d', + # TensorFlow-2.3.0_fix-protoc-build.patch + '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', + # TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch + '1a72f072a764bf66733445ce027c0bad7de7c88092363c0e2a7b91a422608d56', + ], + }), +] + +moduleclass = 'lib' From 97d604f5afbbb65f7aabd975789883995c63bac2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 11:32:47 +0200 Subject: [PATCH 143/698] bump version to 4.3.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index d4601306a5a..1c737902693 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.3.0' +VERSION = '4.3.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 46d3f0336da782f1d1869627ef49229647ac9d8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Sep 2020 11:34:44 +0200 Subject: [PATCH 144/698] adding easyconfigs: EasyBuild-4.3.0.eb --- .../e/EasyBuild/EasyBuild-4.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb new file mode 100644 index 00000000000..9185e8fb088 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.3.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = {'name': 'dummy', 'version': 'dummy'} + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/55/cf/928fb935f0d1648819a46f5b95e84d3f788ac50103e56883a7af1da8be0c/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/ba/d9/41d2be37a3496484cc3b8e6ebc4d8f173455403cdfa953c6f2e22afdcbb3/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/da/16/dd24726c94dabd85debc92f4732c781a90f6fb308824c82736da20960f6f/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '97c42d8f26ebc6fc43748442a9f0bbbc5316ae38b8320f7052695d9b77e101ab', # easybuild-framework-4.3.0.tar.gz + '06598715848db38f6633831d9555b8a1c2aca3023cbe5b33b85778acf8a65174', # easybuild-easyblocks-4.3.0.tar.gz + '48431ddee0d3f36b69dc0dbc2dfca77603a57811ae31f879b9e470a0bf570126', # easybuild-easyconfigs-4.3.0.tar.gz +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 5a7f8db2ec1e04ad6df6fd4ab1c2214eca2e1200 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 14 Sep 2020 09:49:05 +0200 Subject: [PATCH 145/698] adding easyconfigs: CBLAS-20110120-intel-2019b.eb, CBLAS-20110120-intel-2020a.eb --- .../c/CBLAS/CBLAS-20110120-intel-2019b.eb | 25 +++++++++++++++++++ .../c/CBLAS/CBLAS-20110120-intel-2020a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb create mode 100644 easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb new file mode 100644 index 00000000000..ae3da879c7f --- /dev/null +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb @@ -0,0 +1,25 @@ +name = 'CBLAS' +version = '20110120' + +homepage = 'http://www.netlib.org/blas/' +description = "C interface to the BLAS" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/blas/blast-forum/'] +sources = ['cblas.tgz'] +patches = ['CBLAS_shared-lib.patch'] +checksums = [ + '0f6354fd67fabd909baf57ced2ef84e962db58fae126e4f41b21dd4fec60a2a3', # cblas.tgz + '43d049287b91251064c581e8471f4f3323fec6b7d789f43dd93516b35cd1de81', # CBLAS_shared-lib.patch +] + +buildopts = 'all shared' + +# parallel build fails occasionally +parallel = 1 + +runtest = 'runtst' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb new file mode 100644 index 00000000000..9fd6648b6af --- /dev/null +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb @@ -0,0 +1,25 @@ +name = 'CBLAS' +version = '20110120' + +homepage = 'http://www.netlib.org/blas/' +description = "C interface to the BLAS" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.netlib.org/blas/blast-forum/'] +sources = ['cblas.tgz'] +patches = ['CBLAS_shared-lib.patch'] +checksums = [ + '0f6354fd67fabd909baf57ced2ef84e962db58fae126e4f41b21dd4fec60a2a3', # cblas.tgz + '43d049287b91251064c581e8471f4f3323fec6b7d789f43dd93516b35cd1de81', # CBLAS_shared-lib.patch +] + +buildopts = 'all shared' + +# parallel build fails occasionally +parallel = 1 + +runtest = 'runtst' + +moduleclass = 'numlib' From 219f451914ebdf0bc55ad2a1a7f0cf1c3e1b0673 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2020 09:57:26 +0200 Subject: [PATCH 146/698] adding easyconfigs: torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb --- ...sscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb new file mode 100644 index 00000000000..a96311750f8 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.7.0-fosscuda-2019b-Python-3.7.4-PyTorch-1.6.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'torchvision' +version = '0.7.0' +local_pytorch_version = '1.6.0' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_version + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa0a6f44a50451115d1499b3f2aa597e0092a07afce1068750260fa7dd2c85cb'] + +builddependencies = [('CMake', '3.15.3')] + +dependencies = [ + ('Python', '3.7.4'), + ('Pillow-SIMD', '6.0.x.post0'), + ('PyTorch', local_pytorch_version, '-Python-%(pyver)s'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'export TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0 7.2 7.5" && ' + +sanity_pip_check = True + +moduleclass = 'vis' From 9130653bd89c485d9a1a52d8770279e8bfe43a9d Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Mon, 14 Sep 2020 10:54:32 +0200 Subject: [PATCH 147/698] update https --- easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb | 4 ++-- easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb index ae3da879c7f..5dc02932f19 100644 --- a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2019b.eb @@ -1,13 +1,13 @@ name = 'CBLAS' version = '20110120' -homepage = 'http://www.netlib.org/blas/' +homepage = 'https://www.netlib.org/blas/' description = "C interface to the BLAS" toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'pic': True} -source_urls = ['http://www.netlib.org/blas/blast-forum/'] +source_urls = ['https://www.netlib.org/blas/blast-forum/'] sources = ['cblas.tgz'] patches = ['CBLAS_shared-lib.patch'] checksums = [ diff --git a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb index 9fd6648b6af..a1985c637ab 100644 --- a/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb +++ b/easybuild/easyconfigs/c/CBLAS/CBLAS-20110120-intel-2020a.eb @@ -1,13 +1,13 @@ name = 'CBLAS' version = '20110120' -homepage = 'http://www.netlib.org/blas/' +homepage = 'https://www.netlib.org/blas/' description = "C interface to the BLAS" toolchain = {'name': 'intel', 'version': '2020a'} toolchainopts = {'pic': True} -source_urls = ['http://www.netlib.org/blas/blast-forum/'] +source_urls = ['https://www.netlib.org/blas/blast-forum/'] sources = ['cblas.tgz'] patches = ['CBLAS_shared-lib.patch'] checksums = [ From e511d08d36d3e526e62ac81839098e22da55ff87 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Mon, 14 Sep 2020 10:00:29 +0100 Subject: [PATCH 148/698] Changed moduleclass to chem. --- .../easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb index 4267a0b909f..c5e1f61ea24 100644 --- a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb +++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb @@ -46,4 +46,4 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'math' +moduleclass = 'chem' From a4a435c298486809991c6f36a05d339327e4c836 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Mon, 14 Sep 2020 14:37:18 +0100 Subject: [PATCH 149/698] Updated source download text. --- .../easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb index c5e1f61ea24..e3138b934a5 100644 --- a/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb +++ b/easybuild/easyconfigs/f/FHI-aims/FHI-aims-200112_2-intel-2019b.eb @@ -23,7 +23,10 @@ thousands of cores. toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'opt': True, 'precise': True} -# The source code must be downloaded manually from the FHI-aims club. +# The source code must be downloaded manually from the FHI-aims club (https://aimsclub.fhi-berlin.mpg.de/). +# Access to the FHI-aims club requires a valid license and registration. Details on available license options +# and how to register to access FHI-aims club may be found at +# https://aimsclub.fhi-berlin.mpg.de/aims_obtaining_simple.php sources = ['%(namelower)s.%(version)s.tgz'] checksums = ['b591b09c7cb2e0befe59067ae59a63f522a9b5200a4073018f616aea657704d6'] From 63cb2502ca3cb546ddd75e0728d99ef38df959b2 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Mon, 14 Sep 2020 14:55:38 +0100 Subject: [PATCH 150/698] Updated to include POCL to make sure it builds on Power --- .../easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb index 7c62b0eed8b..52775bf9e62 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb @@ -37,6 +37,7 @@ dependencies = [ ('PCRE', '8.43'), ('PROJ', '6.2.1'), ('libgeotiff', '1.5.1'), + ('pocl', '1.4'), # for OpenCL support (particularly on POWER) ('SciPy-bundle', '2019.10', versionsuffix), ] From f38e76cba7232f0da7ea009d65f37eb1fcc0e48b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2020 17:12:46 +0200 Subject: [PATCH 151/698] adding easyconfigs: Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb --- ...s-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb new file mode 100644 index 00000000000..6106ea8a398 --- /dev/null +++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Statistics-R' +version = '0.34' +versionsuffix = '-Perl-%(perlver)s-R-%(rver)s' + +homepage = 'https://metacpan.org/pod/Statistics::R' +description = "Perl interface with the R statistical program" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://cpan.metacpan.org/authors/id/F/FA/FANGLY'] +sources = [SOURCE_TAR_GZ] +checksums = ['782dd064876ac94680d97899f24fb0e727df42c05ba474ec096a9116438fbed4'] + +dependencies = [ + ('Perl', '5.30.2'), + ('R', '4.0.0'), +] + +options = {'modulename': 'Statistics::R'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/Statistics/R.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Statistics/R'], +} + +moduleclass = 'data' From 5579f42e6be46ed6589f111c3f0ead16c9c0e07a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Sep 2020 17:20:57 +0200 Subject: [PATCH 152/698] drop versionsuffix for Statistics-R easyconfig --- ...0a-Perl-5.30.2-R-4.0.0.eb => Statistics-R-0.34-foss-2020a.eb} | 1 - 1 file changed, 1 deletion(-) rename easybuild/easyconfigs/s/Statistics-R/{Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb => Statistics-R-0.34-foss-2020a.eb} (93%) diff --git a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb similarity index 93% rename from easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb rename to easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb index 6106ea8a398..bb8a8f65acb 100644 --- a/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a-Perl-5.30.2-R-4.0.0.eb +++ b/easybuild/easyconfigs/s/Statistics-R/Statistics-R-0.34-foss-2020a.eb @@ -2,7 +2,6 @@ easyblock = 'PerlModule' name = 'Statistics-R' version = '0.34' -versionsuffix = '-Perl-%(perlver)s-R-%(rver)s' homepage = 'https://metacpan.org/pod/Statistics::R' description = "Perl interface with the R statistical program" From a9ae7a7cee1d0bb123961c67f1943ed734f0e5eb Mon Sep 17 00:00:00 2001 From: Rok Zitko Date: Tue, 15 Sep 2020 14:43:05 +0200 Subject: [PATCH 153/698] adding easyconfigs: Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb, TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb, TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb, NFFT-3.5.2-foss-2020a.eb, TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb, TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb --- ...dings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb | 32 +++++++++ .../n/NFFT/NFFT-3.5.2-foss-2020a.eb | 28 ++++++++ ...IQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb | 63 ++++++++++++++++++ ...dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb | 64 ++++++++++++++++++ ...RIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb | 64 ++++++++++++++++++ .../TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb | 66 +++++++++++++++++++ 6 files changed, 317 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2020a.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..0827034d6fd --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-10.0.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'Clang-Python-bindings' +version = '10.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://clang.llvm.org' +description = """Python bindings for libclang""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] +sources = ['clang-%(version)s.src.tar.xz'] +checksums = ['f99afc382b88e622c689b6d96cadfa6241ef55dca90e87fc170352e12ddb2b24'] + +dependencies = [ + ('Clang', version), + ('Python', '3.8.2') +] + +start_dir = 'bindings/python' + +sanity_check_paths = { + 'files': ['clang/cindex.py'], + 'dirs': ['clang'] +} + +sanity_check_commands = ["python -c 'import clang'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2020a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2020a.eb new file mode 100644 index 00000000000..dc2182b4582 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.2-foss-2020a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.2' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c68b22de2b914328d5d9fd33778defc66b226c72ef4c103956bbf36bbcd18e45'] + +dependencies = [('FFTW', '3.3.8')] + +builddependencies = [('Autotools', '20180311')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3.a', 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c1454f3c191 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-cthyb' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://triqs.github.io/cthyb/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + cthyb = continuous-time hybridisation-expansion quantum Monte Carlo + + The TRIQS-based hybridization-expansion solver allows to solve the + generic problem of a quantum impurity embedded in a conduction bath + for an arbitrary local interaction vertex. The “impurity” can be any + set of orbitals, on one or several atoms. +""" + +docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] +sources = ['cthyb-%(version)s.tar.gz'] +checksums = ['64970bfc73f5be819a87044411b4cc9e1f7996d122158c5c011046b7e1aec4e5'] + +dependencies = [ + ('Python', '3.8.2'), + ('TRIQS', '3.0.0', versionsuffix), + ('NFFT', '3.5.2') +] + +builddependencies = [ + ('CMake', '3.16.4') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_cthyb_c.a'], + 'dirs': ['include', 'include/triqs_cthyb', 'lib', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import triqs_cthyb'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_cthyb', +} +modextravars = { + 'TRIQS_CTHYB_ROOT': '%(installdir)s', + 'TRIQS_CTHYB_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..905b5036fab --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-dft_tools' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://triqs.github.io/dft_tools/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + This TRIQS-based-based application is aimed at ab-initio calculations + for correlated materials, combining realistic DFT band-structure calculation + with the dynamical mean-field theory. Together with the necessary tools to + perform the DMFT self-consistency loop for realistic multi-band problems, + the package provides a full-fledged charge self-consistent interface to the + Wien2K package. In addition, if Wien2k is not available, it provides a generic + interface for one-shot DFT+DMFT calculations, where only the single-particle + Hamiltonian in orbital space has to be provided. +""" + +docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] +sources = ['dft_tools-%(version)s.tar.gz'] +checksums = ['646d1d2dca5cf6ad90e18d0706124f701aa94ec39c5236d8fcf36dc5c628a3f6'] + +dependencies = [ + ('Python', '3.8.2'), + ('TRIQS', '3.0.0', versionsuffix), +] + +builddependencies = [ + ('CMake', '3.16.4') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/dmftproj', 'lib/libtriqs_dft_tools_c.a'], + 'dirs': ['include/triqs_dft_tools', 'bin', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_dft_tools'], +} + +sanity_check_commands = ["python -c 'import triqs_dft_tools'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_dft_tools', +} +modextravars = { + 'TRIQS_DFT_TOOLS_ROOT': '%(installdir)s', + 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..912621d4fbe --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,64 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-tprf' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://triqs.github.io/tprf' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + TPRF is a TRIQS-based two-particle response function tool box that + implements basic operations for higher order response functions such + as inversion, products, the random phase approximation, the bethe + salpeter equation (in the local vertex approximation), etc.. + + The aim is to provide efficient (C++/OpenMP/MPI) implementations of + the basic operations needed to compute the two-particle response in + the different two-particle channels (particle-hole, particle-particle). +""" + +docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] +sources = ['tprf-%(version)s.tar.gz'] +checksums = ['8e20620145bb8cbcc187f4637884457c0cacaed79ba6e1709a951046ee5ffc4b'] + +dependencies = [ + ('Python', '3.8.2'), + ('TRIQS', '3.0.0', versionsuffix) +] + +builddependencies = [ + ('CMake', '3.16.4') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_tprf_c.a'], + 'dirs': ['include/triqs_tprf', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_tprf'], +} + +sanity_check_commands = ["python -c 'import triqs_tprf'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_tprf', +} +modextravars = { + 'TRIQS_TPRF_ROOT': '%(installdir)s', + 'TRIQS_TPRF_VERSION': '%(version)s' +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..d583e1f1940 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,66 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS' +version = '3.0.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://triqs.github.io/triqs' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. +""" + +docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] +sources = ['triqs-%(version)s.tar.gz'] +checksums = ['21239fb42ba73f84a77b63abce84c0d2b9162277233d5839aaf39e22e1be8128'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-%(pyver)s'), + ('Boost', '1.72.0'), + ('Clang', '10.0.1'), + ('Clang-Python-bindings', '10.0.1', '-Python-%(pyver)s'), + ('GMP', '6.2.0'), + ('HDF5', '1.10.6'), + ('Mako', '1.1.2'), + ('h5py', '2.10.0', '-Python-%(pyver)s') +] + +builddependencies = [ + ('CMake', '3.16.4') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs.%s' % SHLIB_EXT], + 'dirs': ['include/triqs', 'include/itertools', 'include/mpi', 'include/cpp2py', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = [ + "triqs++ --help", + "c++2py --help", + "python -c 'import triqs'" +] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': ['lib/cmake/triqs', 'lib/cmake/cpp2py'] +} +modextravars = { + 'TRIQS_ROOT': '%(installdir)s', + 'TRIQS_VERSION': '%(version)s' +} + +moduleclass = 'phys' From e8d164a2375661201020aaa97f8e2b0785256ad7 Mon Sep 17 00:00:00 2001 From: Rok Zitko Date: Tue, 15 Sep 2020 17:59:46 +0200 Subject: [PATCH 154/698] Dropping h5py as a dependency: no longer required in TRIQS 3.0.0 --- .../easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb index d583e1f1940..eadd92f648b 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb @@ -30,7 +30,6 @@ dependencies = [ ('GMP', '6.2.0'), ('HDF5', '1.10.6'), ('Mako', '1.1.2'), - ('h5py', '2.10.0', '-Python-%(pyver)s') ] builddependencies = [ From 08ea74c3f1e87bb17ef650ad6875276306ed926f Mon Sep 17 00:00:00 2001 From: fizwit Date: Tue, 15 Sep 2020 09:48:54 -0700 Subject: [PATCH 155/698] fix issues --- .../b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb index 438e1ae5448..50116881235 100644 --- a/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.8.8-foss-2019b-Python-3.7.4.eb @@ -16,15 +16,15 @@ dependencies = [ ('SciPy-bundle', '2019.10', versionsuffix), ] -prebuildopts = "export CPATH=$EBROOTLZO/include/lzo:$CPATH && " use_pip = True - +sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('python-lzo', '1.12', { 'modulename': 'lzo', + 'preinstallopts': 'export PREFIX=$EBROOTLZO && ', 'checksums': ['97a8e46825e8f1abd84c2a3372bc09adae9745a5be5d3af2692cd850dac35345'], }), (name, version, { From 3d35dea2ff457798b274b893c5ee697424752e40 Mon Sep 17 00:00:00 2001 From: Rok Zitko Date: Tue, 15 Sep 2020 19:03:36 +0200 Subject: [PATCH 156/698] Reintroduce h5py as a dependency to fix a linking problem --- .../easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb index eadd92f648b..d583e1f1940 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb @@ -30,6 +30,7 @@ dependencies = [ ('GMP', '6.2.0'), ('HDF5', '1.10.6'), ('Mako', '1.1.2'), + ('h5py', '2.10.0', '-Python-%(pyver)s') ] builddependencies = [ From 11c6a5a8579c3a158830e586684b8354c91e9079 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Sep 2020 21:18:35 +0200 Subject: [PATCH 157/698] add libtirpc as a build dep for HDF to fix installation on RHEL8 --- .../h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb | 14 +++++++--- .../libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb | 28 +++++++++++++++++++ 2 files changed, 38 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index 34afcfde732..fa9fb0921be 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.34'), ('Bison', '3.5.3'), ('flex', '2.6.4'), + ('libtirpc', '1.2.6'), ] dependencies = [ @@ -29,15 +30,20 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '' -configopts += '--with-szlib=$EBROOTSZIP ' +preconfigopts = "LIBS='-ltirpc' " +configopts = '--with-szlib=$EBROOTSZIP ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' modextrapaths = {'CPATH': 'include/hdf'} sanity_check_paths = { - 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], - 'dirs': ['bin', 'include/hdf'], + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'dirs': ['include/hdf'], } +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2ac13a65f04 --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.2.6' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['4278e9a5181d5af9cd7885322fdecebc444f9a3da87c526e7d47f7a12a37d1cc'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.34') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 8800fc5fd3aa39099330cb12750090b3f9f7a0c5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 15 Sep 2020 20:31:56 +0100 Subject: [PATCH 158/698] adding easyconfigs: Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb --- .../Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..391315203bc --- /dev/null +++ b/easybuild/easyconfigs/p/Pingouin/Pingouin-0.3.8-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'Pingouin' +version = '0.3.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pingouin-stats.org/" +description = """Pingouin is an open-source statistical package written in Python 3 and based mostly on Pandas and + NumPy.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('Seaborn', '0.10.0', versionsuffix), + ('statsmodels', '0.11.0', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), + ('xarray', '0.15.1', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], +} + +exts_list = [ + ('littleutils', '0.2.2', { + 'checksums': ['e6cae3a4203e530d51c9667ed310ffe3b1948f2876e3d69605b3de4b7d96916f'], + }), + ('pandas_flavor', '0.2.0', { + 'checksums': ['7871655816de22dc766e916697ccc67449e1863c090ef5fd40d4d0fbd056e489'], + }), + ('outdated', '0.2.0', { + 'checksums': ['bcb145e0e372ba467e998c327d3d1ba72a134b0d5a729749729df6c6244ce643'], + }), + (name, version, { + 'modulename': '%(namelower)s', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['ae12581174740a358ca9127bdc2360edf7af357b094de682c80f993ff402b813'], + }), +] + +moduleclass = 'math' From 43a1a45480e58e636553e7f5f846a289220746a4 Mon Sep 17 00:00:00 2001 From: Rok Zitko Date: Wed, 16 Sep 2020 07:44:08 +0200 Subject: [PATCH 159/698] preconfigopts & configopts to prevent existing installation from interfering with (re)builds --- .../t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb index d583e1f1940..a52a51a72af 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb @@ -29,8 +29,7 @@ dependencies = [ ('Clang-Python-bindings', '10.0.1', '-Python-%(pyver)s'), ('GMP', '6.2.0'), ('HDF5', '1.10.6'), - ('Mako', '1.1.2'), - ('h5py', '2.10.0', '-Python-%(pyver)s') + ('Mako', '1.1.2') ] builddependencies = [ @@ -39,6 +38,9 @@ builddependencies = [ separate_build_dir = True +preconfigopts = "rm -rf %(installdir)s && " +configopts = "-DBuild_Deps=Always" + runtest = 'test' sanity_check_paths = { From 20df39a04e5e0b95d12b8154d966e0e10a9b9a52 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 16 Sep 2020 09:24:11 +0100 Subject: [PATCH 160/698] adding easyconfigs: Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb, geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb, networkx-2.4-fosscuda-2019b-Python-3.7.4.eb --- ...iona-1.8.13-fosscuda-2019b-Python-3.7.4.eb | 51 +++++++++++++++++++ ...andas-0.7.0-fosscuda-2019b-Python-3.7.4.eb | 50 ++++++++++++++++++ ...etworkx-2.4-fosscuda-2019b-Python-3.7.4.eb | 26 ++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..b65b571c300 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.13-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.13' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('GDAL', '3.0.2', versionsuffix), + ('Shapely', '1.7.0', versionsuffix), # optional +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cligj', '0.5.0', { + 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], + }), + ('click', '7.1.1', { + 'checksums': ['8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['5ec34898c8b983a723fb4e949dd3e0ed7e691c303e51f6bfd61e52ac9ac813ae'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..44fc1d3a24e --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.7.0-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.7.0' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('Shapely', '1.7.0', versionsuffix), + ('Fiona', '1.8.13', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('scikit-learn', '0.21.3', versionsuffix), + ('pyproj', '2.4.2', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('descartes', '1.1.0', { + 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Deprecated', '1.2.10', { + 'checksums': ['525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74'], + }), + ('mapclassify', '2.2.0', { + 'checksums': ['d8cce990f2df905ec7ba0d61a0de60a64635822684a2074cb412da9992dbf999'], + }), + (name, version, { + 'checksums': ['19074b090ab928527193c50b383d31a259a9b84b18553562631295fa67f640bc'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..0c35f1395b7 --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-2.4-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '2.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, + and functions of complex networks.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f8f4ff0b6f96e4f9b16af6b84622597b5334bf9cae8cf9b2e42e7985d5c95c64'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 95e6c7e0d8786f43332bc27672820f223222e21e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 12:04:18 +0200 Subject: [PATCH 161/698] use https in source URLs for V8 v2.3 --- easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb | 2 +- easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb b/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb index 7003dbc6917..7e3a93b6d57 100644 --- a/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/v/V8/V8-2.3-foss-2019a-R-3.6.0.eb @@ -10,7 +10,7 @@ description = """R interface to Google's open source JavaScript engine""" toolchain = {'name': 'foss', 'version': '2019a'} source_urls = [ - 'http://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/', 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['f720d772c1d66cac0320230f2e6189e0b8a59af6e589e421e3d2423099d505b3'] diff --git a/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb b/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb index d90249673fc..ea1f3e5179d 100644 --- a/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb +++ b/easybuild/easyconfigs/v/V8/V8-2.3-intel-2019a-R-3.6.0.eb @@ -10,7 +10,7 @@ description = """R interface to Google's open source JavaScript engine""" toolchain = {'name': 'intel', 'version': '2019a'} source_urls = [ - 'http://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/', 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['f720d772c1d66cac0320230f2e6189e0b8a59af6e589e421e3d2423099d505b3'] From da9898916a849a7f566e7db4da34e661d6bc25d1 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 Sep 2020 13:33:08 +0200 Subject: [PATCH 162/698] Fix make 4.2.1 on RHEL 8 --- .../Automake/Automake-1.15.1-GCCcore-7.3.0.eb | 41 +++++++++++++++++++ .../Automake/Automake-1.15.1-GCCcore-8.3.0.eb | 41 +++++++++++++++++++ .../Autotools-20170619-GCCcore-7.3.0.eb | 24 +++++++++++ .../Autotools-20170619-GCCcore-8.3.0.eb | 24 +++++++++++ .../m/make/make-4.2.1-GCC-7.3.0-2.30.eb | 12 +++++- .../m/make/make-4.2.1-GCCcore-8.3.0.eb | 13 +++++- .../easyconfigs/m/make/make-4.2.1_RHEL8.patch | 15 +++++++ 7 files changed, 167 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..907b363772a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15.1" + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260'] + +builddependencies = [ + ('binutils', '2.30'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..3e9a40f622a --- /dev/null +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb @@ -0,0 +1,41 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## + +easyblock = 'ConfigureMake' + +name = 'Automake' +version = "1.15.1" + +homepage = 'http://www.gnu.org/software/automake/automake.html' + +description = "Automake: GNU Standards-compliant Makefile generator" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['988e32527abe052307d21c8ca000aa238b914df363a617e38f4fb89f5abf6260'] + +builddependencies = [ + ('binutils', '2.32'), +] + +dependencies = [ + ('Autoconf', '2.69'), +] + +sanity_check_paths = { + 'files': ['bin/automake', 'bin/aclocal'], + 'dirs': [] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..3be3052c893 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20170619' # date of the most recent change + +homepage = 'http://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15.1'), # 20170619 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..2290af6b865 --- /dev/null +++ b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Bundle' + +name = 'Autotools' +version = '20170619' # date of the most recent change + +homepage = 'http://autotools.io' + +description = """ + This bundle collect the standard GNU build tools: Autoconf, Automake + and libtool +""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +dependencies = [ + ('Autoconf', '2.69'), # 20120424 + ('Automake', '1.15.1'), # 20170619 + ('libtool', '2.4.6'), # 20150215 +] + +# Pure bundle -- no need to specify 'binutils' used when building GCCcore +# toolchain as build dependency + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb index a25d9bda13b..ccc8a7c0e98 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb @@ -21,7 +21,17 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_BZ2] -checksums = ['d6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589'] +patches = ['%(name)s-%(version)s_RHEL8.patch'] +checksums = [ + 'd6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589', # make-4.2.1.tar.bz2 + 'f564f16443979c8398ed325b5d3cd2d6683ca5400433fc67fa29492d2cc4c9ea', # make-4.2.1_RHEL8.patch +] + +builddependencies = [ + # needs specifically aclocal 1.15 + ('Autotools', '20170619'), + ('pkg-config', '0.29.2'), +] sanity_check_paths = { 'files': ['bin/make'], diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb index 0ee7c0b4033..851d90c79f4 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb @@ -21,9 +21,18 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_BZ2] -checksums = ['d6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589'] +patches = ['%(name)s-%(version)s_RHEL8.patch'] +checksums = [ + 'd6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589', # make-4.2.1.tar.bz2 + 'f564f16443979c8398ed325b5d3cd2d6683ca5400433fc67fa29492d2cc4c9ea', # make-4.2.1_RHEL8.patch +] -builddependencies = [('binutils', '2.32')] +builddependencies = [ + # needs specifically aclocal 1.15 + ('Autotools', '20170619'), + ('binutils', '2.32'), + ('pkg-config', '0.29.2'), +] postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] diff --git a/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch b/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch new file mode 100644 index 00000000000..f84b2f2560a --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch @@ -0,0 +1,15 @@ +# http://gnu-make.2324884.n4.nabble.com/undefined-reference-to-alloca-td18308.html +# SEP 16th 2020 by B. Hajgato (UGent) +diff --git a/configure.ac.orig b/configure.ac +index 64ec870..870a70a 100644 +--- a/configure.ac.orig ++++ b/configure.ac +@@ -402,7 +402,7 @@ AC_CACHE_CHECK([if system libc has GNU glob], [make_cv_sys_gnu_glob], + #define GLOB_INTERFACE_VERSION 1 + #if !defined _LIBC && defined __GNU_LIBRARY__ && __GNU_LIBRARY__ > 1 + # include +-# if _GNU_GLOB_INTERFACE_VERSION == GLOB_INTERFACE_VERSION ++# if _GNU_GLOB_INTERFACE_VERSION >= GLOB_INTERFACE_VERSION + gnu glob + # endif + #endif], From 77e3cd8f9d9e5eef3fba3fd81770933104cedc2a Mon Sep 17 00:00:00 2001 From: Rok Zitko Date: Wed, 16 Sep 2020 14:12:02 +0200 Subject: [PATCH 163/698] provide rationale for the rm command in preconfigopts --- .../easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb index a52a51a72af..03f85da785b 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.0.0-foss-2020a-Python-3.8.2.eb @@ -38,7 +38,10 @@ builddependencies = [ separate_build_dir = True +# Remove installation directory before building. This fixes problems with +# failing builds in the presence of preexisting installation. preconfigopts = "rm -rf %(installdir)s && " + configopts = "-DBuild_Deps=Always" runtest = 'test' From 77c05b04a067035b97cde8c8011a3b4cefe68bdd Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 16 Sep 2020 14:18:32 +0200 Subject: [PATCH 164/698] adding easyconfigs: MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb, tsne-0.1.8-intel-2019b-Python-2.7.16.eb, fetchMG-1.0-GCCcore-8.3.0.eb, CD-HIT-4.8.1-iccifort-2019.5.281.eb and patches: MyCC-2017-03-01_fix_paths.patch, tsne-0.1.8_fix_setup_py.patch --- .../CD-HIT-4.8.1-iccifort-2019.5.281.eb | 40 ++++++++++ .../f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb | 36 +++++++++ ...CC-2017-03-01-intel-2019b-Python-2.7.16.eb | 74 +++++++++++++++++++ .../m/MyCC/MyCC-2017-03-01_fix_paths.patch | 33 +++++++++ .../tsne-0.1.8-intel-2019b-Python-2.7.16.eb | 35 +++++++++ .../t/tsne/tsne-0.1.8_fix_setup_py.patch | 24 ++++++ 6 files changed, 242 insertions(+) create mode 100644 easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb create mode 100644 easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01_fix_paths.patch create mode 100644 easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb create mode 100644 easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..f1f1a221380 --- /dev/null +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'MakeCp' + +name = 'CD-HIT' +version = '4.8.1' + +homepage = 'http://weizhongli-lab.org/cd-hit/' +description = """ CD-HIT is a very widely used program for clustering and + comparing protein or nucleotide sequences.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/weizhongli/cdhit/releases/download/V%(version)s/'] +sources = ['%(namelower)s-v%(version)s-2019-0228.tar.gz'] +checksums = ['26172dba3040d1ae5c73ff0ac6c3be8c8e60cc49fc7379e434cdf9cb1e7415de'] + +dependencies = [ + ('Perl', '5.30.0'), + ('zlib', '1.2.11'), +] + +# make sure compilation flags are passed down (e.g. to enable OpenMP) +buildopts = ' CC="$CXX" CCFLAGS="$CPPFLAGS $CXXFLAGS"' + +# put here the list of generated executables when compiling +local_list_of_executables = ['cd-hit', 'cd-hit-est', 'cd-hit-2d', 'cd-hit-est-2d', 'cd-hit-div', 'cd-hit-454'] + +# this is the real EasyBuild line to copy all the executables and perl scripts to "bin" +files_to_copy = [(local_list_of_executables, 'bin'), (['*.pl'], 'bin'), 'README', 'doc', 'license.txt'] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_list_of_executables], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..472087a6202 --- /dev/null +++ b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'fetchMG' +version = '1.0' + +homepage = 'http://vm-lux.embl.de/~mende/fetchMG/about.html' +description = """The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes +in an easy and accurate manner.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['http://vm-lux.embl.de/~kultima/share/mOTU/'] +sources = ['%(name)sv%(version)s.tar.gz'] +checksums = ['e3b835b425525513611b7116f89fc11ed015032ffd0494fa058edec1d6e67b17'] + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Perl', '5.30.0'), +] + +fix_perl_shebang_for = ['%(name)s.pl'] + +sanity_check_paths = { + 'files': ['%(name)s.pl', 'bin/cdbfasta', 'bin/cdbyank', 'bin/hmmsearch'], + 'dirs': [], +} + +sanity_check_commands = [ + "fetchMG.pl -h", + "fetchMG.pl -m extraction -x '' %(installdir)s/example_datasets/example_data.faa" +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..a5ae391748b --- /dev/null +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -0,0 +1,74 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = "CmdCp" + +name = "MyCC" +version = "2017-03-01" +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://docutils.sourceforge.net/" +description = """Docutils is an open-source text processing system for processing plaintext +documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. +It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get +plaintext markup language.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = [('https://sourceforge.net/projects/sb2nhri/files/MyCC/', 'download')] +sources = [{'download_filename': '%s-%s.tar.gz' % (name, version), 'filename': 'Tools.tar.gz'}] +patches = ['%(name)s-%(version)s_fix_paths.patch'] +checksums = [ + '173210a759e90c7b1ff98bf537a88e8b7e893e60fe91fca50407ffede7e08de6', # Tools.tar.gz + 'f20fdf13ccd04c2e523c87a8f0a80194443fa09f7916b4b7ecb5a9751e1f6ee8', # MyCC-2017-03-01_fix_paths.patch +] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('scikit-learn', '0.20.4', versionsuffix), + ('matplotlib', '2.2.4', versionsuffix), + ('prodigal', '2.6.3'), + ('fetchMG', '1.0'), + ('UCLUST', '1.2.22q', '-i86linux64', True), + ('CD-HIT', '4.8.1'), + ('tsne', '0.1.8', versionsuffix), +] + +skipsteps = ['build'] + + +local_bin_files = [ + '1_bhsne.py', '1_ClusterCorrection_Split.py', '1_GetCDHitHeader.py', '1_GetCOG.py', '1_GetRepeatGeneMaskedFa.py', + '1_rename.py', '1_tsne.py', '2_ap.py', '2_ClusterCorrection_Merge_3d.py', '2_ClusterCorrection_Merge.py', + '2_GetFeatures_4mer.py', '2_GetFeatures_5mer_p6mer.py', '2_GetFeatures_5mer.py', '2_GetFeatures_TimeSeries.py', + '3_GetMatrix_4mer.py', '3_GetMatrix.py', '4_AppendToCluster.py', '4_CorrectionAP.py', '5_CorrectionCovAP.py', + '6_GetScfByCluster.py', '7_AppendToCluster_spearman.py', 'AnnotateCluster.py', 'ColorMark.py', + 'ColorMark_ToDraw.py', 'ColorMark_to_Species.py', 'Evaluate.py', 'GetAliasName.py', 'getCentroid.py', + 'Get_Coverage.py', 'GetOutput.py', 'GetPreSen.py', 'GetPreSen_weight.py', 'GetThr.py', 'MyCC.py', 'N50.py', + 'ToDrawAP.py', 'ToDrawPDF.py', 'ToDraw.py', 'UCLUST_GetCOG.py', 'soap2sam.pl' +] + +fix_perl_shebang_for = ['bin/*.pl'] +fix_python_shebang_for = ['bin/*.py'] + + +files_to_copy = [ + # all Python and Perl file + (['*.py'], 'bin'), (['*.pl'], 'bin'), + + # https://www.bioinf.jku.at/software/apcluster/ + # just copy included version for now, never used in other eb. + # Depends on R, likely not worth the effort. + (['ap/apcluster'], 'bin'), (['ap/apclusterunix64.so'], 'lib'), + (['ap/apclusterdemo_linux.c', 'ap/apcluster.h'], 'include'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % f for f in local_bin_files], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = ['MyCC.py'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01_fix_paths.patch b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01_fix_paths.patch new file mode 100644 index 00000000000..f817560e949 --- /dev/null +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01_fix_paths.patch @@ -0,0 +1,33 @@ +As according to instalation ReadMe.txt: https://sourceforge.net/projects/sb2nhri/files/MyCC/ +Update paths manually :D + +author: Pavel Grochal (INUITS) +diff -rub --new-file Tools.orig/MyCC.py Tools/MyCC.py +--- Tools.orig/MyCC.py 2015-09-22 05:16:04.000000000 +0200 ++++ Tools/MyCC.py 2020-08-21 14:03:32.574421384 +0200 +@@ -3,12 +3,12 @@ + import commands + import os + import time +-fetchMGbin='/opt/fetchMG/bin' +-apcluster='/opt/ap' +-prodigal='/opt/prodigal.linux' +-uclust='/opt/uclustq1.2.22_i86linux64' +-cdhit='/opt/cd-hit/cd-hit' +-fetchMG='/opt/fetchMG/fetchMG.pl' ++fetchMGbin=os.path.expandvars('$EBROOTFETCHMG/bin') ++apcluster=os.path.expandvars('$EBROOTMYCC/bin/ap') ++prodigal=os.path.expandvars('$EBROOTPRODIGAL/bin/prodigal') ++uclust=os.path.expandvars('$EBROOTUCLUST/bin/uclust') ++cdhit=os.path.expandvars('$EBROOTCDMINHIT/bin/cd-hit') ++fetchMG=os.path.expandvars('$EBROOTFETCHMG/fetchMG.pl') + argv=sys.argv + mer=4 + p='20' +@@ -345,6 +345,3 @@ + print myTime + logfw.write(myTime+'\n') + os.chdir('../') +- +- +- diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb new file mode 100644 index 00000000000..5e31965ea2c --- /dev/null +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'tsne' +version = '0.1.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/danielfrg/tsne' +description = "Python library containing T-SNE algorithms." + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_fix_setup_py.patch'] +checksums = [ + 'fa6f29fc767ec269003986115aa40713bdd5ed5feb5fe974a1c3c33a5f2a925b', # tsne-0.1.8.tar.gz + '30311baf29935bf2aec8263b1405a81d5d69bebaab5bc15fa1c98565e2ec2ac3', # tsne-0.1.8_fix_setup_py.patch +] + +dependencies = [ + ('Python', '2.7.16'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('CBLAS', '20110120'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': False} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch new file mode 100644 index 00000000000..6572a9068d7 --- /dev/null +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch @@ -0,0 +1,24 @@ +Removed hardcoded flags + +Author: Pavel Grochal (INUITS) +diff -ru tsne-0.1.8.orig/setup.py tsne-0.1.8/setup.py +--- tsne-0.1.8.orig/setup.py 2018-06-06 19:22:12.000000000 +0200 ++++ tsne-0.1.8/setup.py 2020-09-15 12:42:01.908482715 +0200 +@@ -50,11 +50,11 @@ + language='c++')] + else: + extra_link_args = ['-lcblas'] +- dist = platform.linux_distribution(full_distribution_name=0)[0] +- redhat_dists = set(["redhat", "fedora", "centos"]) +- if dist in redhat_dists: +- extra_link_args = ['-lsatlas'] +- ++ # dist = platform.linux_distribution(full_distribution_name=0)[0] ++ # redhat_dists = set(["redhat", "fedora", "centos"]) ++ # if dist in redhat_dists: ++ # extra_link_args = ['-lsatlas'] ++ + # LINUX + ext_modules = [Extension(name='bh_sne', + sources=['tsne/bh_sne_src/quadtree.cpp', 'tsne/bh_sne_src/tsne.cpp', 'tsne/bh_sne.pyx'], + From 2e2ce1c9d9ee5c1bd8b5d400d11e52de96c5307d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 Sep 2020 16:39:31 +0200 Subject: [PATCH 165/698] Fix http addresses --- .../Automake/Automake-1.15.1-GCCcore-7.3.0.eb | 2 +- .../Automake/Automake-1.15.1-GCCcore-8.3.0.eb | 2 +- .../Autotools-20170619-GCCcore-7.3.0.eb | 24 ------------------- .../Autotools-20170619-GCCcore-8.3.0.eb | 24 ------------------- .../m/make/make-4.2.1-GCC-7.3.0-2.30.eb | 13 +++++++--- .../m/make/make-4.2.1-GCCcore-8.3.0.eb | 2 +- 6 files changed, 13 insertions(+), 54 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb delete mode 100644 easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb index 907b363772a..52707b6dc37 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-7.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = "1.15.1" -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" diff --git a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb index 3e9a40f622a..ace43febdba 100644 --- a/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/Automake/Automake-1.15.1-GCCcore-8.3.0.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'Automake' version = "1.15.1" -homepage = 'http://www.gnu.org/software/automake/automake.html' +homepage = 'https://www.gnu.org/software/automake/automake.html' description = "Automake: GNU Standards-compliant Makefile generator" diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb deleted file mode 100644 index 3be3052c893..00000000000 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-7.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20170619' # date of the most recent change - -homepage = 'http://autotools.io' - -description = """ - This bundle collect the standard GNU build tools: Autoconf, Automake - and libtool -""" - -toolchain = {'name': 'GCCcore', 'version': '7.3.0'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15.1'), # 20170619 - ('libtool', '2.4.6'), # 20150215 -] - -# Pure bundle -- no need to specify 'binutils' used when building GCCcore -# toolchain as build dependency - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb deleted file mode 100644 index 2290af6b865..00000000000 --- a/easybuild/easyconfigs/a/Autotools/Autotools-20170619-GCCcore-8.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'Bundle' - -name = 'Autotools' -version = '20170619' # date of the most recent change - -homepage = 'http://autotools.io' - -description = """ - This bundle collect the standard GNU build tools: Autoconf, Automake - and libtool -""" - -toolchain = {'name': 'GCCcore', 'version': '8.3.0'} - -dependencies = [ - ('Autoconf', '2.69'), # 20120424 - ('Automake', '1.15.1'), # 20170619 - ('libtool', '2.4.6'), # 20150215 -] - -# Pure bundle -- no need to specify 'binutils' used when building GCCcore -# toolchain as build dependency - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb index ccc8a7c0e98..0e845ec92b8 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCC-7.3.0-2.30.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'make' version = '4.2.1' -homepage = 'http://www.gnu.org/software/make/make.html' +homepage = 'https://www.gnu.org/software/make/make.html' description = "GNU version of make utility" toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} @@ -29,13 +29,20 @@ checksums = [ builddependencies = [ # needs specifically aclocal 1.15 - ('Autotools', '20170619'), + ('Automake', '1.15.1'), ('pkg-config', '0.29.2'), ] +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + sanity_check_paths = { - 'files': ['bin/make'], + 'files': ['bin/gmake', 'bin/make'], 'dirs': [] } +sanity_check_commands = [ + "gmake --help", + "make --help", +] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb index 851d90c79f4..d8927406731 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb @@ -29,7 +29,7 @@ checksums = [ builddependencies = [ # needs specifically aclocal 1.15 - ('Autotools', '20170619'), + ('Automake', '1.15.1'), ('binutils', '2.32'), ('pkg-config', '0.29.2'), ] From 9244bb6581f9a8faaf6cfa2d60febce5a24e5be0 Mon Sep 17 00:00:00 2001 From: Ben Date: Wed, 16 Sep 2020 10:54:56 -0400 Subject: [PATCH 166/698] LIBS change to fix Ghostscript ZLIB error Ghostscript was not compiling due to failing on: `libpng/1.6.36-GCCcore-8.2.0/lib/libpng16.so.16: undefined reference to inflateValidate@ZLIB_1.2.9'` needed to add `-L$EBROOTZLIB/lib` to the `preconfigopts += 'export LIBS="$LIBS -lz" && '` line --- .../easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb index 9db716ad2c3..1dbe0fed864 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.27-GCCcore-8.2.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" From c71699a195ac1008db4aa4b8f667665511e13d89 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 Sep 2020 17:39:34 +0200 Subject: [PATCH 167/698] fix festival source versioning and add sanity check commands --- .../e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb | 2 ++ .../f/festival/festival-2.5.0-GCCcore-9.3.0.eb | 16 +++++++++++++--- .../MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb | 2 ++ 3 files changed, 17 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb index 3f0ac409613..86a42b12742 100644 --- a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.50-gompi-2020a.eb @@ -45,4 +45,6 @@ sanity_check_paths = { 'dirs': ['lib/pkgconfig'] } +sanity_check_commands = ['%sspeak%s --version' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb index 4c93a96ff12..71f5df63488 100644 --- a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-9.3.0.eb @@ -19,9 +19,11 @@ source_urls = [ 'http://festvox.org/packed/festival/%(version_major_minor)s', 'http://festvox.org/packed/festival/%(version_major_minor)s/voices', ] -sources = [] +sources = [{ + 'filename': '%(name)s-%(version)s-release.tar.gz', + 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', +}] local_sources = [ - '%(name)s-%(version)s-release.tar.gz', 'festlex_CMU.tar.gz', 'festlex_OALD.tar.gz', 'festlex_POSLEX.tar.gz', @@ -60,7 +62,13 @@ local_sources = [ 'festvox_rablpc16k.tar.gz', ] for local_x in local_sources: - sources.append({'filename': local_x, 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1'}) + local_newfilename = local_x.split('.') + local_newfilename[0] = local_newfilename[0] + '-%(version)s' + sources.append({ + 'download_filename': local_x, + 'filename': '.'.join(local_newfilename), + 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', + }) patches = ['%(name)s-%(version)s_speech_tools.patch'] checksums = [ @@ -126,4 +134,6 @@ sanity_check_paths = { 'dirs': ['lib/voices', 'lib/dicts/cmu', 'lib/dicts/oald'] } +sanity_check_commands = ['festival%s --version' % x for x in ['', '_client']] + moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb index 0b4d4106cdc..e21748be660 100644 --- a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-9.3.0-voices-20200330.eb @@ -49,4 +49,6 @@ sanity_check_paths = { 'dirs': ['share/mbrola'] } +sanity_check_commands = ['mbrola -h'] + moduleclass = 'tools' From 061cc233165f7dae88c65e51d003b0d1f93386e4 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 16 Sep 2020 18:46:02 +0000 Subject: [PATCH 168/698] Added CUDA 11.0.2 and related recipes Like #10935 this introduces a new CUDAcore easyconfig to share CUDA between use of GCC and Intel compilers, but unlike #10935 this uses a versionsuffix for UCX+CUDA so it does not need any framework changes or MODULEPATH adjustments. --- .../c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb | 17 +++++ .../c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb | 17 +++++ .../easyconfigs/c/CUDAcore/CUDAcore-11.0.2.eb | 25 ++++++++ .../easyconfigs/f/fosscuda/fosscuda-2020a.eb | 29 +++++++++ .../easyconfigs/g/gcccuda/gcccuda-2020a.eb | 19 ++++++ .../easyconfigs/g/gompic/gompic-2020a.eb | 21 +++++++ .../i/iccifortcuda/iccifortcuda-2020a.eb | 18 ++++++ .../i/intelcuda/intelcuda-2020a.eb | 20 ++++++ .../o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb | 22 +++++++ .../OpenMPI-4.0.3-iccifortcuda-2020a.eb | 22 +++++++ .../UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 62 +++++++++++++++++++ 11 files changed, 272 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb create mode 100644 easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.0.2.eb create mode 100644 easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb create mode 100644 easybuild/easyconfigs/g/gcccuda/gcccuda-2020a.eb create mode 100644 easybuild/easyconfigs/g/gompic/gompic-2020a.eb create mode 100644 easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020a.eb create mode 100644 easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb new file mode 100644 index 00000000000..c193a9b0bcd --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-GCC-9.3.0.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' +name = 'CUDA' +version = '11.0.2' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +dependencies = [('CUDAcore', '11.0.2', '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb new file mode 100644 index 00000000000..7f77cc256bf --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.0.2-iccifort-2020.1.217.eb @@ -0,0 +1,17 @@ +easyblock = 'Bundle' +name = 'CUDA' +version = '11.0.2' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = {'name': 'iccifort', 'version': '2020.1.217'} + +dependencies = [('CUDAcore', '11.0.2', '', True)] + +altroot = 'CUDAcore' + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.0.2.eb b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.0.2.eb new file mode 100644 index 00000000000..cf56d9a5211 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAcore/CUDAcore-11.0.2.eb @@ -0,0 +1,25 @@ +easyblock = "EB_CUDA" +name = 'CUDAcore' +version = '11.0.2' +local_nv_version = '450.51.05' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [ + { + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '48247ada0e3f106051029ae8f70fbd0c238040f58b0880e55026374a959a69c1', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'db06d0f3fbf6f7aa1f106fc921ad1c86162210a26e8cb65b171c5240a3bf75da', + } +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb new file mode 100644 index 00000000000..921ff09c9df --- /dev/null +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb @@ -0,0 +1,29 @@ +easyblock = 'Toolchain' + +name = 'fosscuda' +version = '2020a' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '9.3.0' + +# toolchain used to build fosscuda dependencies +local_comp_mpi_tc = ('gompic', version) + +# compiler toolchain dependencies +# We need GCC, CUDA and OpenMPI as explicit dependencies instead of +# gompic toolchain because of toolchain preperation functions. +dependencies = [ + ('GCC', local_gccver), # part of gompic + ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gompic + ('OpenMPI', '4.0.3', '', ('gcccuda', version)), # part of gompic + ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gcccuda/gcccuda-2020a.eb b/easybuild/easyconfigs/g/gcccuda/gcccuda-2020a.eb new file mode 100644 index 00000000000..c8488c1a27a --- /dev/null +++ b/easybuild/easyconfigs/g/gcccuda/gcccuda-2020a.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gcccuda' +version = '2020a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.""" + +toolchain = SYSTEM + +local_gcc_version = '9.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gcc_version), + ('CUDA', '11.0.2', '', ('GCC', local_gcc_version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompic/gompic-2020a.eb b/easybuild/easyconfigs/g/gompic/gompic-2020a.eb new file mode 100644 index 00000000000..a44a4fa4cb2 --- /dev/null +++ b/easybuild/easyconfigs/g/gompic/gompic-2020a.eb @@ -0,0 +1,21 @@ +easyblock = "Toolchain" + +name = 'gompic' +version = '2020a' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, + including OpenMPI for MPI support with CUDA features enabled.""" + +toolchain = SYSTEM + +local_gccver = '9.3.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # part of gcccuda + ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gcccuda + ('OpenMPI', '4.0.3', '', ('gcccuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020a.eb new file mode 100644 index 00000000000..1239af68d39 --- /dev/null +++ b/easybuild/easyconfigs/i/iccifortcuda/iccifortcuda-2020a.eb @@ -0,0 +1,18 @@ +easyblock = 'Toolchain' + +name = 'iccifortcuda' +version = '2020a' + +homepage = '(none)' +description = "Intel C, C++ & Fortran compilers with CUDA toolkit" + +toolchain = SYSTEM + +local_compver = '2020.1.217' + +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.0.2', '', ('iccifort', local_compver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb new file mode 100644 index 00000000000..49ffa18e384 --- /dev/null +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'intelcuda' +version = '2020a' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = SYSTEM + +local_compver = '2020.1.217' +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.0.2', '', ('iccifort', local_compver)), + ('impi', '2019.7.217', '', ('iccifortcuda', version)), + ('imkl', local_compver, '', ('iimpic', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb new file mode 100644 index 00000000000..02cdab983ee --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb @@ -0,0 +1,22 @@ +name = 'OpenMPI' +version = '4.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'gcccuda', 'version': '2020a'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('UCX', '1.8.0', '-CUDA-11.0.2'), +] + +# to enable SLURM integration (site-specific) +# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb new file mode 100644 index 00000000000..4f474bba1a3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb @@ -0,0 +1,22 @@ +name = 'OpenMPI' +version = '4.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'iccifortcuda', 'version': '2020a'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('UCX', '1.8.0', '-CUDA-11.0.2'), +] + +# to enable SLURM integration (site-specific) +# configopts = '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb new file mode 100644 index 00000000000..6f7472afaf3 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -0,0 +1,62 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.8.0' +local_cudaversion = 11.0.2 +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.7.0_binutils_2.34_api_fix.patch', + 'UCX-1.8.0_fix-undefined-symbol.patch', +] +checksums = [ + 'e400f7aa5354971c8f5ac6b881dc2846143851df868088c37d432c076445628d', # ucx-1.8.0.tar.gz + 'c09ebe4d734d520ae23f56d95ba0b91e464a42ccbaf435675424515ebd3fa3a9', # UCX-1.7.0_binutils_2.34_api_fix.patch + 'eb757242ab3eecd8a851f329cb4baf3c64d46788ab61675f29ab4cc6a0274a45', # UCX-1.8.0_fix-undefined-symbol.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +dependencies = [ + ('numactl', '2.0.13'), + ('CUDAcore', local_cudaversion), +] + +# CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles +# unset LIBS from EB toolchain to avoid unconditional linking to libcudart: +# it only needs to be linked by the CUDA run-time plugins +preconfigopts = 'autoreconf && unset CUDA_CFLAGS && unset LIBS && ' +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' +configopts += '--with-cuda ' + +prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 59a151b25f437e92d7f9308adea7ee823c924bda Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Sep 2020 21:00:08 +0200 Subject: [PATCH 169/698] {vis}[GCC/9.3.0] FLTK v1.3.5 --- .../f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb | 41 +++++++++++++++++++ .../x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb | 32 +++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb new file mode 100644 index 00000000000..a68c6268969 --- /dev/null +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb @@ -0,0 +1,41 @@ +# +# author: Dina Mahmoud Ibrahim ( Cairo University ) +# +easyblock = 'ConfigureMake' + +name = 'FLTK' +version = '1.3.5' + +homepage = 'https://www.fltk.org' +description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, + and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL + and its built-in GLUT emulation.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] +sources = ['%(namelower)s-%(version)s-source.tar.gz'] +patches = ['FLTK-1.3.4_fix-LDFLAGS.patch'] +checksums = [ + '8729b2a055f38c1636ba20f749de0853384c1d3e9d1a6b8d4d1305143e115702', # fltk-1.3.5-source.tar.gz + 'b9d39f6dce92fdb34a149f686a5d56e72912f94fd09c4958f3bb12770603da7d', # FLTK-1.3.4_fix-LDFLAGS.patch +] + +configopts = '--enable-shared --enable-threads --enable-xft' + +dependencies = [ + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('xprop', '1.2.4'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/fltk-config', 'bin/fluid', 'lib/libfltk.a', 'lib/libfltk.%s' % SHLIB_EXT], + 'dirs': ['lib'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9a54190e8dc --- /dev/null +++ b/easybuild/easyconfigs/x/xprop/xprop-1.2.4-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'xprop' +version = '1.2.4' + +homepage = "https://www.x.org/wiki/" +description = """The xprop utility is for displaying window and font properties in an X server. + One window or font is selected using the command line arguments or possibly + in the case of a window, by clicking on the desired window. A list of + properties is then given, possibly with formatting information.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftp.x.org/archive/individual/app/'] +sources = [SOURCE_TAR_GZ] +checksums = ['dddb6e208ffa515e68f001c22077a465f1365a4bcf91d9b37f336a6c0d15400d'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20200222'), +] + +sanity_check_paths = { + 'files': ['bin/xprop'], + 'dirs': [], +} + +moduleclass = 'vis' From f090aa8be0a979b3a379cb8f9be2e4abf4f62640 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 16 Sep 2020 21:00:14 +0200 Subject: [PATCH 170/698] add sanity check commands for speech_tools --- .../speech_tools-2.5.0-GCCcore-9.3.0.eb | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb index b0dd36dd5f0..6666e62d45a 100644 --- a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-9.3.0.eb @@ -45,15 +45,19 @@ buildininstalldir = True maxparallel = 1 +local_sanity = [ + 'align', 'bcat', 'ch_lab', 'ch_track', 'ch_utt', 'ch_wave', 'design_filter', 'est_program', 'na_play', + 'na_record', 'ngram_build', 'ols', 'pda', 'pitchmark', 'raw_to_xgraph', 'resynth', 'scfg_make', 'scfg_parse', + 'scfg_train', 'sig2fv', 'sigfilter', 'siod', 'spectgen', 'tex_to_images', 'tilt_analysis', 'tilt_synthesis', + 'viterbi', 'wagon', 'wfst_build', 'wfst_run', 'wfst_train', 'xml_parser', +] + sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['align', 'bcat', 'ch_lab', 'ch_track', 'ch_utt', 'ch_wave', 'design_filter', - 'est_program', 'Makefile', 'na_play', 'na_record', 'ngram_build', 'ols', 'pda', - 'pitchmark', 'pm', 'raw_to_xgraph', 'resynth', 'scfg_make', 'scfg_parse', - 'scfg_train', 'sig2fv', 'sigfilter', 'siod', 'spectgen', 'tex_to_images', - 'tilt_analysis', 'tilt_synthesis', 'viterbi', 'wagon', 'wfst_build', 'wfst_run', - 'wfst_train', 'xml_parser']] + + 'files': ['bin/%s' % x for x in local_sanity + ['Makefile', 'pm']] + ['lib/lib%s.a' % x for x in ['estbase', 'estools', 'eststring']], 'dirs': [] } +sanity_check_commands = ['%s -h' % x for x in local_sanity] + moduleclass = 'tools' From 10a64ee9eb80139e91a4697c83352a70b15b81ba Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 16 Sep 2020 19:01:50 +0000 Subject: [PATCH 171/698] UCX: quote local_cudaversion --- .../easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index 6f7472afaf3..04c76a0e4da 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -4,7 +4,7 @@ easyblock = 'ConfigureMake' name = 'UCX' version = '1.8.0' -local_cudaversion = 11.0.2 +local_cudaversion = '11.0.2' versionsuffix = '-CUDA-%s' % local_cudaversion homepage = 'http://www.openucx.org/' From dc9bd443bef01a9be21db82c84f168175fba6d8d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 16 Sep 2020 19:22:03 +0000 Subject: [PATCH 172/698] Remove fosscuda/intelcuda for now to focus on basics. --- .../easyconfigs/f/fosscuda/fosscuda-2020a.eb | 29 ------------------- .../i/intelcuda/intelcuda-2020a.eb | 20 ------------- 2 files changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb delete mode 100644 easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb deleted file mode 100644 index 921ff09c9df..00000000000 --- a/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'Toolchain' - -name = 'fosscuda' -version = '2020a' - -homepage = '(none)' -description = """GCC based compiler toolchain __with CUDA support__, and including - OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" - -toolchain = SYSTEM - -local_gccver = '9.3.0' - -# toolchain used to build fosscuda dependencies -local_comp_mpi_tc = ('gompic', version) - -# compiler toolchain dependencies -# We need GCC, CUDA and OpenMPI as explicit dependencies instead of -# gompic toolchain because of toolchain preperation functions. -dependencies = [ - ('GCC', local_gccver), # part of gompic - ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gompic - ('OpenMPI', '4.0.3', '', ('gcccuda', version)), # part of gompic - ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), - ('FFTW', '3.3.8', '', local_comp_mpi_tc), - ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), -] - -moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb deleted file mode 100644 index 49ffa18e384..00000000000 --- a/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb +++ /dev/null @@ -1,20 +0,0 @@ -easyblock = 'Toolchain' - -name = 'intelcuda' -version = '2020a' - -homepage = '(none)' -description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, - Intel MPI & Intel MKL, with CUDA toolkit""" - -toolchain = SYSTEM - -local_compver = '2020.1.217' -dependencies = [ - ('iccifort', local_compver), - ('CUDA', '11.0.2', '', ('iccifort', local_compver)), - ('impi', '2019.7.217', '', ('iccifortcuda', version)), - ('imkl', local_compver, '', ('iimpic', version)), -] - -moduleclass = 'toolchain' From 0eb804bfde04758635f7ff760d12919b942029ba Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Wed, 16 Sep 2020 19:39:53 +0000 Subject: [PATCH 173/698] UCX: make sure CUDAcore comes from SYSTEM. --- .../easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index 04c76a0e4da..38be4f62623 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -38,7 +38,7 @@ osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] dependencies = [ ('numactl', '2.0.13'), - ('CUDAcore', local_cudaversion), + ('CUDAcore', local_cudaversion, '', True), ] # CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles From ad710a48ab54c357d5411d26b6e857cc744c91ee Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 09:47:26 +0200 Subject: [PATCH 174/698] {bio}[fosscuda/2019a] Taiyaki v5.1.0-20200617, Biopython v1.74 w/ Python 3.7.2 --- .../Biopython-1.74-fosscuda-2019a.eb | 56 +++++++++++++++ ....0-20200617-fosscuda-2019a-Python-3.7.2.eb | 68 +++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb create mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb new file mode 100644 index 00000000000..4fe918a3de7 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb @@ -0,0 +1,56 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , +# Thekla Loizou , +# George Tsouloupas +# License:: MIT/GPL +# +# Updated: Pavel Grochal (INUITS) +## +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.74' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0'] + +multi_deps = {'Python': ['3.7.2', '2.7.15']} + +dependencies = [ + ('SciPy-bundle', '2019.03'), # for numpy +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +sanity_pip_check = True + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..1665d07012c --- /dev/null +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'Taiyaki' +local_commit = '589863d' +version = '5.1.0-20200617' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/taiyaki' +description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." + +toolchain = {'name': 'fosscuda', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('h5py', '2.9.0'), + ('Biopython', '1.74'), + ('Pysam', '0.15.2'), + ('matplotlib', '3.0.3', versionsuffix), + # this version of Taiyaki is not compatible with more recent version of PyTorch! + # see hardcoded version requirement for 'torch' in setup.py + ('PyTorch', '1.2.0', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.12.0', { + 'checksums': ['5c7d6707ad3112b67f564abaf1845d3c02ecc7174c2d990d539f45c37e98ad35'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.1.6', { + 'checksums': ['586b819bd48d38f446b33dac4a34f33c1004beeef0baf16ae1253d5fa360b951'], + }), + (name, version, { + 'source_tmpl': '%s.tar.gz' % local_commit, + 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], + 'checksums': ['b7cae83cf3b84844f1eceab909a66f878e5c0eeaa4e03ae0b67a3206b7a5dec2'], + }), +] + +postinstallcmds = ["cp %(builddir)s/Taiyaki/taiyaki-*/misc -a %(installdir)s"] + +fix_python_shebang_for = ['bin/*.py', 'misc/*.py'] + +sanity_check_paths = { + 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py', 'misc/upgrade_model.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "basecall.py --help", + "upgrade_model.py --help", +] + +sanity_pip_check = True + +modextrapaths = {'PATH': 'misc'} + +moduleclass = 'bio' From 968f2fef84a18d88020911cd8d44a7d981181937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 11:52:00 +0200 Subject: [PATCH 175/698] stick to Biopython 1.73 as dep for Taiyaki with fosscuda/2019a + add PyTorch version in versionsuffix --- ...17-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb} | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) rename easybuild/easyconfigs/t/Taiyaki/{Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb => Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb} (83%) diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb similarity index 83% rename from easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb rename to easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb index 1665d07012c..1f2fbec877a 100644 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-fosscuda-2019a-Python-3.7.2-PyTorch-1.2.0.eb @@ -3,7 +3,10 @@ easyblock = 'PythonBundle' name = 'Taiyaki' local_commit = '589863d' version = '5.1.0-20200617' -versionsuffix = '-Python-%(pyver)s' +# this version of Taiyaki is not compatible with more recent version of PyTorch! +# see hardcoded version requirement for 'torch' in setup.py +local_pytorch_ver = '1.2.0' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver homepage = 'https://github.com/nanoporetech/taiyaki' description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." @@ -14,12 +17,10 @@ dependencies = [ ('Python', '3.7.2'), ('SciPy-bundle', '2019.03'), ('h5py', '2.9.0'), - ('Biopython', '1.74'), + ('Biopython', '1.73'), ('Pysam', '0.15.2'), - ('matplotlib', '3.0.3', versionsuffix), - # this version of Taiyaki is not compatible with more recent version of PyTorch! - # see hardcoded version requirement for 'torch' in setup.py - ('PyTorch', '1.2.0', versionsuffix), + ('matplotlib', '3.0.3', '-Python-%(pyver)s'), + ('PyTorch', local_pytorch_ver, '-Python-%(pyver)s'), ] use_pip = True From 1a1053616ec43ca396e95ef49ef518c44236c1ed Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 12:02:26 +0200 Subject: [PATCH 176/698] remove unused Biopython easyconfig --- .../Biopython-1.74-fosscuda-2019a.eb | 56 ------------------- 1 file changed, 56 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb deleted file mode 100644 index 4fe918a3de7..00000000000 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.74-fosscuda-2019a.eb +++ /dev/null @@ -1,56 +0,0 @@ -## -# EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2012-2013 The Cyprus Institute -# Authors:: Andreas Panteli , -# Thekla Loizou , -# George Tsouloupas -# License:: MIT/GPL -# -# Updated: Pavel Grochal (INUITS) -## -easyblock = 'PythonPackage' - -name = 'Biopython' -version = '1.74' - -homepage = 'https://www.biopython.org' -description = """Biopython is a set of freely available tools for biological - computation written in Python by an international team of developers. It is - a distributed collaborative effort to develop Python libraries and - applications which address the needs of current and future work in - bioinformatics. """ - -toolchain = {'name': 'fosscuda', 'version': '2019a'} - -source_urls = ['https://biopython.org/DIST'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['25152c1be2c9205bf80901fc49adf2c2efff49f0dddbcf6e6b2ce31dfa6590c0'] - -multi_deps = {'Python': ['3.7.2', '2.7.15']} - -dependencies = [ - ('SciPy-bundle', '2019.03'), # for numpy -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -# Run only tests that don't require internet connection -runtest = 'python setup.py test --offline' - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', - 'lib/python%(pyshortver)s/site-packages/BioSQL'] -} - -# extra check to ensure numpy dependency is available -sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] - -sanity_pip_check = True - -options = {'modulename': 'Bio'} - -moduleclass = 'bio' From 7fcecfedbcf7cef20dc1d348d0de08bf6185f872 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 12:03:58 +0200 Subject: [PATCH 177/698] add easyconfig for Taiyaki with foss/2019a --- ...7-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb new file mode 100644 index 00000000000..e5752ccc2d5 --- /dev/null +++ b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.1.0-20200617-foss-2019a-Python-3.7.2-PyTorch-1.2.0.eb @@ -0,0 +1,69 @@ +easyblock = 'PythonBundle' + +name = 'Taiyaki' +local_commit = '589863d' +version = '5.1.0-20200617' +# this version of Taiyaki is not compatible with more recent version of PyTorch! +# see hardcoded version requirement for 'torch' in setup.py +local_pytorch_ver = '1.2.0' +versionsuffix = '-Python-%%(pyver)s-PyTorch-%s' % local_pytorch_ver + +homepage = 'https://github.com/nanoporetech/taiyaki' +description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." + +toolchain = {'name': 'foss', 'version': '2019a'} + +dependencies = [ + ('Python', '3.7.2'), + ('SciPy-bundle', '2019.03'), + ('h5py', '2.9.0'), + ('Biopython', '1.73'), + ('Pysam', '0.15.2'), + ('matplotlib', '3.0.3', '-Python-%(pyver)s'), + ('PyTorch', local_pytorch_ver, '-Python-%(pyver)s'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('patsy', '0.5.1', { + 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], + }), + ('statsmodels', '0.12.0', { + 'checksums': ['5c7d6707ad3112b67f564abaf1845d3c02ecc7174c2d990d539f45c37e98ad35'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.1.6', { + 'checksums': ['586b819bd48d38f446b33dac4a34f33c1004beeef0baf16ae1253d5fa360b951'], + }), + (name, version, { + 'source_tmpl': '%s.tar.gz' % local_commit, + 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], + 'checksums': ['b7cae83cf3b84844f1eceab909a66f878e5c0eeaa4e03ae0b67a3206b7a5dec2'], + }), +] + +postinstallcmds = ["cp %(builddir)s/Taiyaki/taiyaki-*/misc -a %(installdir)s"] + +fix_python_shebang_for = ['bin/*.py', 'misc/*.py'] + +sanity_check_paths = { + 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py', 'misc/upgrade_model.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "basecall.py --help", + "upgrade_model.py --help", +] + +sanity_pip_check = True + +modextrapaths = {'PATH': 'misc'} + +moduleclass = 'bio' From 731e972a0b8d3e7968bea939550aff4bba2ad566 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 17 Sep 2020 18:41:48 +0800 Subject: [PATCH 178/698] adding easyconfigs: R-3.6.2-intel-2019b.eb --- .../easyconfigs/r/R/R-3.6.2-intel-2019b.eb | 2459 +++++++++++++++++ 1 file changed, 2459 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb new file mode 100644 index 00000000000..c8ee1e0d04a --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb @@ -0,0 +1,2459 @@ +name = 'R' +version = '3.6.2' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'intel', 'version': '2019b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix_long_dbl_on_ppc.patch', +] +checksums = [ + 'bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954', # R-3.6.2.tar.gz + '833b80f9a62751eae9cfbad6116542acf932e9c6511235145be32264aacdce69', # R-3.6.2_fix_long_dbl_on_ppc.patch +] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('X11', '20190717'), + ('Mesa', '19.1.7'), + ('libGLU', '9.0.1'), + ('cairo', '1.16.0'), + ('libreadline', '8.0'), + ('ncurses', '6.1'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.4'), + ('zlib', '1.2.11'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('libpng', '1.6.37'), # for plotting in R + ('libjpeg-turbo', '2.0.3'), # for plottting in R + ('LibTIFF', '4.0.10'), + ('Java', '11', '', True), + ('Tk', '8.6.9'), # for tcltk + ('cURL', '7.66.0'), # for RCurl + ('libxml2', '2.9.9'), # for XML + ('GMP', '6.1.2'), # for igraph + ('NLopt', '2.6.1'), # for nloptr + ('FFTW', '3.3.8'), # for fftw + ('libsndfile', '1.0.28'), # for seewave + ('ICU', '64.2'), # for rJava & gdsfmt + ('HDF5', '1.10.5'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.6'), # for RcppGSL + ('ImageMagick', '7.0.9-5'), # for animation + # OS dependency should be preferred if the os version is more recent then + # this version, it's nice to have an up to date openssl for security + # reasons + # ('OpenSSL', '1.1.1b'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 16 December 2019 +exts_list = [ + 'base', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'splines', + 'stats', + 'stats4', + 'tools', + 'utils', + ('Rmpi', '0.6-9', { + 'patches': ['Rmpi-0.6-5_impi5.patch'], + 'checksums': [ + 'b2e1eac3e56f6b26c7ce744b29d8994ab6507ac88df64ebbb5af439414651ee6', # Rmpi_0.6-9.tar.gz + 'f753f0b6434295be70fe29d36edb2047c091e465b7ff0cab56b93d55883c8dd3', # Rmpi-0.6-5_impi5.patch + ], + }), + ('abind', '1.4-5', { + 'checksums': ['3a3ace5afbcb86e56889efcebf3bf5c3bb042a282ba7cc4412d450bb246a3f2c'], + }), + ('magic', '1.5-9', { + 'checksums': ['fa1d5ef2d39e880f262d31b77006a2a7e76ea38e306aae4356e682b90d6cd56a'], + }), + ('Rcpp', '1.0.3', { + 'checksums': ['2b3500dd3aca16f7b3cb5442625e76dcf4f7c974b4249d33041e9184a5ff030e'], + }), + ('RcppProgress', '0.4.1', { + 'checksums': ['11764105922f763d4c75c502599ec7dcc2fd629a029964caf53f98b41d0c607a'], + }), + ('lpSolve', '5.6.13.3', { + 'checksums': ['e64165428c40d730f7686d233c22936bf4b3b91a618a600bdf87acaa905f5ff5'], + }), + ('linprog', '0.9-2', { + 'checksums': ['8937b2e30692e38de1713f1513b78f505f73da6f5b4a576d151ad60bac2221ce'], + }), + ('geometry', '0.4.5', { + 'checksums': ['8fedd17c64468721d398e3c17a39706321ab71098b29f5e8d8039dd115a220d8'], + }), + ('bit', '1.1-14', { + 'checksums': ['5cbaace1fb643a665a6ca69b90f7a6d624270de82420ca7a44f306753fcef254'], + }), + ('filehash', '2.4-2', { + 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], + }), + ('ff', '2.2-14', { + 'checksums': ['1c6307847275b1b8ad9e2ffdce3f4df3c9d955dc2e8a45e3fd7bfd2b0926e2f0'], + }), + ('bnlearn', '4.5', { + 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], + }), + ('bootstrap', '2019.6', { + 'checksums': ['5252fdfeb944cf1fae35016d35f9333b1bd1fc8c6d4a14e33901160e21968694'], + }), + ('combinat', '0.0-8', { + 'checksums': ['1513cf6b6ed74865bfdd9f8ca58feae12b62f38965d1a32c6130bef810ca30c1'], + }), + ('deal', '1.2-39', { + 'checksums': ['a349db8f1c86cbd8315c068da49314ce9eb585dbb50d2e5ff09300506bd8806b'], + }), + ('fdrtool', '1.2.15', { + 'checksums': ['65f964aa768d0703ceb7a199adc5e79ca79a6d29d7bc053a262eb533697686c0'], + }), + ('formatR', '1.7', { + 'checksums': ['a366621b3ff5f8e86a499b6f87858ad47eefdace138341b1377ecc307a5e5ddb'], + }), + ('gtools', '3.8.1', { + 'checksums': ['051484459bd8ad1b03425b8843d24f6828fea18f7357cfa1c192198cc3f4ba38'], + }), + ('gdata', '2.18.0', { + 'checksums': ['4b287f59f5bbf5fcbf18db16477852faac4a605b10c5284c46b93fa6e9918d7f'], + }), + ('GSA', '1.03.1', { + 'checksums': ['e192d4383f53680dbd556223ea5f8cad6bae62a80a337ba5fd8d05a8aee6a917'], + }), + ('highr', '0.8', { + 'checksums': ['4bd01fba995f68c947a99bdf9aca15327a5320151e10bd0326fad50a6d8bc657'], + }), + ('infotheo', '1.2.0', { + 'checksums': ['9b47ebc3db5708c88dc014b4ffec6734053a9c255a9241fcede30fec3e63aaa3'], + }), + ('lars', '1.2', { + 'checksums': ['64745b568f20b2cfdae3dad02fba92ebf78ffee466a71aaaafd4f48c3921922e'], + }), + ('lazy', '1.2-16', { + 'checksums': ['c796c8b987ed1bd9dfddd593e17312ed681fc4fa3a1ecfe51da2def0ac1e50df'], + }), + ('kernlab', '0.9-29', { + 'checksums': ['c3da693a0041dd34f869e7b63a8d8cf7d4bc588ac601bcdddcf7d44f68b3106f'], + }), + ('mime', '0.7', { + 'checksums': ['11083ee44c92569aadbb9baf60a2e079ab7a721c849b74d102694975cc8d778b'], + }), + ('xfun', '0.11', { + 'checksums': ['3cc24b5a67a11204255b71e5fadbb4c303dfb34a32e79c95b787aa8997e1cc36'], + }), + ('markdown', '1.1', { + 'checksums': ['8d8cd47472a37362e615dbb8865c3780d7b7db694d59050e19312f126e5efc1b'], + }), + ('mlbench', '2.1-1', { + 'checksums': ['748141d56531a39dc4d37cf0a5165a40b653a04c507e916854053ed77119e0e6'], + }), + ('NLP', '0.2-0', { + 'checksums': ['fc64c80124c4e53b20f92b60c68e2fd33ee189653d0ceea410c32dd66d9e7075'], + }), + ('mclust', '5.4.5', { + 'checksums': ['75f2963082669485953e4306ffa93db98335ee6afdc1318b95d605d56cb30a72'], + }), + ('RANN', '2.6.1', { + 'checksums': ['b299c3dfb7be17aa41e66eff5674fddd2992fb6dd3b10bc59ffbf0c401697182'], + }), + ('rmeta', '3.0', { + 'checksums': ['b9f9d405935cffcd7a5697ff13b033f9725de45f4dc7b059fd68a7536eb76b6e'], + }), + ('segmented', '1.1-0', { + 'checksums': ['d081d0efaec708d717bf1248ba3df099876389c22796aad676655efb706e9d19'], + }), + ('som', '0.3-5.1', { + 'checksums': ['a6f4c0e5b36656b7a8ea144b057e3d7642a8b71972da387a7133f3dd65507fb9'], + }), + ('SuppDists', '1.1-9.4', { + 'checksums': ['fcb571150af66b95dcf0627298c54f7813671d60521a00ed157f63fc2247ddb9'], + }), + ('stabledist', '0.7-1', { + 'checksums': ['06c5704d3a3c179fa389675c537c39a006867bc6e4f23dd7e406476ed2c88a69'], + }), + ('survivalROC', '1.0.3', { + 'checksums': ['1449e7038e048e6ad4d3f7767983c0873c9c7a7637ffa03a4cc7f0e25c31cd72'], + }), + ('pspline', '1.0-18', { + 'checksums': ['f71cf293bd5462e510ac5ad16c4a96eda18891a0bfa6447dd881c65845e19ac7'], + }), + ('timeDate', '3043.102', { + 'checksums': ['377cba03cddab8c6992e31d0683c1db3a73afa9834eee3e95b3b0723f02d7473'], + }), + ('longmemo', '1.1-1', { + 'checksums': ['0dd88e84a8376141d117bba39fe44f7d3c29d46fc103557fe98357f06e17d657'], + }), + ('ADGofTest', '0.3', { + 'checksums': ['9cd9313954f6ecd82480d373f6c5371ca84ab33e3f5c39d972d35cfcf1096846'], + }), + ('MASS', '7.3-51.4', { + 'checksums': [('9911d546a8d29dc906b46cb53ef8aad76d23566f4fc3b52778a1201f8a9b2c74', + '844270a2541eaed420871dfb61d681aa67ee57126645fb6b144b436c25698eeb')], + }), + ('ade4', '1.7-13', { + 'checksums': ['f5d0a7356ae63f82d3adb481a39007e7b0d70211b8724aa686af0c89c994e99b'], + }), + ('AlgDesign', '1.2.0', { + 'checksums': ['ff86c9e19505770520e7614970ad19c698664d08001ce888b8603e44c2a3b52a'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('BH', '1.69.0-1', { + 'checksums': ['a0fd4364b7e368f09c56dec030823f52c16da0787580af7e4615eddeb99baca2'], + }), + ('brew', '1.0-6', { + 'checksums': ['d70d1a9a01cf4a923b4f11e4374ffd887ad3ff964f35c6f9dc0f29c8d657f0ed'], + }), + ('Brobdingnag', '1.2-6', { + 'checksums': ['19eccaed830ce9d93b70642f6f126ac66722a98bbd48586899cc613dd9966ad4'], + }), + ('corpcor', '1.6.9', { + 'checksums': ['2e4fabd1d3936fecea67fa365233590147ca50bb45cf80efb53a10345a8a23c2'], + }), + ('longitudinal', '1.1.12', { + 'checksums': ['d4f894c38373ba105b1bdc89e3e7c1b215838e2fb6b4470b9f23768b84e603b5'], + }), + ('backports', '1.1.5', { + 'checksums': 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('tibble', '2.1.3', { + 'checksums': ['9a8cea9e6b5d24a7e9bf5f67ab38c40b2b6489eddb0d0edb8a48a21ba3574e1a'], + }), + ('lazyeval', '0.2.2', { + 'checksums': ['d6904112a21056222cfcd5eb8175a78aa063afe648a562d9c42c6b960a8820d4'], + }), + ('withr', '2.1.2', { + 'checksums': ['41366f777d8adb83d0bdbac1392a1ab118b36217ca648d3bb9db763aa7ff4686'], + }), + ('nlme', '3.1-143', { + 'checksums': ['42b48586c3ec4eba7de0cef6312aff63f4596cd92a1f9acb618dae28f4ea318e'], + }), + ('mgcv', '1.8-31', { + 'checksums': ['736de462a0ac43a6ed38cd57dfb0ba2942c941dfbb538128782727ab7125c3c5'], + }), + ('ggplot2', '3.2.1', { + 'checksums': ['e39114a90af69041645b0751ac469d8919c5a7e8cb044a3b56a0728623e65a56'], + }), + ('pROC', '1.15.3', { + 'checksums': ['b010988a646a642657ec72d908c2e0ca2f9df0898c05b9f1f5ab6b739353a8cb'], + }), + ('quadprog', '1.5-8', { + 'checksums': ['22128dd6b08d3516c44ff89276719ad4fe46b36b23fdd585274fa3a93e7a49cd'], + }), + ('BB', '2019.10-1', { + 'checksums': 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'7.3-12', { + 'checksums': ['2723523e8581cc0e2215435ac773033577a16087a3f41d111757dd96b8c5559d'], + }), + ('minqa', '1.2.4', { + 'checksums': ['cfa193a4a9c55cb08f3faf4ab09c11b70412523767f19894e4eafc6e94cccd0c'], + }), + ('RcppEigen', '0.3.3.7.0', { + 'checksums': ['62ea627284425bfdb56613bc315cca492ed3483a56a03c1f9dc9821a25c3e8ac'], + }), + ('MatrixModels', '0.4-1', { + 'checksums': ['fe878e401e697992a480cd146421c3a10fa331f6b37a51bac83b5c1119dcce33'], + }), + ('quantreg', '5.54', { + 'checksums': ['703b2c67d88e95eaf1bf3c09fc64c1964bcc1145244c8bc8c0e5ac99713ad0a6'], + }), + ('robustbase', '0.93-5', { + 'checksums': ['bde564dbd52f04ab32f9f2f9dd09b9578f3ccd2541cf5f8ff430da42a55e7f56'], + }), + ('sp', '1.3-2', { + 'checksums': ['940a22add254fbb5ebd80a380f4777fcd1af282975ebad400d177f3a20d6f24e'], + }), + ('zoo', '1.8-6', { + 'checksums': ['2217a4f362f2201443b5fdbfd9a77d9a6caeecb05f02d703ee8b3b9bf2af37cc'], + }), + ('lmtest', '0.9-37', { + 'checksums': ['ddc929f94bf055974832fa4a20fdd0c1eb3a84ee11f716c287936f2141d5ca0a'], + }), + ('vcd', '1.4-4', { + 'checksums': ['a561adf120b5ce41b66e0c0c321542fcddc772eb12b3d7020d86e9cd014ce9d2'], + }), + ('snowfall', '1.84-6.1', { + 'checksums': ['5c446df3a931e522a8b138cf1fb7ca5815cc82fcf486dbac964dcbc0690e248d'], + }), + ('rpart', '4.1-15', { + 'checksums': ['2b8ebe0e9e11592debff893f93f5a44a6765abd0bd956b0eb1f70e9394cfae5c'], + }), + ('survival', '3.1-8', { + 'checksums': ['cecf393e8e27df79f3bf4aa7bc186d161f0e4b46a8572504e6eb80c09027d295'], + }), + ('bindr', '0.1.1', { + 'checksums': ['7c785ca77ceb3ab9282148bcecf64d1857d35f5b800531d49483622fe67505d0'], + }), + ('plogr', '0.2.0', { + 'checksums': ['0e63ba2e1f624005fe25c67cdd403636a912e063d682eca07f2f1d65e9870d29'], + }), + ('bindrcpp', '0.2.2', { + 'checksums': ['48130709eba9d133679a0e959e49a7b14acbce4f47c1e15c4ab46bd9e48ae467'], + }), + ('purrr', '0.3.3', { + 'checksums': ['0f31a89a424e12e35bd6e0581dee1d160f1f8be1f0a883a7d33ccbde8ef69e9e'], + }), + ('tidyselect', '0.2.5', { + 'checksums': ['5ce2e86230fa35cfc09aa71dcdd6e05e1554a5739c863ca354d241bfccb86c74'], + }), + ('dplyr', '0.8.3', { + 'checksums': ['68b4aac65a69ea6390e90991d9c7ce7a011a07e5db439d60cce911a078424c0c'], + }), + ('tidyr', '1.0.0', { + 'checksums': ['92a1a30b5636c3c1c68acbff0c1f5b301df64bf3198d23f1c9808ed43a900390'], + }), + ('mnormt', '1.5-5', { + 'checksums': ['ff78d5f935278935f1814a69e5a913d93d6dd2ac1b5681ba86b30c6773ef64ac'], + }), + ('foreign', '0.8-72', { + 'checksums': ['439c17c9cd387e180b1bb640efff3ed1696b1016d0f7b3b3b884e89884488c88'], + }), + ('psych', '1.8.12', { + 'checksums': ['6e175e049bc1ee5b79a9e51ccafb22b962b4e6c839ce5c9cfa1ad83967037743'], + }), + ('generics', '0.0.2', { + 'checksums': ['71b3d1b719ce89e71dd396ac8bc6aa5f1cd99bbbf03faff61dfbbee32fec6176'], + }), + ('broom', '0.5.3', { + 'checksums': ['0d59b135bfa11c633c8ceec640342f026c5468c620984484bbc9adde1211f59c'], + }), + ('nloptr', '1.2.1', { + 'checksums': ['1f86e33ecde6c3b0d2098c47591a9cd0fa41fb973ebf5145859677492730df97'], + }), + ('boot', '1.3-23', { + 'checksums': [('30c89e19dd6490b943233e87dfe422bfef92cfbb7a7dfb5c17dfd9b2d63fa02f', + '79236a5a770dc8bf5ce25d9aa303c5dc0574d94aa043fd00b8b4c8ccc877357f')], + }), + ('lme4', '1.1-21', { + 'checksums': ['7f5554b69ff8ce9bac21e8842131ea940fb7a7dfa2de03684f236d3e3114b20c'], + }), + ('ucminf', '1.1-4', { + 'checksums': ['a2eb382f9b24e949d982e311578518710f8242070b3aa3314a331c1e1e7f6f07'], + }), + ('numDeriv', '2016.8-1.1', { + 'checksums': ['d8c4d19ff9aeb31b0c628bd4a16378e51c1c9a3813b525469a31fe89af00b345'], + }), + ('ordinal', '2019.12-10', { + 'checksums': ['7a41e7b7e852a8fa3e911f8859d36e5709ccec5ca42ee3de14a813b7aaac7725'], + }), + ('jomo', '2.6-10', { + 'checksums': ['4063d48e259e936dc0bd9dc616a09043f695703848cb1bf8faa08c07922034cd'], + }), + ('hms', '0.5.2', { + 'checksums': ['d445c98c36b224e73c76dd4fc2a700e0b1abf0ade3d8ac8ac96c12fb946e4440'], + }), + ('clipr', '0.7.0', { + 'checksums': ['03a4e4b72ec63bd08b53fe62673ffc19a004cc846957a335be2b30d046b8c2e2'], + }), + ('readr', '1.3.1', { + 'checksums': ['33f94de39bb7f2a342fbb2bd4e5afcfec08798eac39672ee18042ac0b349e4f3'], + }), + ('forcats', '0.4.0', { + 'checksums': ['7c83cb576aa6fe1379d7506dcc332f7560068b2025f9e3ab5cd0a5f28780d2b2'], + }), + ('haven', '2.2.0', { + 'checksums': ['199ee9b14e1ff70a0b0c3b9ce33dfdec8ed3b5e857a2a36bfb82e78a7b352d3d'], + }), + ('pan', '1.6', { + 'checksums': ['adc0df816ae38bc188bce0aef3aeb71d19c0fc26e063107eeee71a81a49463b6'], + }), + ('mitml', '0.3-7', { + 'checksums': ['c6f796d0059f1b093b599a89d955982fa257de9c45763ecc2cbbce10fdec1e7b'], + }), + ('mice', '3.7.0', { + 'checksums': ['4eab2959bcfe28eae068e5e697901b47b05a6c88e0a34af8303f1ec05ed0a1f3'], + }), + ('urca', '1.3-0', { + 'checksums': ['621cc82398e25b58b4a16edf000ed0a1484d9a0bc458f734e97b6f371cc76aaa'], + }), + ('fracdiff', '1.5-0', { + 'checksums': [('3a837326a6cdeed5ab1b8a83f57adb2e861886736fbde49fede79b6150081b70', + '792f2684074a8583f162e201f141a8e7615af188bf34773db6b57792d62de338')], + }), + ('logistf', '1.23', { + 'checksums': ['5adb22a40569883395dc048c877f849dd08d07582a991f1b160f0338f0b13838'], + }), + ('akima', '0.6-2', { + 'checksums': ['61da3e556553eea6d1f8db7c92218254441da31e365bdef82dfe5da188cc97ce'], + }), + ('bitops', '1.0-6', { + 'checksums': ['9b731397b7166dd54941fb0d2eac6df60c7a483b2e790f7eb15b4d7b79c9d69c'], + }), + ('mixtools', '1.1.0', { + 'checksums': ['543fd8d8dc8d4b6079ebf491cf97f27d6225e1a6e65d8fd48553ada23ba88d8f'], + }), + ('cluster', '2.1.0', { + 'checksums': ['eaf955bef8f616ea563351ec7f597c445aec43e65991ca975e382ef1fd70aa14'], + }), + ('gclus', '1.3.2', { + 'checksums': ['9cc61cdff206c11213e73afca3d570a7234250cf6044a9202c2589932278e0b3'], + }), + ('coda', '0.19-3', { + 'checksums': ['d3df1fc848bcf1af8fae13d61eeab60e99a3d4b4db384bec4326f909f502c5d6'], + }), + ('codetools', '0.2-16', { + 'checksums': ['f67a66175cb5d8882457d1e9b91ea2f16813d554fa74f80c1fd6e17cf1877501'], + }), + ('foreach', '1.4.7', { + 'checksums': ['95632c0b1182fc01490718d82fa3b2bce864f2a011ae53282431c7c2a3f5f160'], + }), + ('doMC', '1.3.6', { + 'checksums': ['2977fc9e2dc54d85d45b4a36cd286dff72834fbc73f38b6ee45a6eb8557fc9b2'], + }), + ('DBI', '1.1.0', { + 'checksums': ['a96db7fa39a58f1ed34c6e78d8f5f7e4cf0882afb301323b5c6975d6729203e4'], + }), + ('gam', '1.16.1', { + 'checksums': ['80d04102c6152143e8ed364f91eb312e413f73b8fcab7cf15d677867a16e74b9'], + }), + ('gamlss.data', '5.1-4', { + 'checksums': ['0d3777d8c3cd76cef273aa6bde40a91688719be401195ed9bfd1e85bd7d5eeb5'], + }), + ('gamlss.dist', '5.1-5', { + 'checksums': ['1c6f42d17e32eae848217bc5115bc440ff8f95869d7fef0756fbf6f2da8787e6'], + }), + ('gamlss', '5.1-5', { + 'checksums': ['6ca1297418e514a7b89f59789908d040e3160cb32e7cf024cc623630997b963d'], + }), + ('gamlss.tr', '5.1-0', { + 'checksums': ['f9e1c4935d8876bfc80dddc0a9bc2c82b4deeda9482df208297a84a638a4a9df'], + }), + ('hwriter', '1.3.2', { + 'checksums': ['6b3531d2e7a239be9d6e3a1aa3256b2745eb68aa0bdffd2076d36552d0d7322b'], + }), + ('KernSmooth', '2.23-16', { + 'checksums': ['b8c251fea1483a8ade005faf31dff9d85d2b6da08dcd661bf1e4a861db9a99a9'], + }), + ('xts', '0.11-2', { + 'checksums': ['12772f6a66aab5b84b0665c470f11a3d8d8a992955c027261cfe8e6077ee13b8'], + }), + ('curl', '4.3', { + 'checksums': ['7406d485bb50a6190e3ed201e3489063fd249b8b3b1b4f049167ac405a352edb'], + }), + ('TTR', '0.23-6', { + 'checksums': ['afc10a89d3a18f121ddf0f7256408eeb05cc64e18ee94e654bfa803e5415e265'], + }), + ('quantmod', '0.4-15', { + 'checksums': ['7ef2e798d4d8e4d2af0a5b2b9fecebec30568087afbd24bfd923cdeb8b53df53'], + }), + ('mvtnorm', '1.0-11', { + 'checksums': ['0321612de99aa9bc75a45c7e029d3372736014223cbdefb80d8cae600cbc7252'], + }), + ('pcaPP', '1.9-73', { + 'checksums': ['ca4566b0babfbe83ef9418283b08a12b3420dc362f93c6562f265df7926b53fc'], + }), + ('SQUAREM', '2017.10-1', { + 'checksums': ['9b89905b436f1cf3faa9e3dabc585a76299e729e85ca659bfddb4b7cba11b283'], + }), + ('lava', '1.6.6', { + 'checksums': ['7abc84dd99cce450a45ac4f232812cde3a322e432da3472f43b057fb5c59ca59'], + }), + ('prodlim', '2019.11.13', { + 'checksums': ['6809924f503a14681de84730489cdaf9240d7951c64f5b98ca37dc1ce7809b0f'], + }), + ('pscl', '1.5.2', { + 'checksums': ['2c9fe648485c6b54c6f95a54b6e00ffe3cf06fa8c5c68f1d669664a7b91a0ede'], + }), + ('memoise', '1.1.0', { + 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], + }), + ('bit64', '0.9-7', { + 'checksums': ['7b9aaa7f971198728c3629f9ba1a1b24d53db5c7e459498b0fdf86bbd3dff61f'], + }), + ('prettyunits', '1.0.2', { + 'checksums': ['35a4980586c20650538ae1e4fed4d80fdde3f212b98546fc3c7d9469a1207f5c'], + }), + ('blob', '1.2.0', { + 'checksums': ['1af1cfa28607bc0e2f1f01598a00a7d5d1385ef160a9e79e568f30f56538e023'], + }), + ('RSQLite', '2.1.4', { + 'checksums': ['64b80063833d4cdbc4b44b7d70c605bf87c2595300049a8c519e46ecbec10aee'], + }), + ('data.table', '1.12.8', { + 'checksums': ['d3a75f3a355ff144cc20a476041617e21fcf2a9f79265fd9bbd4693f3671f9dc'], + }), + ('BatchJobs', '1.8', { + 'checksums': ['35cc2dae31994b1df982d11939509ce965e12578418c4fbb8cd7a422afd6e4ff'], + }), + ('sandwich', '2.5-1', { + 'checksums': ['dbef6f4d12b83e166f9a2508b7c732b04493641685d6758d29f3609e564166d6'], + }), + ('sfsmisc', '1.1-4', { + 'checksums': ['44b6a9c859922e86b7182e54eb781d3264f3819f310343518ebc66f54f305c7d'], + }), + ('spatial', '7.3-11', { + 'checksums': ['624448d2ac22e1798097d09fc5dc4605908a33f490b8ec971fc6ea318a445c11'], + }), + ('VGAM', '1.1-2', { + 'checksums': ['f8071339f127121945954c98168749efcc179c67c70437d35b5d684fd4b0ca4f'], + }), + ('waveslim', '1.7.5.1', { + 'checksums': ['b323018c92674b1b49fe01ec7e3900641a1c9ce0bd1e7497cfe8f64e96057e56'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('profileModel', '0.6.0', { + 'checksums': ['a829ceec29c817d6d15947b818e28f9cf5a188a231b9b5d0a75018388887087b'], + }), + ('brglm', '0.6.2', { + 'checksums': ['c2af432a43ccf37e9de50317f770b9703a4c80b4ef79ec40aa8e7ec3987e3631'], + }), + ('deSolve', '1.25', { + 'checksums': ['773170a7b9f82db3a8dfb563942ee0e71ebdebc388e59f93e918d257eef0651c'], + }), + ('tseriesChaos', '0.1-13.1', { + 'checksums': ['23cb5fea56409a305e02a523ff8b7642ec383942d415c9cffdc92208dacfd961'], + }), + ('tseries', '0.10-47', { + 'patches': ['tseries-0.10-47_ifort_explicit_free_form.patch'], + 'checksums': [ + '202377df56806fe611c2e12c4d9732c71b71220726e2defa7e568d2b5b62fb7b', # tseries_0.10-47.tar.gz + # tseries-0.10-47_ifort_explicit_free_form.patch + 'b5a5b342e3b647ea2d7db145cb81eedcb82ea09c993a19a17b0148691ab0813c', + ], + }), + ('fastICA', '1.2-2', { + 'checksums': ['32223593374102bf54c8fdca7b57231e4f4d0dd0be02d9f3500ad41b1996f1fe'], + }), + ('R.methodsS3', '1.7.1', { + 'checksums': ['44b840399266cd27f8f9157777b4d9d85ab7bd31bfdc143b3fc45079a2d8e687'], + }), + ('R.oo', '1.23.0', { + 'checksums': ['f5124ce3dbb0a62e8ef1bfce2de2d1dc2f776e8c48fd8cac358f7f5feb592ea1'], + }), + ('jsonlite', '1.6', { + 'checksums': ['88c5b425229966b7409145a6cabc72db9ed04f8c37ee95901af0146bb285db53'], + }), + ('sys', '3.3', { + 'checksums': ['a6217c2a7240ed68614006f392c6d062247dab8b9b0d498f95e947110df19b93'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), + ('openssl', '1.4.1', { + 'checksums': ['f7fbecc75254fc43297a95a4338c674ab9ba2ec056b59e027d16d23122161fc6'], + }), + ('httr', '1.4.1', { + 'checksums': ['675c7e07bbe82c48284ee1ab929bb14a6e653abae2860d854dc41a3c028de156'], + }), + ('cgdsr', '1.3.0', { + 'checksums': ['4aa2a3564cee2449c3ff39ab2ad631deb165d4c78b8107e0ff77a9095340cc1f'], + }), + ('R.utils', '2.9.2', { + 'checksums': ['ac6b3b8e814fbb855c38fbdb89a4f0cf0ed65ce7fa308445bd74107fbc0d32cf'], + }), + ('R.matlab', version, { + 'checksums': ['1ba338f470a24b7f6ef68cadbd04eb468ead4a689f263d2642408ad591b786bb'], + }), + ('gridExtra', '2.3', { + 'checksums': ['81b60ce6f237ec308555471ae0119158b115463df696d2eca9b177ded8988e3b'], + }), + ('gbm', '2.1.5', { + 'checksums': ['06fbde10639dfa886554379b40a7402d1f1236a9152eca517e97738895a4466f'], + }), + ('Formula', '1.2-3', { + 'checksums': ['1411349b20bd09611a9fd0ee6d15f780c758ad2b0e490e908facb49433823872'], + }), + ('acepack', '1.4.1', { + 'checksums': ['82750507926f02a696f6cc03693e8d4a5ee7e92500c8c15a16a9c12addcd28b9'], + }), + ('proto', '1.0.0', { + 'checksums': ['9294d9a3b2b680bb6fac17000bfc97453d77c87ef68cfd609b4c4eb6d11d04d1'], + }), + ('chron', '2.3-54', { + 'checksums': ['0df3ac3e96e0469a8fd727ef65a1edfada90c088cd74f535ff5882ce716f876d'], + }), + ('viridis', '0.5.1', { + 'checksums': ['ddf267515838c6eb092938133035cee62ab6a78760413bfc28b8256165701918'], + }), + ('yaml', '2.2.0', { + 'checksums': ['55bcac87eca360ab5904914fcff473a6981a1f5e6d2215d2634344d0ac30c546'], + }), + ('htmltools', '0.4.0', { + 'checksums': ['5b18552e1183b1b90b5cca8e7f95b57e8124c9d517b22aa64783b829513b811a'], + }), + ('htmlwidgets', '1.5.1', { + 'checksums': ['d42e59144552d9b4131f11ddd6169dfb9bd538c7996669a09acbdb400d18d781'], + }), + ('knitr', '1.26', { + 'checksums': ['38db354bec68f25cf8a05e5162ebbac45811309c75a7bcfc8bcb5a565a5bc321'], + }), + ('rstudioapi', '0.10', { + 'checksums': ['80c5aa3063bcab649904cb92f0b164edffa2f6b0e6a8f7ea28ae317b80e1ab96'], + }), + ('htmlTable', '1.13.3', { + 'checksums': ['d459c43675f6ee0a1ae8232ea8819b2a842e795a833b28127081fa344d09393d'], + }), + ('Hmisc', '4.3-0', { + 'checksums': ['7ff2f9adcfd67f2e70345e73db3608ed46f8e07e2f696d0d591f533482a96165'], + }), + ('fastcluster', '1.1.25', { + 'checksums': ['f3661def975802f3dd3cec5b2a1379f3707eacff945cf448e33aec0da1ed4205'], + }), + ('registry', '0.5-1', { + 'checksums': ['dfea36edb0a703ec57e111016789b47a1ba21d9c8ff30672555c81327a3372cc'], + }), + ('bibtex', '0.4.2', { + 'checksums': ['1f06ab3660c940405230ad16ff6e4ba38d4418a59cd9b16d78a4349f8b488372'], + }), + ('pkgmaker', '0.27', { + 'checksums': [('17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a', + 'e5eb9058e68702c15e8dc6fee6ede41cdbe8e3914d190a5a1113079db26fb003')], + }), + ('rngtools', '1.4', { + 'checksums': [('3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce', + '0a54eaea0d9024ef42bfc12b8cdebf51f34c26a28714f7971f0b7af72c5f0970')], + }), + ('doParallel', '1.0.15', { + 'checksums': ['71ad7ea69616468996aefdd8d02a4a234759a21ddde9ed1657e3c537145cd86e'], + }), + ('gridBase', '0.4-7', { + 'checksums': ['be8718d24cd10f6e323dce91b15fc40ed88bccaa26acf3192d5e38fe33e15f26'], + }), + ('NMF', '0.21.0', { + 'checksums': ['3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3'], + }), + ('irlba', '2.3.3', { + 'checksums': ['6ee233697bcd579813bd0af5e1f4e6dd1eea971e8919c748408130d970fef5c0'], + }), + ('igraph', '1.2.4.2', { + 'checksums': ['ad67b58e9132128d8ea7ec0dee5c071a21f4674e8f2cbaa642555d23165e9969'], + }), + ('GeneNet', '1.2.13', { + 'checksums': ['3798caac3bef7dc87f97b3628eb29eb12365d571ce0837b5b6285b0be655a270'], + }), + ('ape', '5.3', { + 'checksums': ['08b0df134c523feb00a86896d1aa2a43f0f0dab20a53bc6b5d6268d867988b23'], + }), + ('RJSONIO', '1.3-1.3', { + 'checksums': ['bc5e97dac4d6e935ba530f60be9364ea5f2aebaf5b9a907135e8d7c0d56d22b9'], + }), + ('caTools', '1.17.1.3', { + 'checksums': ['d78735c5adb54ba31a4d529cc2fbf7d3c72a6e12fc24afda8d36acdefcdaa712'], + }), + ('gplots', '3.0.1.1', { + 'checksums': ['7db103f903a25d174cddcdfc7b946039b61e236c95084b90ad17f1a41da3770c'], + }), + ('ROCR', '1.0-7', { + 'checksums': ['e7ef710f847e441a48b20fdc781dbc1377f5a060a5ee635234053f7a2a435ec9'], + }), + ('later', '1.0.0', { + 'checksums': ['277b9848ef2e5e1ac7257aefeb58f6b20cca17693460e7c4eee0477de456b287'], + }), + ('promises', '1.1.0', { + 'checksums': ['c8ea0f3e3256cf3010439b3a6111966db419c3dcff9a561e73caf8bd65f38006'], + }), + ('httpuv', '1.5.2', { + 'checksums': ['93b32be974e0f531a3cb343685165c0caadf30cfea07683f8d69302a34045d8d'], + }), + ('rjson', '0.2.20', { + 'checksums': ['3a287c1e5ee7c333ed8385913c0a307daf99335fbdf803e9dcca6e3d5adb3f6c'], + }), + ('sourcetools', '0.1.7', { + 'checksums': ['47984406efb3b3face133979ccbae9fefb7360b9a6ca1a1c11473681418ed2ca'], + }), + ('fastmap', '1.0.1', { + 'checksums': ['4778b05dfebd356f8df980dfeff3b973a72bca14898f870e5c40c1d84db9faec'], + }), + ('shiny', '1.4.0', { + 'checksums': ['0c070459387cea98ca7c6df7318370116df42afb5f76a8625eb4f5b681ee6c4b'], + }), + ('seqinr', '3.6-1', { + 'checksums': ['c44fc8922ef410da3c3b5ca117cdbec55ccb546c9e6d96c01ede44398dfa6048'], + }), + ('LearnBayes', '2.15.1', { + 'checksums': ['9b110858456523ca0b2a63f22013c4e1fbda6674b9d84dc1f4de8bffc5260532'], + }), + ('deldir', '0.1-23', { + 'checksums': ['e0112bce9fc94daf73596a0fff9b3958b80872e3bbb487be73e157b13a6f201d'], + }), + ('gmodels', '2.18.1', { + 'checksums': ['626140a34eb8c53dd0a06511a76c71bc61c48777fa76fcc5e6934c9c276a1369'], + }), + ('expm', '0.999-4', { + 'checksums': ['58d06427a08c9442462b00a5531e2575800be13ed450c5a1546261251e536096'], + }), + ('spData', '0.3.2', { + 'checksums': ['7c7d93e7b722e67695f89e1961592733393298229359768fe846087b73d615a4'], + }), + ('units', '0.6-5', { + 'checksums': ['50b759fe0c91f7e098cabb348f3d14067f3dbeb26574a2259d27870c2ad2d40a'], + }), + ('classInt', '0.4-2', { + 'checksums': ['bb0da1e7db779831cf5cea80722ade90bf83a9aa51b7d2bc6bee69c433042871'], + }), + ('vegan', '2.5-6', { + 'checksums': ['b3c00aceb3db38101960515658e2b9ec1552439c3ed4e26e72989f18eccbc03c'], + }), + ('progress', '1.2.2', { + 'checksums': ['b4a4d8ed55db99394b036a29a0fb20b5dd2a91c211a1d651c52a1023cc58ff35'], + }), + ('rncl', '0.8.3', { + 'checksums': ['daaef6874438233c73a62b59a9ee10261e1e10d7ef18b7178d2d8b517fd4880d'], + }), + ('XML', '3.98-1.20', { + 'checksums': ['46af86376ea9a0fb1b440cf0acdf9b89178686a05c4b77728fcff1f023aa4858'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('ps', '1.3.0', { + 'checksums': ['289193d0ccd2db0b6fe8702e8c5711e935219b17f90f01a6e9684982413e98d1'], + }), + ('processx', '3.4.1', { + 'checksums': ['f1abddb48fa78f2b176552e2ec5d808d4d87d79ce72e9b3d25c9a7d715bbd1bc'], + }), + ('callr', '3.4.0', { + 'checksums': ['99ea44fa5b9ce3db1c3811f57021b04c172611ec6caa6e317808ff489fe07dc3'], + }), + ('rprojroot', '1.3-2', { + 'checksums': ['df5665834941d8b0e377a8810a04f98552201678300f168de5f58a587b73238b'], + }), + ('desc', '1.2.0', { + 'checksums': ['e66fb5d4fc7974bc558abcdc107a1f258c9177a29dcfcf9164bc6b33dd08dae8'], + }), + ('pkgbuild', '1.0.6', { + 'checksums': ['bd736cadcb9938df9fafddd362f9f032934a93b9853b981eb3754db8a3f9d476'], + }), + ('pkgload', '1.0.2', { + 'checksums': ['3186564e690fb05eabe76e1ac0bfd4312562c3ac8794b29f8850399515dcf27c'], + }), + ('testthat', '2.3.1', { + 'checksums': ['7eae9574b8baf80a95b529aff982fb691794bf211c8bf58ce431d9771b641d55'], + }), + ('tinytex', '0.18', { + 'checksums': ['39cf729b11138f55949901facd346452b17192640603f995ad7df5d8145cb712'], + }), + ('rmarkdown', '2.0', { + 'checksums': ['87ba0499555719cf3793bfd6ff4fa3577401ac5d90577c300bee02c54fb0a3ae'], + }), + ('reshape', '0.8.8', { + 'checksums': ['4d5597fde8511e8fe4e4d1fd7adfc7ab37ff41ac68c76a746f7487d7b106d168'], + }), + ('xml2', '1.2.2', { + 'checksums': ['3050f147c4335be2925a576557bbda36bd52a5bba3110d47b740a2dd811a78f4'], + }), + ('triebeard', '0.3.0', { + 'checksums': ['bf1dd6209cea1aab24e21a85375ca473ad11c2eff400d65c6202c0fb4ef91ec3'], + }), + ('urltools', '1.7.3', { + 'checksums': ['6020355c1b16a9e3956674e5dea9ac5c035c8eb3eb6bbdd841a2b5528cafa313'], + }), + ('httpcode', '0.2.0', { + 'checksums': ['fbc1853db742a2cc1df11285cf27ce2ea43bc0ba5f7d393ee96c7e0ee328681a'], + }), + ('crul', '0.9.0', { + 'checksums': ['a7b42c69ca31648a419b93c618d32d0613f3ea053e45d584e84ef422ccf531c0'], + }), + ('bold', '0.9.0', { + 'checksums': ['45e844a83f4545a2f84887e36db83113da824a8673fa039f067a3bd7ee82ed5e'], + }), + ('rredlist', '0.5.0', { + 'checksums': ['404db668f94aea7fe8c4da75085ea82b0bc9994f023ef4a52f4d75cf198db889'], + }), + ('rentrez', '1.2.2', { + 'checksums': ['e5cb4265fd06d2ed0e11da3667ba79f7f2c8816005ba72cf5f53b8cf02dc193e'], + }), + ('rotl', '3.0.10', { + 'checksums': ['38b4679fe2d5407f7d0799d624ae8ea5d73ec0b6531b0e3d48246dea5575073a'], + }), + ('solrium', '1.1.4', { + 'checksums': ['5fccdb455746493c56e4df91f01ea9e89cdf0d67cfa5f958ca246b9207d20375'], + }), + ('ritis', '0.8.0', { + 'checksums': ['23bc11599a64c25fe7a60e86fa3cd8c4078e140bc338c6d51d8d75b81564ecbd'], + }), + ('worrms', '0.4.0', { + 'checksums': ['8480c56a4412662a383103fef68e73fcf14e94fcb878c25df8c6d5a8c0146059'], + }), + ('natserv', '0.3.0', { + 'checksums': ['3c207d45bbba75dfd16f40d6eaaac122e40b3d3ca05b3b98aa8ed3c092638e5e'], + }), + ('WikipediR', '1.5.0', { + 'checksums': ['f8d0e6f04fb65f7ad9c1c068852a6a8b699ffe8d39edf1f3fa07d32d087e8ff0'], + }), + ('WikidataR', '1.4.0', { + 'checksums': ['64b1d53d7023249b73a77a7146adc3a8957b7bf3d808ebd6734795e9f58f4b2a'], + }), + ('wikitaxa', '0.3.0', { + 'checksums': ['10dbabac6c56c1d0f33a66ff9b4f48b0bcb470711808a86863b48dc1140ec86c'], + }), + ('phangorn', '2.5.5', { + 'checksums': ['c58dc1ace26cb4358619a15da3ea4765dbdde1557acccc5103c85589a7571346'], + }), + ('taxize', '0.9.91', { + 'checksums': ['ce3d05c5c7c2d2cf2612264b24b9880b587d459efa3f5b7703667e0b64a58f59'], + }), + ('uuid', '0.1-2', { + 'checksums': ['dd71704dc336b0857981b92a75ed9877d4ca47780b1682def28839304cd3b1be'], + }), + ('RNeXML', '2.4.0', { + 'checksums': ['e162a896f895199061a0c537f65aeae480be8190fcae2a1be2b80fbc54cb9398'], + }), + ('phylobase', '0.8.6', { + 'checksums': ['e7117b210ef406115e5523b794d8c2c5779640cee8c06e73751dc14c69322fd9'], + }), + ('magick', '2.2', { + 'checksums': ['05d13050be37d158e66fd895ef03a34184ed96a5a3258d790c930f3d15ac05f6'], + }), + ('animation', '2.6', { + 'checksums': ['90293638920ac436e7e4de76ebfd92e1643ccdb0259b62128f16dd0b13245b0a'], + }), + ('bigmemory.sri', '0.1.3', { + 'checksums': ['55403252d8bae9627476d1f553236ea5dc7aa6e54da6980526a6cdc66924e155'], + }), + ('bigmemory', '4.5.33', { + 'patches': ['bigmemory-4.5.19_icpc-wd308.patch'], + 'checksums': [ + '7237d9785d8ce3eab4e36ad3ce2c95cbae926326031661b4f237b7517f4b9479', # bigmemory_4.5.33.tar.gz + 'cf673010f63baff60bf5fe4521a3740aa6891bcfb64c1979a8f1e1aa21532549', # bigmemory-4.5.19_icpc-wd308.patch + ], + }), + ('calibrate', '1.7.5', { + 'checksums': ['33f4f6874f0a979af3ce592ed1105e829d3df1fbf05c6e0cd3829a13b21d82e8'], + }), + ('clusterGeneration', '1.3.4', { + 'checksums': ['7c591ad95a8a9d7fb0e4d5d80dfd78f7d6a63cf7d11eb53dd3c98fdfb5b868aa'], + }), + ('raster', '3.0-7', { + 'checksums': ['764f1c3d66ad2d1242c9fad6cff30291f351bfdb41df11d7a66b760ac3d95d39'], + }), + ('dismo', '1.1-4', { + 'checksums': ['f2110f716cd9e4cca5fd2b22130c6954658aaf61361d2fe688ba22bbfdfa97c8'], + }), + ('extrafontdb', '1.0', { + 'checksums': ['faa1bafee5d4fbc24d03ed237f29f1179964ebac6e3a46ac25b0eceda020b684'], + }), + ('Rttf2pt1', '1.3.7', { + 'checksums': ['4a4e50578b5c1dbfb90c289ee388c102de1f9c84f8b8ddb8d2294b58474e0e8a'], + }), + ('extrafont', '0.17', { + 'checksums': ['2f6d7d79a890424b56ddbdced361f8b9ddede5edd33e090b816b88a99315332d'], + }), + ('fields', '10.0', { + 'checksums': ['3406a04034429ef3a68a68782a0f73099e3e28f0f8880d706cde0c9177a97f9c'], + }), + ('shapefiles', '0.7', { + 'checksums': ['eeb18ea4165119519a978d4a2ba1ecbb47649deb96a7f617f5b3100d63b3f021'], + }), + ('fossil', '0.3.7', { + 'checksums': ['3feba6ceecaa6f2f68fdc1ceb0019395ccfadb0cf033e1709dddb690c7f210a1'], + }), + ('geiger', '2.0.6.2', { + 'checksums': ['9153047b608d652821251206d1450bb3f517c8884379f498a695315574ae001d'], + }), + ('shape', '1.4.4', { + 'checksums': ['f4cb1b7d7c84cf08d2fa97f712ea7eb53ed5fa16e5c7293b820bceabea984d41'], + }), + ('glmnet', '3.0-2', { + 'checksums': ['f48956a75af7e2be045198873fc9eb637a549af1db83dcf76cac3774bfb3762c'], + }), + ('crosstalk', '1.0.0', { + 'checksums': ['b31eada24cac26f24c9763d9a8cbe0adfd87b264cf57f8725027fe0c7742ca51'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('webshot', '0.5.2', { + 'checksums': ['f183dc970157075b51ac543550a7a48fa3428b9c6838abb72fe987c21982043f'], + }), + ('manipulateWidget', '0.10.0', { + 'checksums': ['3d61a3d0cedf5c8a850a3e62ed6af38c600dc3f25b44c4ff07a5093bf9ca4ffd'], + }), + ('rgl', '0.100.30', { + 'checksums': ['8575f51160b43057e5992f0d38480309fae3b8cca50b933d814a38cea6fef867'], + }), + ('Rtsne', '0.15', { + 'patches': ['Rtsne-0.15_icpc-wd308.patch'], + 'checksums': [ + '56376e4f0a382fad3d3d40e2cb0562224be5265b827622bcd235e8fc63df276c', # Rtsne_0.15.tar.gz + '150eedeb0ce59d1f9fe9f24a63be19961a32df5b2ec734c43deceb377940070d', # Rtsne-0.15_icpc-wd308.patch + ], + }), + ('labdsv', '2.0-1', { + 'checksums': ['5a4d55e9be18222dc47e725008b450996448ab117d83e7caaa191c0f13fd3925'], + }), + ('stabs', '0.6-3', { + 'checksums': ['e961ae21d45babc1162b6eeda874c4e3677fc286fd06f5427f071ad7a5064a9f'], + }), + ('modeltools', '0.2-22', { + 'checksums': ['256a088fc80b0d9182f984f9bd3d6207fb7c1e743f72e2ecb480e6c1d4ac34e9'], + }), + ('strucchange', '1.5-2', { + 'checksums': ['7d247c5ae6f5a63c80e478799d009c57fb8803943aa4286d05f71235cc1002f8'], + }), + ('TH.data', '1.0-10', { + 'checksums': ['618a1c67a30536d54b1e48ba3af46a6edcd6c2abef17935b5d4ba526a43aff55'], + }), + ('multcomp', '1.4-11', { + 'checksums': ['0bd22d9c978eac17ac6ed65ef15890df6730551e93ba9d3e3769100d8331894b'], + }), + ('libcoin', '1.0-5', { + 'checksums': ['0a744164e00557d2f3e888d14cfd6108d17c14e983db620f74c7a5475be8a9b2'], + }), + ('matrixStats', '0.55.0', { + 'patches': ['matrixStats-0.53.1_O1.patch'], + 'checksums': [ + '16d6bd90eee4cee8df4c15687de0f9b72730c03e56603c2998007d4533e8db19', # matrixStats_0.55.0.tar.gz + '96ef21a1d5ee4ccd1f4a6b74ef5aa2699a52c38b34613d8ff9f3c4af952aa8fd', # matrixStats-0.53.1_O1.patch + ], + }), + ('coin', '1.3-1', { + 'checksums': ['5de2519a6e2b059bba9d74c58085cccaff1aaaa0454586ed164a108ebd1b2062'], + }), + ('party', '1.3-3', { + 'checksums': ['9f72eea02d43a4cee105790ae7185b0478deb6011ab049cc9d31a0df3abf7ce9'], + }), + ('inum', '1.0-1', { + 'checksums': ['3c2f94c13c03607e05817e4859595592068b55e810fed94e29bc181ad248a099'], + }), + ('partykit', '1.2-5', { + 'checksums': ['f48e30790f93fa5d03e68e8ce71ce33d009d107d46d45d85da2016b38b27629c'], + }), + ('mboost', '2.9-1', { + 'checksums': ['67ed26093fc2c1e57d7fac842a51a0de0162e448d4dab09c0054baee801f2a0a'], + }), + ('msm', '1.6.7', { + 'checksums': ['7503c0f61916033ed0efad54727368bce629ff2d370f302b71bc1cb924d2e23a'], + }), + ('nor1mix', '1.3-0', { + 'checksums': ['9ce4ee92f889a4a4041b5ea1ff09396780785a9f12ac46f40647f74a37e327a0'], + }), + ('np', '0.60-9', { + 'checksums': ['fe31a8985f0b1a576a7775022b7131093b1c9a8337734136d5fcad85fa6592fc'], + }), + ('polynom', '1.4-0', { + 'checksums': ['c5b788b26f7118a18d5d8e7ba93a0abf3efa6603fa48603c70ed63c038d3d4dd'], + }), + ('polspline', '1.1.17', { + 'checksums': ['d67b269d01105d4a6ea774737e921e66e065a859d1931ae38a70f88b6fb7ee30'], + }), + ('rms', '5.1-4', { + 'checksums': ['38f5844c4944a95b2adebea6bb1d163111270b8662399ea0349c45c0758076a6'], + }), + ('RWekajars', '3.9.3-2', { + 'checksums': ['16e6b019aab1646f89c5203f0d6fc1cb800129e5169b15aaef30fd6236f5da1a'], + }), + ('RWeka', '0.4-41', { + 'checksums': ['ae3a87ee572c2207cb047490a778a7d9f9785ce63f65b6818622b23db9c13abf'], + }), + ('slam', '0.1-46', { + 'checksums': ['0b64989a639b196b6f217b301a8a233cefa66296112efdcad09ec76a4e5f10c6'], + }), + ('tm', '0.7-7', { + 'checksums': ['d0dbe41ff8414bdc2eee06a1b0d6db4567850135c4c6ff0a9c9ca8239166d15f'], + }), + ('TraMineR', '2.0-13', { + 'checksums': ['679a73f4e75268a60060941f476929142b8fc4bf0ea8708b64a72635566d688d'], + }), + ('chemometrics', '1.4.2', { + 'checksums': ['b705832fa167dc24b52b642f571ed1efd24c5f53ba60d02c7797986481b6186a'], + }), + ('FNN', '1.1.3', { + 'checksums': ['de763a25c9cfbd19d144586b9ed158135ec49cf7b812938954be54eb2dc59432'], + }), + ('ipred', '0.9-9', { + 'checksums': ['0da87a70730d5a60b97e46b2421088765e7d6a7cc2695757eba0f9d31d86416f'], + }), + ('statmod', '1.4.32', { + 'checksums': ['2f67a1cfa66126e6345f8a40564a3077d08f1748f17cb8c8fb05c94ed0f57e20'], + }), + ('miscTools', '0.6-26', { + 'checksums': ['be3c5a63ca12ce7ce4d43767a1815cd3dcf32664728ade251cfb03ea6f77fc9a'], + }), + ('maxLik', '1.3-6', { + 'checksums': ['95e92124776d70c5aaf5af99f184b0fac0ec726a98537d32518a8d7acf43924a'], + }), + ('gbRd', '0.4-11', { + 'checksums': ['0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b'], + }), + ('Rdpack', '0.11-1', { + 'checksums': ['58020f150be07209fd1fdd7f5e58c138863e850f4e4c1512d69250286e091e20'], + }), + ('mlogit', '1.0-2', { + 'checksums': ['5cc3afefb37c065dc39a9c01ec610a66a3775f91246313a946575309f4e2b6a1'], + }), + ('getopt', '1.20.3', { + 'checksums': ['531f5fdfdcd6b96a73df2b39928418de342160ac1b0043861e9ea844f9fbf57f'], + }), + ('gsalib', '2.1', { + 'checksums': ['e1b23b986c18b89a94c58d9db45e552d1bce484300461803740dacdf7c937fcc'], + }), + ('optparse', '1.6.4', { + 'checksums': ['cd7855ebc2303da4ab0615282667c7eeef5329faf51bd2bf2e4b0d250561d973'], + }), + ('labelled', '2.2.1', { + 'checksums': ['51851d8a50acadb144e0d2300f65d0962d617aa963b2a3051fb56495bdd237d7'], + }), + ('questionr', '0.7.0', { + 'checksums': ['c4566880a1ca8f01faad396e20d907d913f4a252acaf83a0cb508a3738874cb3'], + }), + ('klaR', '0.6-14', { + 'checksums': ['51e9d9149ba77874ccecc816a2a75619e2f9615c091f6e8969da20615c2b29bd'], + }), + ('neuRosim', '0.2-12', { + 'checksums': ['f4f718c7bea2f4b61a914023015f4c71312f8a180124dcbc2327b71b7be256c3'], + }), + ('locfit', '1.5-9.1', { + 'patches': ['locfit-1.5-9.1_Fix_logical_operators_icc.patch'], + 'checksums': [ + 'f524148fdb29aac3a178618f88718d3d4ac91283014091aa11a01f1c70cd4e51', # locfit_1.5-9.1.tar.gz + # locfit-1.5-9.1_Fix_logical_operators_icc.patch + 'e12c995539c039a8f2a1fb1a4d2b34c488f942b0fd4e31a2b9d5bd1543bce0fc', + ], + }), + ('GGally', '1.4.0', { + 'checksums': ['9a47cdf004c41f5e4024327b94227707f4dad3a0ac5556d8f1fba9bf0a6355fe'], + }), + ('beanplot', '1.2', { + 'checksums': ['49da299139a47171c5b4ccdea79ffbbc152894e05d552e676f135147c0c9b372'], + }), + ('clValid', '0.6-6', { + 'checksums': ['c13ef1b6258e34ba53615b78f39dbe4d8ba47b976b3c24a3eedaecf5ffba19ed'], + }), + ('DiscriMiner', '0.1-29', { + 'checksums': ['5aab7671086ef9940e030324651976456f0e84dab35edb7048693ade885228c6'], + }), + ('ellipse', '0.4.1', { + 'checksums': ['1a9a9c52195b26c2b4d51ad159ab98aff7aa8ca25fdc6b2198818d1a0adb023d'], + }), + ('leaps', '3.0', { + 'checksums': ['55a879cdad5a4c9bc3b5697dd4d364b3a094a49d8facb6692f5ce6af82adf285'], + }), + ('pbkrtest', '0.4-7', { + 'checksums': ['5cbb03ad2b2468720a5a610a0ebda48ac08119a34fca77810a85f554225c23ea'], + }), + ('carData', '3.0-3', { + 'checksums': ['986b84bdd289159eead8b050ea82600a4f77bf0bbe0293a7c7b25d607ff7e231'], + }), + ('maptools', '0.9-9', { + 'checksums': ['69ba3b2cd50260f78fb6c25cf0557b4a0d31498d6a4f4ff00e466334fba4946c'], + }), + ('zip', '2.0.4', { + 'checksums': ['ab5dd0c63bd30b478d0f878735e7baf36e2e76e4d12d2b4b8eddd03b665502b0'], + }), + ('openxlsx', '4.1.4', { + 'checksums': ['07a38b21f6ce6e92d58d7a51ea9f4b5fd77db49b019a18ba9ecea69878a39dd7'], + }), + ('rematch', '1.0.1', { + 'checksums': ['a409dec978cd02914cdddfedc974d9b45bd2975a124d8870d52cfd7d37d47578'], + }), + ('cellranger', '1.1.0', { + 'checksums': ['5d38f288c752bbb9cea6ff830b8388bdd65a8571fd82d8d96064586bd588cf99'], + }), + ('readxl', '1.3.1', { + 'checksums': ['24b441713e2f46a3e7c6813230ad6ea4d4ddf7e0816ad76614f33094fbaaaa96'], + }), + ('rio', '0.5.16', { + 'checksums': ['d3eb8d5a11e0a3d26169bb9d08f834a51a6516a349854250629072d59c29d465'], + }), + ('car', '3.0-5', { + 'checksums': ['7ed4f7e79b39089796ca07ca78de560f517967b6ad79b93ecf98037b03aaee70'], + }), + ('flashClust', '1.01-2', { + 'checksums': ['48a7849bb86530465ff3fbfac1c273f0df4b846e67d5eee87187d250c8bf9450'], + }), + ('ggrepel', '0.8.1', { + 'checksums': ['d5d03a77ab6d8c831934bc46e840cc4e3df487272ab591fa72767ad42bcb7283'], + }), + ('FactoMineR', '2.0', { + 'checksums': ['48828a7491a9210aa908f77e8aaacc774b1205a269898f752f6e0d773d303c62'], + }), + ('flexclust', '1.4-0', { + 'checksums': ['82fe445075a795c724644864c7ee803c5dd332a89ea9e6ccf7cd1ae2d1ecfc74'], + }), + ('flexmix', '2.3-15', { + 'checksums': ['ba444c0bfe33ab87d440ab590c06b03605710acd75811c1622253171bb123f43'], + }), + ('prabclus', '2.3-1', { + 'checksums': ['ef3294767d43bc3f72478fdaf0d1f13c8de18881bf9040c9f1add68af808b3c0'], + }), + ('diptest', '0.75-7', { + 'checksums': ['462900100ca598ef21dbe566bf1ab2ce7c49cdeab6b7a600a50489b05f61b61b'], + }), + ('trimcluster', '0.1-2.1', { + 'checksums': ['b64a872a6c2ad677dfeecc776c9fe5aff3e8bab6bc6a8c86957b5683fd5d2300'], + }), + ('fpc', '2.2-3', { + 'checksums': ['8100a74e6ff96b1cd65fd22494f2d200e54ea5ea533cfca321fa494914bdc3b7'], + }), + ('BiasedUrn', '1.07', { + 'checksums': ['2377c2e59d68e758a566452d7e07e88663ae61a182b9ee455d8b4269dda3228e'], + }), + ('TeachingDemos', '2.10', { + 'checksums': ['2ef4c2e36ba13e32f66000e84281a3616584c86b255bca8643ff3fe4f78ed704'], + }), + ('kohonen', '3.0.10', { + 'patches': ['kohonen-3.0.8_intel-wd308.patch'], + 'checksums': [ + '996956ea46a827c9f214e4f940a19304a0ff35bda707d4d7312f80d3479067b2', # kohonen_3.0.10.tar.gz + '816d22f6aec48691e3383c66274df9c83fcabcf68250d627a3e0cfd694dbe78e', # kohonen-3.0.8_intel-wd308.patch + ], + }), + ('base64', '2.0', { + 'checksums': ['8e259c2b12446197d1152b83a81bab84ccb5a5b77021a9b5645dd4c63c804bd1'], + }), + ('doRNG', '1.7.1', { + 'checksums': [('27533d54464889d1c21301594137fc0f536574e3a413d61d7df9463ab12a67e9', + 'bda8143e2b5554fb39fdea81af6482f8938160fdbf5c45014f3a5de40aacf4c4')], + }), + ('nleqslv', '3.3.2', { + 'checksums': ['f54956cf67f9970bb3c6803684c84a27ac78165055745e444efc45cfecb63fed'], + }), + ('Deriv', '4.0', { + 'checksums': ['76788764177b24dc27f4e27046fa563ad97014e0d53e14a880ebff2f9177b40e'], + }), + ('RGCCA', '2.1.2', { + 'checksums': ['20f341fca8f616c556699790814debdf2ac7aa4dd9ace2071100c66af1549d7d'], + }), + ('pheatmap', '1.0.12', { + 'checksums': ['579d96ee0417203b85417780eca921969cda3acc210c859bf9dfeff11539b0c1'], + }), + ('pvclust', '2.2-0', { + 'checksums': ['7892853bacd413b5a921006429641ad308a344ca171b3081c15e4c522a8b0201'], + }), + ('RCircos', '1.2.1', { + 'checksums': ['3b9489ab05ea83ead99ca6e4a1e6830467a2064779834aff1317b42bd41bb8fd'], + }), + ('lambda.r', '1.2.4', { + 'checksums': ['d252fee39065326c6d9f45ad798076522cec05e73b8905c1b30f95a61f7801d6'], + }), + ('futile.options', '1.0.1', { + 'checksums': ['7a9cc974e09598077b242a1069f7fbf4fa7f85ffe25067f6c4c32314ef532570'], + }), + ('futile.logger', '1.4.3', { + 'checksums': ['5e8b32d65f77a86d17d90fd8690fc085aa0612df8018e4d6d6c1a60fa65776e4'], + }), + ('VennDiagram', '1.6.20', { + 'checksums': ['e51cb3fff23c6ec8191966490bf875a7415f8725d4054bae881a25febb9281c5'], + }), + ('xlsxjars', '0.6.1', { + 'checksums': ['37c1517f95f8bca6e3514429394d2457b9e62383305eba288416fb53ab2e6ae6'], + }), + ('xlsx', '0.6.1', { + 'checksums': ['a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4'], + }), + ('uroot', '2.1-0', { + 'checksums': ['3c02a9dadd22aa67a59e99007ab6f576dc428859fa746d3a8f3ffa2bb43d18c2'], + }), + ('forecast', '8.10', { + 'patches': ['forecast-6.1_icpc-wd308.patch'], + 'checksums': [ + '798e15d15be9af0b8f505e826db83d5f09d7a7434567ec291a31eaf3b8c88c49', # forecast_8.10.tar.gz + '5100dce59858960fc2ade7c599ecda13f3473984fb2bd90f8fa6598653e7ddc2', # forecast-6.1_icpc-wd308.patch + ], + }), + ('fma', '2.3', { + 'checksums': ['f516eff79e14d4ffefcdc2db06d97ae57f998e37e871264457078f671384fafc'], + }), + ('expsmooth', '2.3', { + 'checksums': ['ac7da36347f983d6ec71715daefd2797fe2fc505c019f4965cff9f77ce79982a'], + }), + ('fpp', '0.5', { + 'checksums': ['9c87dd8591b8a87327cae7a03fd362a5492495a96609e5845ccbeefb96e916cb'], + }), + ('tensor', '1.5', { + 'checksums': ['e1dec23e3913a82e2c79e76313911db9050fb82711a0da227f94fc6df2d3aea6'], + }), + ('polyclip', '1.10-0', { + 'checksums': ['74dabc0dfe5a527114f0bb8f3d22f5d1ae694e6ea9345912909bae885525d34b'], + }), + ('goftest', '1.2-2', { + 'checksums': ['e497992666b002b6c6bed73bf05047ad7aa69eb58898da0ad8f1f5b2219e7647'], + }), + ('spatstat.utils', '1.15-0', { + 'checksums': ['90e07d730b6939f47f93c939afae10874b2c82bd402960ede4133de67dca2a0c'], + }), + ('spatstat.data', '1.4-0', { + 'checksums': ['121e5bb92beb7ccac920f921e760f429fd71bcfe11cb9b07a7e7326c7a72ec8c'], + }), + ('spatstat', '1.62-2', { + 'checksums': ['57cc1dc51b3d74fb4e3edfa30e6441db98c99e354ff65ffc82d5419a49a8353b'], + }), + ('pracma', '2.2.9', { + 'checksums': ['0cea0ff5e88643df121e07b9aebfe57084c61e11801680039752f371fe87bf1e'], + }), + ('RCurl', '1.95-4.12', { + 'checksums': ['393779efafdf40823dac942a1e028905d65c34f3d41cfd21bcd225e411385ff4'], + }), + ('bio3d', '2.4-0', { + 'checksums': ['9ab86e299adee14e9a87ec87284f4c52a0114d303f21d166aaa0dc766f987746'], + }), + ('AUC', '0.3.0', { + 'checksums': ['e705f2c63d336249d19187f3401120d738d42d323fce905f3e157c2c56643766'], + }), + ('interpretR', '0.2.4', { + 'checksums': ['4c08a6dffd6fd5764f27812f3a085c53e6a21d59ae82d903c9c0da93fd1dd059'], + }), + ('cvAUC', '1.1.0', { + 'checksums': ['c4d8ed53b93869650aa2f666cf6d1076980cbfea7fa41f0b8227595be849738d'], + }), + ('SuperLearner', '2.0-26', { + 'checksums': ['4462922c8daae2773f79ecdea7ca3cc4ea51bfd101c5e6c1ad22f9190e746081'], + }), + ('mediation', '4.5.0', { + 'checksums': ['210206618787c395a67689be268283df044deec7199d9860ed95218ef1e60845'], + }), + ('ModelMetrics', '1.2.2', { + 'checksums': ['66d6fc75658287fdbae4d437b51d26781e138b8baa558345fb9e5a2df86a0d95'], + }), + ('CVST', '0.2-2', { + 'checksums': ['854b8c983427ecf9f2f7798c4fd1c1d06762b5b0bcb1045502baadece6f78316'], + }), + ('DRR', '0.0.3', { + 'checksums': ['7493389c1fb9ddc4d4261e15bf2d4198603227275688b1d3e3994d47e976a1f9'], + }), + ('dimRed', '0.2.3', { + 'checksums': ['e6e56e3f6999ebdc326e64ead5269f3aaf61dd587beefafb7536ac3890370d84'], + }), + ('lubridate', '1.7.4', { + 'checksums': ['510ca87bd91631c395655ee5029b291e948b33df09e56f6be5839f43e3104891'], + }), + ('ddalpha', '1.3.10', { + 'checksums': ['5f52e0aae9917476078daf031f2213b0b6b83d225530394bdb759e86fc79c480'], + }), + ('gower', '0.2.1', { + 'checksums': ['af3fbe91cf818c0841b2c0ec4ddf282c182a588031228c8d88f7291b2cdff100'], + }), + ('RcppRoll', '0.3.0', { + 'checksums': ['cbff2096443a8a38a6f1dabf8c90b9e14a43d2196b412b5bfe5390393f743f6b'], + }), + ('recipes', '0.1.7', { + 'checksums': ['28e96953355749dd1deb6786b22ec825a6fdb9f336e2785d45611e89f7e988bf'], + }), + ('caret', '6.0-84', { + 'checksums': ['a1831c086a9c71b469f7405649ba04517683cdf229e119c005189cf57244090d'], + }), + ('adabag', '4.2', { + 'checksums': ['47019eb8cefc8372996fbb2642f64d4a91d7cedc192690a8d8be6e7e03cd3c81'], + }), + ('parallelMap', '1.4', { + 'checksums': ['fb6f15e325f729f1c5218768b17c20909ee857069c6cc5d8df50e1dafe26ed5b'], + }), + ('ParamHelpers', '1.13', { + 'checksums': ['b9b5212a485f441504716fcddf4fd7376bf3b909aae049c7394245e853424e79'], + }), + ('ggvis', '0.4.5', { + 'checksums': ['82373c3565c299279f6849f798cc39127b2b3f7ff2deee1946528474824b3124'], + }), + ('mlr', '2.16.0', { + 'checksums': ['3db8141d9cbb71139c9bf3a3ea995524322512221b56e6bcf44338d24f84e76a'], + }), + ('unbalanced', '2.0', { + 'checksums': ['9be32b1ce9d972f1abfff2fbe18f5bb5ba9c3f4fb1282063dc410b82ad4d1ea2'], + }), + ('RSNNS', '0.4-12', { + 'checksums': ['b18dfeda71573bc92c6888af72da407651bff7571967965fd3008f0d331743b9'], + }), + ('abc.data', '1.0', { + 'checksums': ['b242f43c3d05de2e8962d25181c6b1bb6ca1852d4838868ae6241ca890b161af'], + }), + ('abc', '2.1', { + 'checksums': ['0bd2dcd4ee1915448d325fb5e66bee68e0497cbd91ef67a11b400b2fbe52ff59'], + }), + ('lhs', '1.0.1', { + 'checksums': ['a4d5ac0c6f585f2880364c867fa94e6554698beb65d3678ba5938dd84fc6ea53'], + }), + ('tensorA', '0.36.1', { + 'checksums': ['c7ffe12b99867675b5e9c9f31798f9521f14305c9d9f9485b171bcbd8697d09c'], + }), + ('EasyABC', '1.5', { + 'checksums': ['1dd7b1383a7c891cafb34d9cec65d92f1511a336cff1b219e63c0aa791371b9f'], + }), + ('whisker', '0.4', { + 'checksums': ['7a86595be4f1029ec5d7152472d11b16175737e2777134e296ae97341bf8fba8'], + }), + ('commonmark', '1.7', { + 'checksums': ['d14a767a3ea9778d6165f44f980dd257423ca6043926e3cd8f664f7171f89108'], + }), + ('roxygen2', '7.0.2', { + 'checksums': ['5823937df68ea558e5e85771b8b6e090775b82f7f797ca5d539e7378c4535d98'], + }), + ('git2r', '0.26.1', { + 'checksums': ['13d609286a0af4ef75ba76f2c2f856593603b8014e311b88896243a50b417435'], + }), + ('rversions', '2.0.1', { + 'checksums': ['51ec1f64e7d628e88d716a020d5d521eba71d472e3c9ae7b694428ef6dd786c5'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('sessioninfo', '1.1.1', { + 'checksums': ['166b04678448a7decd50f24afabe5e2ad613e3c55b180ef6e8dd7a870a1dae48'], + }), + ('rcmdcheck', '1.3.3', { + 'checksums': ['1ab679eb1976d74cd3be5bcad0af7fcc673dbdfd4406bbce32591c8fddfb93b4'], + }), + ('remotes', '2.1.0', { + 'checksums': ['8944c8f6fc9f0cd0ca04d6cf1221b716eee08facef9f4b4c4d91d0346d6d68a7'], + }), + ('fs', '1.3.1', { + 'checksums': ['d6934dca8f835d8173e3fb9fd4d5e2740c8c04348dd2bcc57df1b711facb46bc'], + }), + ('clisymbols', '1.2.0', { + 'checksums': ['0649f2ce39541820daee3ed408d765eddf83db5db639b493561f4e5fbf88efe0'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gh', '1.0.1', { + 'checksums': ['f3c02b16637ae390c3599265852d94b3de3ef585818b260d00e7812595b391d2'], + }), + ('usethis', '1.5.1', { + 'checksums': ['9e3920a04b0df82adf59eef2c1b2b4d835c4a757a51b3c163b8fc619172f561d'], + }), + ('DT', '0.10', { + 'checksums': ['3cc6dfc9697b52aef21d30dcfd355831c6216edcc6dd6bfb9a106cce6ab0906f'], + }), + ('rex', '1.1.2', { + 'checksums': ['bd3c74ceaf335336f5dd04314d0a791f6311e421a2158f321f5aab275f539a2a'], + }), + ('covr', '3.4.0', { + 'checksums': ['e57d9c656b4ab50a7f9557dee422d8777efaf08ecde0fd8bfa5897ef4d9e845c'], + }), + ('devtools', '2.2.1', { + 'checksums': ['2e988fb56b068ba958ea471224d2462427868ce7706e157a90c0ce0e13294e44'], + }), + ('Rook', '1.1-1', { + 'checksums': ['00f4ecfa4c5c57018acbb749080c07154549a6ecaa8d4130dd9de79427504903'], + }), + ('Cairo', '1.5-10', { + 'patches': ['Cairo-1.5-10.patch'], + 'checksums': [ + '7837f0c384cd49bb3342cb39a916d7a80b02fffbf123913a58014e597f69b5d5', # Cairo_1.5-10.tar.gz + 'da36002db4d70583ef3c772ae56b507f19970d16fd35c412ce52b19ffb6466d8', # Cairo-1.5-10.patch + ], + }), + ('RMTstat', '0.3', { + 'checksums': ['81eb4c5434d04cb66c749a434c33ceb1c07d92ba79765d4e9233c13a092ec2da'], + }), + ('Lmoments', '1.3-1', { + 'checksums': ['7c9d489a08f93fa5877e2f233ab9732e0d1b2761596b3f6ac91f2295e41a865d'], + }), + ('distillery', '1.0-6', { + 'checksums': ['4910e2952f767c1062d7cbe648c90a97009e2b3da316c6b33f6d022cd38b23d6'], + }), + ('extRemes', '2.0-11', { + 'checksums': ['75fbdeef677c81cf5661b8df3df4090c55f53e9bb96bb138b498eb0fbbf5af42'], + }), + ('pixmap', '0.4-11', { + 'checksums': ['6fa010749a59cdf56aad9f81271473b7d55697036203f2cd5d81372bcded7412'], + }), + ('tkrplot', '0.0-24', { + 'checksums': ['2873630a37d7ae1e09a5803d9a89ca0494edd83526c7b1860d9246543722f311'], + }), + ('misc3d', '0.8-4', { + 'checksums': ['75de3d2237f67f9e58a36e80a6bbf7e796d43eb46789f2dd1311270007bf5f62'], + }), + ('multicool', '0.1-11', { + 'patches': ['multicool-0.1-10_icpc-wd308.patch'], + 'checksums': [ + '1c907e64af2ac39facdf431a5691e69649f64af1f50e198ae39da5bf30026476', # multicool_0.1-11.tar.gz + '2afcb15d37d0e4adc43530e448325cb97bc46ebf4d1da9fe6c07cf0070fe0a0c', # multicool-0.1-10_icpc-wd308.patch + ], + }), + ('plot3D', '1.1.1', { + 'checksums': ['f6fe4a001387132626fc553ed1d5720d448b8064eb5a6917458a798e1d381632'], + }), + ('plot3Drgl', '1.0.1', { + 'checksums': ['466d428d25c066c9c96d892f24da930513d42b1bdf76d3b53628c3ba13c3e48a'], + }), + ('OceanView', '1.0.4', { + 'checksums': ['e67f6f376737e1e5cf22fdfe2769a8f674e90c886b0e43942e97d9a3e6924f1c'], + }), + ('ks', '1.11.6', { + 'checksums': ['d8f1ccb99281eed092b8f950cfbf422330e88f2a0ce1ef6c9dbd7d8b9d648c41'], + }), + ('logcondens', '2.1.5', { + 'checksums': ['72e61abc1f3eb28830266fbe5b0da0999eb5520586000a3024e7c26be93c02eb'], + }), + ('Iso', '0.0-18', { + 'checksums': ['2d7e8c4452653364ee086d95cea620c50378e30acfcff129b7261e1756a99504'], + }), + ('penalized', '0.9-51', { + 'checksums': ['eaa80dca99981fb9eb576261f30046cfe492d014cc2bf286c447b03a92e299fd'], + }), + ('clusterRepro', '0.9', { + 'checksums': ['940d84529ff429b315cf4ad25700f93e1156ccacee7b6c38e4bdfbe2d4c6f868'], + }), + ('randomForestSRC', '2.9.2', { + 'checksums': ['780fbc07ca0b2676fadf576d4d278887672b431ba42cd49b769ed8ccbc4e6d74'], + }), + ('sm', '2.2-5.6', { + 'checksums': ['b890cd7ebe8ed711ab4a3792c204c4ecbe9e6ca1fd5bbc3925eba5833a839c30'], + }), + ('pbivnorm', '0.6.0', { + 'checksums': ['07c37d507cb8f8d2d9ae51a9a6d44dfbebd8a53e93c242c4378eaddfb1cc5f16'], + }), + ('lavaan', '0.6-5', { + 'checksums': ['feeb6e1b419aa1d54fd5af1d67260b5d13ff251c19de8136a4df565305d47b12'], + }), + ('matrixcalc', '1.0-3', { + 'checksums': ['17e6caeeecd596b850a6caaa257984398de9ec5d2b41ce83c428f112614b9cb0'], + }), + ('arm', '1.10-1', { + 'checksums': ['6f1158c9295e65bd649139224497d3356189b931ff143f9b374daae72548776f'], + }), + ('mi', '1.0', { + 'checksums': ['34f44353101e8c3cb6bf59c5f4ff5b2391d884dcbb9d23066a11ee756b9987c0'], + }), + ('visNetwork', '2.0.9', { + 'checksums': ['5e0b3dc3a91e66e0a359433f03cc856d04b981b0f9ad228d8fa9c96b7fcaa420'], + }), + ('rgexf', '0.15.3', { + 'checksums': ['2e8a7978d1fb977318e6310ba65b70a9c8890185c819a7951ac23425c6dc8147'], + }), + ('influenceR', '0.1.0', { + 'checksums': ['4fc9324179bd8896875fc0e879a8a96b9ef2a6cf42a296c3b7b4d9098519e98a'], + }), + ('downloader', '0.4', { + 'checksums': ['1890e75b028775154023f2135cafb3e3eed0fe908138ab4f7eff1fc1b47dafab'], + }), + ('DiagrammeR', '1.0.1', { + 'checksums': ['ccee8acf608fc909e73c6de4374cef5a570cb62e5f454ac55dda736f22f3f013'], + }), + ('sem', '3.1-9', { + 'checksums': ['4a33780202506543da85877cd2813250114420d6ec5e75457bc67477cd332cb9'], + }), + ('jpeg', '0.1-8.1', { + 'checksums': ['1db0a4976fd9b2ae27a37d3e856cca35bc2909323c7a40724846a5d3c18915a9'], + }), + ('network', '1.16.0', { + 'checksums': ['a24f51457439c7186ffa1fe53719742c501929ac1a354e458754a83f280fce36'], + }), + ('statnet.common', '4.3.0', { + 'checksums': ['834a3359eac967df0420eee416ae4983e3b502a3de56bb24f494a7ca4104e959'], + }), + ('sna', '2.5', { + 'checksums': ['13b508cacb0bf1e79b55d5c8f7e9ada3b173468d4d6d5f1dc606990ac03071c8'], + }), + ('glasso', '1.11', { + 'checksums': ['4c37844b26f55985184a734e16b8fe880b192e3d2763614b0ab3f99b4530e30a'], + }), + ('huge', '1.3.4', { + 'checksums': ['23165f49ec9e67ca3506cc83abbbf8eb3f38c5e19c092133189b7ca17690c31e'], + }), + ('d3Network', '0.5.2.1', { + 'checksums': ['5c798dc0c87c6d574abb7c1f1903346e6b0fec8adfd1df7aef5e4f9e7e3a09be'], + }), + ('ggm', '2.3', { + 'checksums': ['832ffe81ff87c6f1a6644e689ebbfb172924b4c4584ac8108d1244d153219ed8'], + }), + ('BDgraph', '2.62', { + 'checksums': ['7e5de4406f4a7873bf948852291d2851a2ab312288467687dd5c0392b2723bac'], + }), + ('pbapply', '1.4-2', { + 'checksums': ['ac19f209f36f4fa3d0f5b14b6cc5b0c279996fb9d3e86c848c0f6d03c025b3f6'], + }), + ('graphlayouts', '0.5.0', { + 'checksums': ['83f61ce07580c5a64c7044c12b20d98ccf138c7e78ff12855cdfc206e1fab10d'], + }), + ('tweenr', '1.0.1', { + 'checksums': ['efd68162cd6d5a4f6d833dbf785a2bbce1cb7b9f90ba3fb060931a4bd705096b'], + }), + ('ggforce', '0.3.1', { + 'checksums': ['a05271da9b226c12ae5fe6bc6eddb9ad7bfe19e1737e2bfcd6d7a89631332211'], + }), + ('tidygraph', '1.1.2', { + 'checksums': ['5642001d4cccb122d66481b7c61a06c724c02007cbd356ee61cb29726a56fafe'], + }), + ('ggraph', '2.0.0', { + 'checksums': ['4307efe85bfc6a0496797f6b86d6b174ba196538c51b1a6b6af55de0d4e04762'], + }), + ('qgraph', '1.6.4', { + 'checksums': ['43865a096cd9af122c75594a268bac342e80626a8137539d0c94bb0349408fbe'], + }), + ('HWxtest', '1.1.9', { + 'checksums': ['a37309bed4a99212ca104561239d834088217e6c5e5e136ff022544c706f25e6'], + }), + ('diveRsity', '1.9.90', { + 'checksums': ['b8f49cdbfbd82805206ad293fcb2dad65b962fb5523059a3e3aecaedf5c0ee86'], + }), + ('doSNOW', '1.0.18', { + 'checksums': ['70e7bd82186e477e3d1610676d4c6a75258ac08f104ecf0dcc971550ca174766'], + }), + ('geepack', '1.3-1', { + 'checksums': ['823153ca28e1a8bd8a45de778279480c1c35e063d62c8955b6cea1602f28d6df'], + }), + ('biom', '0.3.12', { + 'checksums': ['4ad17f7811c7346dc4923bd6596a007c177eebb1944a9f46e5674afcc5fdd5a1'], + }), + ('pim', '2.0.1', { + 'checksums': ['174568a01f68b9601a4ea89ca5857bf4888242f00e4212bfb7a422d6292300d5'], + }), + ('minpack.lm', '1.2-1', { + 'checksums': ['14cb7dba3ef2b46da0479b46d46c76198e129a31f6157cd8b37f178adb15d5a3'], + }), + ('rootSolve', '1.8.1', { + 'checksums': ['1dde127817cfb2273724c63f662143cc7eb449a833243e0e56ef347df0d5796a'], + }), + ('diagram', '1.6.4', { + 'checksums': ['7c2bc5d5d634c3b8ca7fea79fb463e412962d88f47a77a74c811cc62f375ce38'], + }), + ('FME', '1.3.5', { + 'checksums': ['3619d88df2a41ca8819b93bb7dff3b8233f76ff8ab0ca67c664f530f835935e4'], + }), + ('bmp', '0.3', { + 'checksums': ['bdf790249b932e80bc3a188a288fef079d218856cf64ffb88428d915423ea649'], + }), + ('tiff', '0.1-5', { + 'checksums': ['9514e6a9926fcddc29ce1dd12b1072ad8265900373f738de687ef4a1f9124e2b'], + }), + ('readbitmap', '0.1.5', { + 'checksums': ['737d7d585eb33de2c200da64d16781e3c9522400fe2af352e1460c6a402a0291'], + }), + ('imager', '0.41.2', { + 'patches': ['imager-0.41.2_icpc-wd308.patch'], + 'checksums': [ + '9be8bc8b3190d469fcb2883045a404d3b496a0380f887ee3caea11f0a07cd8a5', # imager_0.41.2.tar.gz + 'ad90b664505ccb630cc6c517da787e81d6a1e042a74fe5be413da47dbd29a817', # imager-0.41.2_icpc-wd308.patch + ], + }), + ('signal', '0.7-6', { + 'checksums': ['6b60277b07cf0167f8272059b128cc82f27a9bab1fd33d74c2a9e1f2abca5def'], + }), + ('tuneR', '1.3.3', { + 'checksums': ['bdc3c2017b162d2ba0a249e80361a4f47202e763c21aecfc57380a482a3a692b'], + }), + ('pastecs', '1.3.21', { + 'checksums': ['8c1ef2affe88627f0b23295aa5edb758b8fd6089ef09f60f37c46445128b8d7c'], + }), + ('audio', '0.1-6', { + 'checksums': ['3f261413ba2d3e9ae58c44abffe5188cc7c21a78a0c93448c7d384d3913d73b8'], + }), + ('fftw', '1.0-5', { + 'checksums': ['afc94fe8e5bed9195c191606239cd37f1b88e24e7422e9c5249cca0781b3f20c'], + }), + ('seewave', '2.1.5', { + 'checksums': ['718b1fb1c289f92be50de099da36d20380d113cb1577569333fca6195f71e8e1'], + }), + ('gsw', '1.0-5', { + 'checksums': ['eb468918ee91e429b47fbcac43269eca627b7f64b61520de5bbe8fa223e96453'], + }), + ('oce', '1.1-1', { + 'checksums': ['2ce8f8d3adb3da5c8a09fda060e1ff79cad0f0f6f918f8fe64f51a6cd6b58e43'], + }), + ('ineq', '0.2-13', { + 'checksums': ['e0876403f59a3dfc2ea7ffc0d965416e1ecfdecf154e5856e5f54800b3efda25'], + }), + ('soundecology', '1.3.3', { + 'checksums': ['276164d5eb92c78726c647be16232d2443acbf7061371ddde2672b4fdb7a069a'], + }), + ('memuse', '4.0-0', { + 'checksums': ['fbf8716a1388692ee439f69ac99643fa427eb100027d8911ff0fbfdcb5b6c3bc'], + }), + ('pinfsc50', '1.1.0', { + 'checksums': ['b6b9b6365a3f408533264d7ec820494f57eccaf362553e8478a46a8e5b474aba'], + }), + ('vcfR', '1.8.0', { + 'checksums': ['5ffcf9980c1936b9be41b92d5887c56a7ec6e3cf197e5ef7c78aefa8aba20499'], + }), + ('glmmML', '1.1.0', { + 'checksums': ['34f088a73ccf6092908502a5bdaaf8209e9134d38abbbd7c4dd559832e653188'], + }), + ('cowplot', '1.0.0', { + 'checksums': ['70f9a7c46d10f409d1599f1afc9fd3c947051cf2b430f01d903c64ef1e6c98a5'], + }), + ('tsne', '0.1-3', { + 'checksums': ['66fdf5d73e69594af529a9c4f261d972872b9b7bffd19f85c1adcd66afd80c69'], + }), + ('sn', '1.5-4', { + 'checksums': ['46677ebc109263a68f62b5cf53ec59916cda490e5bc5bbb08276757a677f8674'], + }), + ('tclust', '1.4-1', { + 'checksums': ['4b0be612c8ecd7b4eb19a44ab6ac8f5d40515600ae1144c55989b6b41335ad9e'], + }), + ('ranger', '0.11.2', { + 'checksums': ['13ac8a9433fdd92f62f66de44abc52477dcbb436b2045c1947951a266bffbeeb'], + }), + ('hexbin', '1.28.0', { + 'checksums': ['cda0d4b637ddd63eaaed70eb7b3ced09216dbf63e7803d6dfe3c8d3fc392a82c'], + }), + ('pryr', '0.1.4', { + 'checksums': ['d39834316504c49ecd4936cbbcaf3ee3dae6ded287af42475bf38c9e682f721b'], + }), + ('moments', '0.14', { + 'checksums': ['2a3b81e60dafdd092d2bdd3513d7038855ca7d113dc71df1229f7518382a3e39'], + }), + ('laeken', '0.5.0', { + 'checksums': ['ea529f9e45a3825e1f13f8dbd8e7c5f5a42933525ca529230c893eb08e1f39bd'], + }), + ('VIM', '4.8.0', { + 'checksums': ['3c6b4fdc10c0375e3fdc56b34a8c05661155bd3166a8b3f36b0addf73d51a423'], + }), + ('proxy', '0.4-23', { + 'checksums': ['9dd4eb0978f40e4fcb55c8a8a26266d32eff9c63ac9dfe70cf1f664ca9c3669d'], + }), + ('smoother', '1.1', { + 'checksums': ['91b55b82f805cfa1deedacc0a4e844a2132aa59df593f3b05676954cf70a195b'], + }), + ('dynamicTreeCut', '1.63-1', { + 'checksums': ['831307f64eddd68dcf01bbe2963be99e5cde65a636a13ce9de229777285e4db9'], + }), + ('beeswarm', '0.2.3', { + 'checksums': ['0115425e210dced05da8e162c8455526a47314f72e441ad2a33dcab3f94ac843'], + }), + ('vipor', '0.4.5', { + 'checksums': ['7d19251ac37639d6a0fed2d30f1af4e578785677df5e53dcdb2a22771a604f84'], + }), + ('ggbeeswarm', '0.6.0', { + 'checksums': ['bbac8552f67ff1945180fbcda83f7f1c47908f27ba4e84921a39c45d6e123333'], + }), + ('shinydashboard', '0.7.1', { + 'checksums': ['51a49945c6b8a684111a2ba4b2a5964e3a50610286ce0378e37ae02316620a4e'], + }), + ('rrcov', '1.4-9', { + 'checksums': ['e757369d70de4def182f4ede8bb066b156fd1a96abeedf8a14f986455becfb87'], + }), + ('WriteXLS', '5.0.0', { + 'checksums': ['5aeb631c7f4dee300a19ded493110d7241e1b79744be05beca770a01ffc1d7bf'], + }), + ('bst', '0.3-17', { + 'checksums': ['1ed161d33a7304abfa2fb23daeda2f870ad8483b7fa9b91e6fc8ced21fd8f074'], + }), + ('mpath', '0.3-20', { + 'checksums': ['0299b11bdd346a7825cd0bba302f09e7a0a15b9491f9179651b2f1154c80d392'], + }), + ('timereg', '1.9.4', { + 'checksums': ['fbf4eeee1648fceb98773156764c32b3a9481f0fb9f8dc3a9d0331a9051cb54b'], + }), + ('peperr', '1.1-7.1', { + 'checksums': ['5d4eff0f0b61c0b3e479c2ac2978c8e32373b9630565bf58fee48ead6166698a'], + }), + ('heatmap3', '1.1.6', { + 'checksums': ['5d5a3d574e9e3699490c93a523ce242006257e5be110935d58c74c135a4e4a8d'], + }), + ('GlobalOptions', '0.1.1', { + 'checksums': ['4249ef78424128050af83bbb8e71b4af82f8490c87f6a9d927782b80be830975'], + }), + ('circlize', '0.4.8', { + 'checksums': ['22d6908b9d2e496105d9b70b73a74152398e5e9e38c60042ffe041df2b4c794b'], + }), + ('GetoptLong', '0.1.7', { + 'checksums': ['b9a98881db407eae9b711c4fa9170168fd5f3be1f8485cd8f28d0a60ace083ba'], + }), + ('dendextend', '1.13.2', { + 'checksums': ['79543002ab3147c283fa659c4a16a1df4c5740b5fe207565236d32cf52db94c5'], + }), + ('RInside', '0.2.15', { + 'checksums': ['1e1d87a3584961f3aa4ca6acd4d2f3cda26abdab027ff5be2fd5cd76a98af02b'], + }), + ('limSolve', '1.5.6', { + 'checksums': ['b97ea9930383634c8112cdbc42f71c4e93fe0e7bfaa8f401921835cb44cb49a0'], + }), + ('dbplyr', '1.4.2', { + 'checksums': ['b783f0da2c09a1e63f41168b02c0715b08820f02a351f7ab0aaa688432754de0'], + }), + ('modelr', '0.1.5', { + 'checksums': ['45bbee387c6ba154f9f8642e9f03ea333cce0863c324ff15d23096f33f85ce5a'], + }), + ('debugme', '1.1.0', { + 'checksums': ['4dae0e2450d6689a6eab560e36f8a7c63853abbab64994028220b8fd4b793ab1'], + }), + ('reprex', '0.3.0', { + 'checksums': ['203c2ae6343f6ff887e7a5a3f5d20bae465f6e8d9745c982479f5385f4effb6c'], + }), + ('selectr', '0.4-2', { + 'checksums': ['5588aed05f3f5ee63c0d29953ef53da5dac7afccfdd04b7b22ef24e1e3b0c127'], + }), + ('rvest', '0.3.5', { + 'checksums': ['0e7f41be4ce6501d7af50575a2532d4bfd9153ca57900ee62dbc27c0a22c0a64'], + }), + ('tidyverse', '1.3.0', { + 'checksums': ['6d8acb81e994f9bef5e4dcf908bcea3786d108adcf982628235b6c8c80f6fe09'], + }), + ('R.cache', '0.14.0', { + 'checksums': ['18af4e372440b9f28b4b71346c8ed9de220232f9903730ccee2bfb3c612c16d9'], + }), + ('R.rsp', '0.43.2', { + 'checksums': ['f291a78ce9955943e0ebad1291f729dc4d9a8091f04b83fc4b1526bcb6c71f89'], + }), + ('listenv', '0.8.0', { + 'checksums': ['fd2aaf3ff2d8d546ce33d1cb38e68401613975117c1f9eb98a7b41facf5c485f'], + }), + ('globals', '0.12.5', { + 'checksums': ['1519a7668b4b549c081f60a5f6b71d8d1dc8833f618125f6c0e4caf8b48a48c1'], + }), + ('future', '1.15.1', { + 'checksums': ['ed4f7f356ca1cb3294f9a5181e4087b2a7781c4ab7304393bf40e1ac388a3080'], + }), + ('gdistance', '1.2-2', { + 'checksums': ['c8c923f02ae4e9ef8376d1b195e0246b6941356c8c790c0a5673c5009eee1753'], + }), + ('vioplot', '0.3.4', { + 'checksums': ['4914262f2e7913ffa5741e74b20157f4a904ba31e648fa5df9ff6a1aaba753bb'], + }), + ('emulator', '1.2-20', { + 'checksums': ['7cabf2cf74d879ad9dbaed8fdee54a5c94a8658a0645c021d160b2ef712ce287'], + }), + ('gmm', '1.6-4', { + 'checksums': ['03ad5ff37d174e9cef13fa41d866412c57b7cbd9155312831e16a1fcda70bc95'], + }), + ('tmvtnorm', '1.4-10', { + 'checksums': ['1a9f35e9b4899672e9c0b263affdc322ecb52ec198b2bb015af9d022faad73f0'], + }), + ('IDPmisc', '1.1.19', { + 'checksums': ['0d5e35252c7ec2654a3d64949bdc0977cc8479f8ada97bccd0d90d70aadb0c8f'], + }), + ('gap', '1.2.1', { + 'checksums': ['5a20adcc7e503b9a2123048510d56ce3ec9f00d5855629b4cbf0d7c7ad8c6fb5'], + }), + ('qrnn', '2.0.5', { + 'checksums': ['3bd83ee8bd83941f9defdab1b5573d0ceca02bf06759a67665e5b9358ff92f52'], + }), + ('TMB', '1.7.15', { + 'checksums': ['facbc7cc44f993e0d827a6eb84928f8e35b0b3f263582d885a307e150b434de4'], + }), + ('glmmTMB', '0.2.3', { + 'checksums': ['6b6f62addaa54b32b975bc984110e245330749ebf69bed4a297f9da1b89fb00c'], + }), + ('spaMM', '3.0.0', { + 'checksums': ['5aca7eebd38d93f3ad6bec6bb01b213879551b4320f6fc17bdebdd4d09e48fe7'], + }), + ('DHARMa', '0.2.6', { + 'checksums': ['d2a17c994e59c4fb4c82825b97a78ac120a350bf94261511d437659a00296957'], + }), + ('mvnfast', '0.2.5', { + 'checksums': ['21b9fa72d1e3843513908aaacd6c4d876cc7a9339782d0151b24910df2975f88'], + }), + ('bridgesampling', '0.7-2', { + 'checksums': ['64a44e92ccc2828261a71e2298901a8064b36df1bc2b8796d47a1bf26fb9a44d'], + }), + ('BayesianTools', '0.1.7', { + 'checksums': ['af49389bdeb794da3c39e1d63f59e6219438ecb8613c5ef523b00c6fed5a600c'], + }), + ('gomms', '1.0', { + 'checksums': ['52828c6fe9b78d66bde5474e45ff153efdb153f2bd9f0e52a20a668e842f2dc5'], + }), + ('feather', '0.3.5', { + 'checksums': ['50ff06d5e24d38b5d5d62f84582861bd353b82363e37623f95529b520504adbf'], + }), + ('dummies', '1.5.6', { + 'checksums': ['7551bc2df0830b98c53582cac32145d5ce21f5a61d97e2bb69fd848e3323c805'], + }), + ('SimSeq', '1.4.0', { + 'checksums': ['5ab9d4fe2cb1b7634432ff125a9e04d2f574fed06246a93859f8004e10790f19'], + }), + ('uniqueAtomMat', '0.1-3-2', { + 'checksums': ['f7024e73274e1e76a870ce5e26bd58f76e8f6df0aa9775c631b861d83f4f53d7'], + }), + ('PoissonSeq', '1.1.2', { + 'checksums': ['6f3dc30ad22e33e4fcfa37b3427c093d591c02f1b89a014d85e63203f6031dc2'], + }), + ('aod', '1.3.1', { + 'checksums': ['052d8802500fcfdb3b37a8e3e6f3fbd5c3a54e48c3f68122402d2ea3a15403bc'], + }), + ('cghFLasso', '0.2-1', { + 'checksums': ['6e697959b35a3ceb2baa1542ef81f0335006a5a9c937f0173c6483979cb4302c'], + }), + ('svd', '0.5', { + 'checksums': ['d042d448671355d0664d37fd64dc90932eb780e6494c479d4431d1faae2071a1'], + }), + ('Rssa', '1.0', { + 'checksums': ['9cc20a7101d8dff4c6cfb789f9bdc14e2b3bb128d7613a67b0f9633cf006902a'], + }), + ('JBTools', '0.7.2.9', { + 'checksums': ['b33cfa17339df7113176ad1832cbb0533acf5d25c36b95e888f561d586c5d62f'], + }), + ('RUnit', '0.4.32', { + 'checksums': ['23a393059989000734898685d0d5509ece219879713eb09083f7707f167f81f1'], + }), + ('DistributionUtils', '0.6-0', { + 'checksums': ['7443d6cd154760d55b6954142908eae30385672c4f3f838dd49876ec2f297823'], + }), + ('gapfill', '0.9.6', { + 'checksums': ['850d0be9d05e3f3620f0f5143496321f1004ed966299bffd6a67a9abd8d9040d'], + }), + ('gee', '4.13-20', { + 'checksums': ['53014cee059bd87dc22f9679dfbf18fe6813b9ab41dfe90361921159edfbf798'], + }), + ('Matching', '4.9-6', { + 'checksums': ['8e0dced7d1242e52de68a6e3010484bb29eb0633733549c82a06e9c6508b66dc'], + }), + ('MatchIt', '3.0.2', { + 'checksums': ['782b159a2b5172e758e3993177930d604140ae668fd8a7c98c30792df80de9de'], + }), + ('RItools', '0.1-17', { + 'checksums': ['75654780e9ca39cb3c43acfaca74080ad74de50f92c5e36e95694aafdfdc0cea'], + }), + ('optmatch', '0.9-13', { + 'patches': ['optmatch-0.9-10_icpc-wd308.patch'], + 'checksums': [ + 'f8f327faa95c808773376570793bbabdbc185a6c7fcdce3b96a09c998134d0d8', # optmatch_0.9-13.tar.gz + '1f0f2a6665267e7c5693f858afddc80a9912301e82c62a5b58c5694d28f3f7ec', # optmatch-0.9-10_icpc-wd308.patch + ], + }), + ('SKAT', '1.3.2.1', { + 'checksums': ['7442408ccd1b9d2abb3f3dbd27e1b46e50b87042195bc46ce25fe0d887f98e7a'], + }), + ('GillespieSSA', '0.6.1', { + 'checksums': ['272e9b6b26001d166fd7ce8d04f32831ba23c676075fbd1e922e27ba2c962052'], + }), + ('startupmsg', '0.9.6', { + 'checksums': ['1d60ff13bb260630f797bde66a377a5d4cd65d78ae81a3936dc4374572ec786e'], + }), + ('distr', '2.8.0', { + 'checksums': ['bb7df05d6b946bcdbbec2e3397c7c7e349b537cabfcbb13a34bcf6312a71ceb7'], + }), + ('distrEx', '2.8.0', { + 'checksums': ['b064cde7d63ce93ec9969c8c4463c1e327758b6f8ea7765217d77f9ba9d590bf'], + }), + ('KODAMA', '1.5', { + 'checksums': ['8ecf53732c1be2bd1e111b3c6de65b66caf28360306e683fe945dc76d4c267dd'], + }), + ('locfdr', '1.1-8', { + 'checksums': ['42d6e12593ae6d541e6813a140b92591dabeb1df94432a515507fc2eee9a54b9'], + }), + ('ica', '1.0-2', { + 'checksums': ['e721596fc6175d3270a60d5e0b5b98be103a8fd0dd93ef16680af21fe0b54179'], + }), + ('dtw', '1.21-3', { + 'checksums': ['1aa46b285b7a31ba19759e83562671ed9076140abec79fe0df0316af43871e0a'], + }), + ('SDMTools', '1.1-221.2', { + 'checksums': ['f0dd8c5f98d2f2c012536fa56d8f7a58aaf0c11cbe3527e66d4ee3194f6a6cf7'], + }), + ('ggridges', '0.5.1', { + 'checksums': ['01f87cdcdf2052ed9c078d9352465cdeda920a41e2ca55bc154c1574fc651c36'], + }), + ('TFisher', '0.2.0', { + 'checksums': ['bd9b7484d6fba0165841596275b446f85ba446d40e92f3b9cb37381a3827e76f'], + }), + ('lsei', '1.2-0', { + 'checksums': ['4781ebd9ef93880260d5d5f23066580ac06061e95c1048fb25e4e838963380f6'], + }), + ('npsurv', '0.4-0', { + 'checksums': ['404cf7135dc40a04e9b81224a543307057a8278e11109ba1fcaa28e87c6204f3'], + }), + ('fitdistrplus', '1.0-14', { + 'checksums': ['85082590f62aa08d99048ea3414c5cc1e5b780d97b3779d2397c6cb435470083'], + }), + ('reticulate', '1.13', { + 'checksums': ['adbe41d556b667c4419d563680f8608a56b0f792b8bc427b3bf4c584ff819de3'], + }), + ('hdf5r', '1.3.0', { + 'installopts': '--configure-args="--with-hdf5=$EBROOTHDF5/bin/h5pcc"', + 'preinstallopts': "unset LIBS && ", + 'checksums': ['0ef18eed2683f5dda34601a20a842ab346a6c66b7277c5ed576c77ece61601df'], + }), + ('DTRreg', '1.5', { + 'checksums': ['eb9b4d98b25eec304a447db302f618a75180f8d8fe0f5728ecd7e85957613456'], + }), + ('pulsar', '0.3.6', { + 'checksums': ['b5851bf365003ace07542fd21ccff015c4b21ffd73e21ec3a539563e9ef53564'], + }), + ('bayesm', '3.1-4', { + 'checksums': ['061b216c62bc72eab8d646ad4075f2f78823f9913344a781fa53ea7cf4a48f94'], + }), + ('energy', '1.7-7', { + 'checksums': ['67b88fb33ee6e7bec2e4fe356a4efd36f70c3cf9b0ebe2f6d9da9ec96de9968f'], + }), + ('compositions', '1.40-3', { + 'checksums': ['e42d90950a63aa7f707bc5025dbf265b63fc02a5b7137bc71836b8bc625d7080'], + }), + ('clustree', '0.4.1', { + 'checksums': ['1d4c0c44826a656b649ce224f94a35fea808e9faef0d550646a0a9221a764e4b'], + }), + ('plotly', '4.9.1', { + 'checksums': ['85a08c64d1bf839786951b3574986eacce78dacd589f2bef4b38208e49554d3d'], + }), + ('tweedie', '2.3.2', { + 'checksums': ['9a6226e64e3d56eb7eb2a408f8b825c2ad6ee0ea203a9220e85e7789514adb81'], + }), + ('RcppGSL', '0.3.7', { + 'checksums': ['45e95c4170fc8421ae9b32134b3a402f76ea9657030969723a3563c7ce14dc32'], + }), + ('mvabund', '4.0.1', { + 'checksums': ['1399fa0a5f7a3673d788abe36b520f476c05246e21f71e3f60cee7a85f194951'], + }), + ('fishMod', '0.29', { + 'checksums': ['5989e49ca6d6b2c5d514655e61f75b019528a8c975f0d6056143f17dc4277a5d'], + }), + ('gllvm', '1.1.7', { + 'checksums': ['cc0331b034e14aa8d47a491cedeb76717b4085a61fb0b1cc75d424c58ca9b8d4'], + }), + ('grpreg', '3.2-1', { + 'checksums': ['6be37719a74d59582107273385d70963b4ccc6c394948c7617e65246d713cb88'], + }), + ('trust', '0.1-7', { + 'checksums': ['e3d15aa84a71becd2824253d4a8156bdf1ab9ac3b72ced0cd53f3bb370ac6f04'], + }), + ('ergm', '3.10.4', { + 'checksums': ['885f0b1a23c5a2c1947962350cfab66683dfdfd1db173c115e90396d00831f22'], + }), + ('networkDynamic', '0.10.0', { + 'checksums': ['eb31d72c73a06a145d231ad3489d450d63b9fecc069aeb19331d7417241df3b5'], + }), + ('tergm', '3.6.1', { + 'checksums': ['21de2eca943d89ba63af14951655d626f241bafccc4b2709fa39aa130625cd0f'], + }), + ('ergm.count', '3.4.0', { + 'checksums': ['7c24c79d0901c18991cce907306a1531cca676ae277c6b0a0e4962ad27c36baf'], + }), + ('tsna', '0.3.0', { + 'checksums': ['29f599d3e774289614608b0fa49e05a09e76e6b15dd1d46988785eaacf2e1a35'], + }), + ('statnet', '2019.6', { + 'checksums': ['0903e1a81ed1b6289359cefd12da1424c92456d19e062c3f74197b69e536b29d'], + }), + ('aggregation', '1.0.1', { + 'checksums': ['86f88a02479ddc8506bafb154117ebc3b1a4a44fa308e0193c8c315109302f49'], + }), + ('ComICS', '1.0.4', { + 'checksums': ['0af7901215876f95f309d7da6e633c38e4d7faf04112dd6fd343bc15fc593a2f'], + }), + ('dtangle', '2.0.9', { + 'checksums': ['c375068c1877c2e8cdc5601cfd5a9c821645c3dff90ddef64817f788f372e179'], + }), + ('mcmc', '0.9-6', { + 'checksums': ['443a189fff907830627029dd55d925db9a70562d8bda7bfae97414ab955186b9'], + }), + ('MCMCpack', '1.4-5', { + 'patches': ['MCMCpack-1.4-4_intel_wd308.patch'], + 'checksums': [ + 'da949cfa44f71bfff1c6ae06caf8fe4252dd6391aa4c8f0fb6e02c7d6b1cdfb5', # MCMCpack_1.4-5.tar.gz + '8820c9153c4717614ed5f3fce9b8507fca1194d4296ea3426e0a3ca7b92bb74a', # MCMCpack-1.4-4_intel_wd308.patch + ], + }), + ('shinythemes', '1.1.2', { + 'checksums': ['2e13d4d5317fc61082e8f3128b15e0b10ed9736ce81e152dd7ae7f6109f9b18a'], + }), + ('csSAM', '1.2.4', { + 'checksums': ['3d6442ad8c41fa84633cbbc275cd67e88490a160927a5c55d29da55a36e148d7'], + }), + ('bridgedist', '0.1.0', { + 'checksums': ['dc7c1c8874d6cfa34d550d9af194389e13471dfbc55049a1ab66db112fbf1343'], + }), + ('asnipe', '1.1.12', { + 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], + }), + ('liquidSVM', '1.2.4', { + 'patches': ['liquidSVM-1.2.2_intel.patch'], + 'checksums': [ + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz + 'a670a6de7c8a7755a9f6f0cc658772f40aebe342512be4a20dea6c56595ff44e', # liquidSVM-1.2.2_intel.patch + ], + }), + ('oddsratio', '2.0.0', { + 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], + }), + ('mltools', '0.3.5', { + 'checksums': ['7093ffceccdf5d4c3f045d8c8143deaa8ab79935cc6d5463973ffc7d3812bb10'], + }), + ('h2o', '3.26.0.2', { + 'checksums': ['cabef231e65991a6fd40b83022eb6d47a0fa09548ed62ce6fe6549535f98b2d1'], + }), + ('mlegp', '3.1.7', { + 'checksums': ['d4845eaf9260f8b8112726dd7ceb5c2f5ce75125fa313191db9de121f2ee15e0'], + }), + ('itertools', '0.1-3', { + 'checksums': ['b69b0781318e175532ad2d4f2840553bade9637e04de215b581704b5635c45d3'], + }), + ('missForest', '1.4', { + 'checksums': ['f785804b03bdf424e1c76095989a803afb3b47d6bebca9a6832074b6326c0278'], + }), + ('bartMachineJARs', '1.1', { + 'checksums': ['f2c31cb94d7485174a2519771127a102e35b9fe7f665e27beda3e76a56feeef2'], + }), + ('bartMachine', '1.2.4.2', { + 'checksums': ['28a5f7363325021bd93f9bd060cc48f20c689dae2f2f6f7100faae66d7651f80'], + }), + ('lqa', '1.0-3', { + 'checksums': ['3889675dc4c8cbafeefe118f4f20c3bd3789d4875bb725933571f9991a133990'], + }), + ('PresenceAbsence', '1.1.9', { + 'checksums': ['1a30b0a4317ea227d674ac873ab94f87f8326490304e5b08ad58953cdf23169f'], + }), + ('GUTS', '1.1.1', { + 'checksums': ['094b8f51719cc36ddc56e3412dbb146eafc93c5e8fbb2c5999c2e80ea7a7d216'], + }), + ('GenSA', '1.1.7', { + 'checksums': ['9d99d3d0a4b7770c3c3a6de44206811272d78ab94481713a8c369f7d6ae7b80f'], + }), + ('rematch2', '2.1.0', { + 'checksums': ['78677071bd44b40e562df1da6f0c6bdeae44caf973f97ff8286b8c994db59f01'], + }), + ('parsedate', '1.2.0', { + 'checksums': ['39ab3c507cb3efcd677c6cf453f46d6b1948662bd70c7765845e755ea1e1633d'], + }), + ('circular', '0.4-93', { + 'checksums': ['76cee2393757390ad91d3db3e5aeb2c2d34c0a46822b7941498571a473417142'], + }), + ('cobs', '1.3-3', { + 'checksums': [('6b1e760cf8dec6b6e63f042cdc3e5e633de5f982e8bc743a891932f6d9f91bdf', + 'f3fca282c9a258cc5e4976780f4907aca1051796524d6861fc15204ab22ab7d2')], + }), + ('resample', '0.4', { + 'checksums': ['f0d5f735e1b812612720845d79167a19f713a438fd10a6a3206e667045fd93e5'], + }), + ('MIIVsem', '0.5.4', { + 'checksums': ['de918d6b1820c59a7d4324342ad15444c2370ce1d843397a136c307397ed64b9'], + }), + ('medflex', '0.6-6', { + 'checksums': ['b9d04fb5281d0ea0555ec4f327a0ee951a7f312a3af944578dc175183dc49211'], + }), + ('Rserve', '1.7-3.1', { + 'checksums': ['3ba1e919706e16a8632def5f45d666b6e44eafa6c14b57064d6ddf3415038f99'], + }), + ('spls', '2.2-3', { + 'checksums': ['bbd693da80487eef2939c37aba199f6d811ec289828c763d9416a05fa202ab2e'], + }), + ('Boruta', '6.0.0', { + 'checksums': ['1c9a7aabe09f040e147f6c614f5fe1d0b951d3b0f0024161fbb4c31da8fae8de'], + }), + ('dr', '3.0.10', { + 'checksums': ['ce523c1bdb62a9dda30afc12b1dd96975cc34695c61913012236f3b80e24bf36'], + }), + ('CovSel', '1.2.1', { + 'checksums': ['b375d00cc567e125ff106b4357654f43bba3abcadeed2238b6dea4b7a68fda09'], + }), + ('tmle', '1.4.0.1', { + 'checksums': ['075e7b7fe0496e02785eb35aed0db84476db756c6f14a0047808af2565b33501'], + }), + ('ctmle', '0.1.2', { + 'checksums': ['e3fa0722cd87aa0e0b209c2dddf3fc44c6d09993f1e66a6c43285fe950948161'], + }), + ('BayesPen', '1.0', { + 'checksums': ['772df9ae12cd8a3da1d5b7d1f1629602c7693f0eb03945784df2809e2bb061b0'], + }), + ('inline', '0.3.15', { + 'checksums': ['ff043fe13c1991a3b285bed256ff4a9c0ba10bee764225a34b285875b7d69c68'], + }), + ('BMA', '3.18.11', { + 'checksums': ['bf4ce8fdb21a4da754dffa4c1869efb11f6bdcfaa7f43a1b009b2695f553698d'], + }), + ('BCEE', '1.2', { + 'checksums': ['0b1183458d625ef5dd0962fc77ca1326e77754a2c04be11fb002057abcb65a22'], + }), + ('bacr', '1.0.1', { + 'checksums': ['c847272e2c03fd08ed79b3b739f57fe881af77404b6fd087caa0c398c90ef993'], + }), + ('clue', '0.3-57', { + 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], + }), + ('bdsmatrix', '1.3-3', { + 'checksums': ['70ea81708c97dedd483a5d3866d2e906fa0e9098ff854c41cf0746fbc8dfad9d'], + }), + ('fftwtools', '0.9-8', { + 'checksums': ['4641c8cd70938c2a8bde0b6da6cf7f83e96175ef52f1ca42ec3920a1dabf1bdb'], + }), + ('imagerExtra', '1.3.2', { + 'checksums': ['0ebfa1eabb89459d774630ab73c7a97a93b9481ea5afc55482975475acebd5b8'], + }), + ('MALDIquant', '1.19.3', { + 'checksums': ['a730327c1f8d053d29e558636736b7b66d0671a009e0004720b869d2c76ff32c'], + }), + ('threejs', '0.3.1', { + 'checksums': ['71750b741672a435ecf749b69c72f0681aa8bb795e317f4e3056d5e33f6d79e8'], + }), + ('LaplacesDemon', '16.1.1', { + # two alternate checksums due updated source tarball with changed package description + 'checksums': [('779ed1dbfed523a15701b4d5d891d4f1f11ab27518826a8a7725807d4c42bd77', + '98d30fbc5594f46818632a6795febaa81df12e9598d31d17500bc7300289aea1')], + }), + ('rda', '1.0.2-2.1', { + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + }), + ('sampling', '2.8', { + 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], + }), + ('lda', '1.4.2', { + 'checksums': ['5606a1e1bc24706988853528023f7a004c725791ae1a7309f1aea2fc6681240f'], + }), + ('jiebaRD', '0.1', { + 'checksums': ['045ee670f5378fe325a45b40fd55136b355cbb225e088cb229f512c51abb4df1'], + }), + ('jiebaR', '0.11', { + 'checksums': ['adde8b0b21c01ec344735d49cd33929511086719c99f8e10dce4ca9479276623'], + }), + ('hdm', '0.3.1', { + 'checksums': ['ba087565e9e0a8ea30a6095919141895fd76b7f3c05a03e60e9e24e602732bce'], + }), + ('abe', '3.0.1', { + 'checksums': ['66d2e9ac78ba64b7d27b22b647fc00378ea832f868e51c18df50d6fffb8029b8'], + }), + ('SignifReg', '2.1', { + 'checksums': ['d21959ce5b1ee20efd1483f6020b57e5f6616bd525af77a7bd325501cc670606'], + }), + ('bbmle', '1.0.20', { + 'checksums': ['6c0fe8df7243f8a039e62d14014065df2002b9329c0e8a3c2df4e7ccf591f1f7'], + }), + ('emdbook', '1.3.11', { + 'checksums': ['f848d4c0a2da50dc8a5af76429d8f9d4960dee3fad1e98f7b507bdfd9b2ca128'], + }), + ('SOAR', '0.99-11', { + 'checksums': ['d5a0fba3664087308ce5295a1d57d10bad149eb9771b4fe67478deae4b7f68d8'], + }), + ('rasterVis', '0.47', { + 'checksums': ['123ebe870895c2ba3a4b64d8a18bccab5287c831fa14bb0fe07f0d7de61e51d3'], + }), + ('tictoc', '1.0', { + 'checksums': ['47da097c1822caa2d8e262381987cfa556ad901131eb96109752742526b2e2fe'], + }), + ('ISOcodes', '2019.04.22', { + 'checksums': ['2386440c3bed8391ee3a029aab86c107d435d0dd6a970236512d7c105d146b6e'], + }), + ('stopwords', '1.0', { + 'checksums': ['9b727a5d827ac8dcfa6329140d294dcf964a06d80132b4ca434330d0ee02b1da'], + }), + ('janeaustenr', '0.1.5', { + 'checksums': ['992f6673653daf7010fe176993a01cd4127d9a88be428da8da7a28241826d6f3'], + }), + ('SnowballC', '0.6.0', { + 'checksums': ['61617d344444235940f5b9ac1cd6b86938e74a8c76791235724b16b755c3f72c'], + }), + ('tokenizers', '0.2.1', { + 'checksums': ['28617cdc5ddef5276abfe14a2642999833322b6c34697de1d4e9d6dc7670dd00'], + }), + ('hunspell', '3.0', { + 'checksums': ['01fb9c87f7cf094aaad3b7098378134f2e503286224351e91d08c00b6ee19857'], + }), + ('topicmodels', '0.2-9', { + 'checksums': ['40770fb7de6ab6bd6e3ef6a0c777fa6db65d0322e67503c26c84ea857ac9a79c'], + }), + ('tidytext', '0.2.2', { + 'checksums': ['188f294cf3177fe6fc85e9b7e16a05211cebeab0e0f7b05a9443416790bf2ec0'], + }), + ('splitstackshape', '1.4.8', { + 'checksums': ['656032c3f1e3dd5b8a3ee19ffcae617e07104c0e342fc3da4d863637a770fe56'], + }), + ('grImport2', '0.2-0', { + 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], + }), + ('preseqR', '4.0.0', { + 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], + }), + ('idr', '1.2', { + 'checksums': ['8bbfdf82c8c2b5c73eb079127e198b6cb65c437bb36729f502c7bcd6037fdb16'], + }), + ('entropy', '1.2.1', { + 'checksums': ['edb27144b8f855f1ef21de6b93b6b6c5cf7d4f2c3d592bf625e5158c02226f83'], + }), + ('kedd', '1.0.3', { + 'checksums': ['38760abd8c8e8f69ad85ca7992803060acc44ce68358de1763bd2415fdf83c9f'], + }), + ('HiddenMarkov', '1.8-11', { + 'checksums': ['4a1614249eee9f428bc182ea9ced443dff4eafa7babf4259c720e5b4da2d08fa'], + }), + ('lmerTest', '3.1-1', { + 'checksums': ['520ef83e9a7c58e3c5b7175fbda902b747b2e01c24b53714ede81a6a87de5b64'], + }), + ('loo', '2.2.0', { + 'checksums': ['466df60953a89fcb135b32909197c3ff26ecea719c191667faa5747324fb01c3'], + }), + ('StanHeaders', '2.21.0-1', { + 'checksums': ['4e94148af2960f203b208c2b725d8be628ca282c7a1e967a7e6e78aa5eb90d3f'], + }), + ('rstan', '2.19.2', { + 'checksums': ['31e4ceb9c327cd62873225097ffa538c2ac4cb0547c52271e52e4c7652d508da'], + }), + ('Rborist', '0.2-3', { + 'checksums': ['f3b3f953ca99e0d17425ac6ba9a7b1e9d6098343abace575cdb492bca2a9c461'], + }), + ('VSURF', '1.1.0', { + 'checksums': ['eee99e0c441795c2ccb21cc6e0a37b24f580241e494c83e811b726b43469eeab'], + }), + ('mRMRe', '2.1.0', { + 'checksums': ['fe23c5c1e7b5b653e0358e98f25ebd8c0c74c6c871606d1b24cd02a5534181d4'], + }), + ('dHSIC', '2.1', { + 'checksums': ['94c86473790cf69f11c68ed8ba9d6ae98218c7c69b7a9a093f235d175cf83db0'], + }), + ('ggsci', '2.9', { + 'checksums': ['4af14e6f3657134c115d5ac5e65a2ed74596f9a8437c03255447cd959fe9e33c'], + }), + ('ggsignif', '0.6.0', { + 'checksums': ['6fe13efda31386483e64d466ba2f5a53a2a235ae04f5c17bba3ccc63d283499e'], + }), + ('corrplot', '0.84', { + 'checksums': ['0dce5e628ead9045580a191f60c58fd7c75b4bbfaaa3307678fc9ed550c303cc'], + }), + ('rstatix', '0.5.0', { + 'checksums': ['06b2ba1b16698c93203474eb67e59169fa4127283d46cf694e032a5472956b46'], + }), + ('ggfan', '0.1.3', { + 'checksums': ['5c888b203ecf5e3dc7a317a790ca059c733002fbca4b4bc1a4f62b7ded5f70dc'], + }), + ('ggpubr', '0.3.0', { + 'checksums': ['b82ffc6bd5974c3036d08393fa1f2bafeaf6f567e0b3faf43e38226b19399eb6'], + }), + ('yaImpute', '1.0-32', { + 'checksums': ['08eee5d851b80aad9c7c80f9531aadd50d60e4b16b3a80657a50212269cd73ff'], + }), + ('intrinsicDimension', '1.2.0', { + 'checksums': ['6cc9180a83aa0d123f1e420136bb959c0d5877867fa170b79536f5ee22106a32'], + }), + ('patchwork', '1.0.0', { + 'checksums': ['8bfb59b91775781848f39eedcaaaf92c147e2637f384085fcdd41fc8355b3c63'], + }), + ('leiden', '0.3.3', { + 'checksums': ['c2b5e1c061c8bbea494639a0d7f0fa22f5b41ff5fd911409e5f832f3575d06c2'], + }), + ('future.apply', '1.4.0', { + 'checksums': ['737e5a8e2d0ce2678835f5be15c96d491f690d307662ed6719be41937633f8cd'], + }), + ('sctransform', '0.2.1', { + 'checksums': ['d6430a81a66c93da770b1a7c55344df42187321038b4eee80b7066cdd8a7631f'], + }), + ('packrat', '0.5.0', { + 'checksums': ['d6a09290fbe037a6c740921c5dcd70b500e5b36e4713eae4010adf0c456bc5f7'], + }), + ('shinyjs', '1.1', { + 'checksums': ['8986181baa68fb2863eea65b9df1b04b9b4e1293685298531d42de3bc2f06892'], + }), + ('colourpicker', '1.0', { + 'checksums': ['f1dacbafb05c09f61b9bdd0fdcee5344409759b042a71ec46d7c9e3710107b7c'], + }), + ('ggExtra', '0.9', { + 'checksums': ['f22db92d6e3e610901998348acbcaa6652fa6c62a285a622d3b962ba9e89aba2'], + }), + ('findpython', '1.0.5', { + 'checksums': ['3e9a21988cb78833769b02680d128a0cc01bcb41aa9c9725ab1742f349759145'], + }), + ('argparse', '2.0.1', { + 'checksums': ['949843920d14fc7c162aedab331a936499541736e7dafbb103fbfd79be8147ab'], + }), + ('intergraph', '2.0-2', { + 'checksums': ['6cbe77f1e87fa1c110db2d46010f2f3ae72bfdb708ce2ca84c1cdc2cd6eb47a1'], + }), + ('ggnetwork', '0.5.8', { + 'checksums': ['a8c7c19a2bafce898c95d0b2401ef052925db57b85058c7203f0122b3af7bbbd'], + }), + ('qqman', '0.1.4', { + 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], + }), +] + +moduleclass = 'lang' From 20f5d326cbf76ecb4c1621ed227ebcc192722d96 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 17 Sep 2020 13:30:59 +0200 Subject: [PATCH 179/698] adding easyconfigs: fetchMG-1.0-GCCcore-9.3.0.eb --- .../f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..ee652238cbe --- /dev/null +++ b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'fetchMG' +version = '1.0' + +homepage = 'http://vm-lux.embl.de/~mende/fetchMG/about.html' +description = """The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes +in an easy and accurate manner.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://vm-lux.embl.de/~kultima/share/mOTU/'] +sources = ['%(name)sv%(version)s.tar.gz'] +checksums = ['e3b835b425525513611b7116f89fc11ed015032ffd0494fa058edec1d6e67b17'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Perl', '5.30.2'), +] + +fix_perl_shebang_for = ['%(name)s.pl'] + +sanity_check_paths = { + 'files': ['%(name)s.pl', 'bin/cdbfasta', 'bin/cdbyank', 'bin/hmmsearch'], + 'dirs': [], +} + +sanity_check_commands = [ + "fetchMG.pl -h", + "fetchMG.pl -m extraction -x '' %(installdir)s/example_datasets/example_data.faa" +] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 27ab0e5551eae50edc1f23156619f320c6af62b8 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 17 Sep 2020 13:34:14 +0200 Subject: [PATCH 180/698] adding easyconfigs: Tkinter-2.7.18-GCCcore-9.3.0.eb --- .../t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..63794a7c9c4 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-2.7.18-GCCcore-9.3.0.eb @@ -0,0 +1,22 @@ +name = 'Tkinter' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Tkinter module, built with the Python buildsystem""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', version), + ('Tk', '8.6.10'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' From b02c9aec70163d32751511534685aefca7e2e09a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 15:17:58 +0200 Subject: [PATCH 181/698] remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 --- ...-5.0.1-20200316-foss-2019b-Python-3.7.4.eb | 58 ------------------- ....1-20200316-fosscuda-2019b-Python-3.7.4.eb | 58 ------------------- 2 files changed, 116 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb delete mode 100644 easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb deleted file mode 100644 index 0edb2e0be25..00000000000 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-foss-2019b-Python-3.7.4.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Taiyaki' -local_commit = '486b76a' -version = '5.0.1-20200316' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/nanoporetech/taiyaki' -description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." - -toolchain = {'name': 'foss', 'version': '2019b'} - -dependencies = [ - ('Python', '3.7.4'), - ('SciPy-bundle', '2019.10', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('Biopython', '1.75', versionsuffix), - ('Pysam', '0.15.3'), - ('PyTorch', '1.3.1', versionsuffix), - ('matplotlib', '3.1.1', versionsuffix), -] - -use_pip = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} - -exts_list = [ - ('patsy', '0.5.1', { - 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], - }), - ('statsmodels', '0.11.1', { - 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], - }), - ('progressbar33', '2.4', { - 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], - 'modulename': 'progressbar', - }), - ('ont-fast5-api', '3.1.1', { - 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], - }), - (name, version, { - 'source_tmpl': '486b76a.tar.gz', - 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], - 'checksums': ['5fe92fd7db2311ef3c59b1e77275a434ad3ee8107c918f5937746a6ca7615e00'], - 'preinstallopts': "sed -i 's/torch == 1.2/torch/g' setup.py && " - }), -] - -fix_python_shebang_for = ['bin/*.py'] - -sanity_check_paths = { - 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_pip_check = True - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb deleted file mode 100644 index 989abf0702b..00000000000 --- a/easybuild/easyconfigs/t/Taiyaki/Taiyaki-5.0.1-20200316-fosscuda-2019b-Python-3.7.4.eb +++ /dev/null @@ -1,58 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Taiyaki' -local_commit = '486b76a' -version = '5.0.1-20200316' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/nanoporetech/taiyaki' -description = "Taiyaki is research software for training models for basecalling Oxford Nanopore reads." - -toolchain = {'name': 'fosscuda', 'version': '2019b'} - -dependencies = [ - ('Python', '3.7.4'), - ('SciPy-bundle', '2019.10', versionsuffix), - ('h5py', '2.10.0', versionsuffix), - ('Biopython', '1.75', versionsuffix), - ('Pysam', '0.15.3'), - ('PyTorch', '1.3.1', versionsuffix), - ('matplotlib', '3.1.1', versionsuffix), -] - -use_pip = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} - -exts_list = [ - ('patsy', '0.5.1', { - 'checksums': ['f115cec4201e1465cd58b9866b0b0e7b941caafec129869057405bfe5b5e3991'], - }), - ('statsmodels', '0.11.1', { - 'checksums': ['5bde3fa0a35a91b45dba7cbc28270b5b649ff1d721c89290883f6e831672d5f0'], - }), - ('progressbar33', '2.4', { - 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], - 'modulename': 'progressbar', - }), - ('ont-fast5-api', '3.1.1', { - 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], - }), - (name, version, { - 'source_tmpl': '486b76a.tar.gz', - 'source_urls': ['https://github.com/nanoporetech/taiyaki/archive/'], - 'checksums': ['5fe92fd7db2311ef3c59b1e77275a434ad3ee8107c918f5937746a6ca7615e00'], - 'preinstallopts': "sed -i 's/torch == 1.2/torch/g' setup.py && " - }), -] - -fix_python_shebang_for = ['bin/*.py'] - -sanity_check_paths = { - 'files': ['bin/basecall.py', 'bin/prepare_mapped_reads.py', 'bin/train_flipflop.py'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_pip_check = True - -moduleclass = 'bio' From 578f8c3610ec16dce19b31adc8c8c6b0338371b5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 17:14:18 +0200 Subject: [PATCH 182/698] adding easyconfigs: PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb --- .../PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..a9c68e2075e --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('MDTraj', '1.9.4', versionsuffix), + ('tqdm', '4.47.0') +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From a13ca2f48d0fef0f12639d5b9451a1eba1bb9527 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 17:28:47 +0200 Subject: [PATCH 183/698] adding easyconfigs: PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb, MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb --- .../MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb | 42 ++++++++++++++++++ .../PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb | 43 +++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..8cfe3cbed2a --- /dev/null +++ b/easybuild/easyconfigs/m/MDTraj/MDTraj-1.9.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,42 @@ +# Updated: Pavel Grochal (INUITS) + +easyblock = 'PythonBundle' + +name = 'MDTraj' +version = '1.9.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://mdtraj.org' +description = "Read, write and analyze MD trajectories with only a few lines of Python code." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('zlib', '1.2.11'), +] + +use_pip = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('pymbar', '3.0.5', { + 'checksums': ['b079a7d0b9fbc8a92850277b664bb582991ef5ac399b3607e695569148f6c784'], + }), + ('mdtraj', version, { + 'checksums': ['d5d28be24dd5f38e8b272c3a445a6cdbffc374b30e891c5535f65bb20f7e8b24'], + }), +] + +# The unit tests of MDTraj are a pain to get to work: they require +# a massive number of extra dependencies. See +# https://github.com/mdtraj/mdtraj/blob/master/devtools/conda-recipe/meta.yaml + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..22cc5c5ec3a --- /dev/null +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'PyRETIS' +version = '2.5.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.pyretis.org' +description = """PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based + on transition interface sampling and replica exchange transition interface sampling.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('MDTraj', '1.9.4', versionsuffix), + ('tqdm', '4.47.0') +] + +use_pip = True + +exts_list = [ + ('colorama', '0.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/colorama/'], + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'source_urls': ['https://pypi.python.org/packages/source/s/sphinx-bootstrap-theme/'], + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + (name, version, { + 'source_tmpl': 'pyretis-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/p/pyretis'], + 'checksums': ['b4b842a83f39e97a9bbf2d9797f53823b9e741b479b5a6744aeb42daf1c7ad2b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyretisanalyse', 'bin/pyretisrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'chem' From d389814d47f00d3b0e775a770a0f781ea1c16cd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 17:34:10 +0200 Subject: [PATCH 184/698] fix sources spec in MyCC easyconfig --- .../m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb index a5ae391748b..cf70c9fe661 100644 --- a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -16,7 +16,7 @@ plaintext markup language.""" toolchain = {'name': 'intel', 'version': '2019b'} source_urls = [('https://sourceforge.net/projects/sb2nhri/files/MyCC/', 'download')] -sources = [{'download_filename': '%s-%s.tar.gz' % (name, version), 'filename': 'Tools.tar.gz'}] +sources = [{'download_filename': 'Tools.tar.gz', 'filename': '%s-%s.tar.gz' % (name, version)}] patches = ['%(name)s-%(version)s_fix_paths.patch'] checksums = [ '173210a759e90c7b1ff98bf537a88e8b7e893e60fe91fca50407ffede7e08de6', # Tools.tar.gz From b0d0f434f2688111b612ca7ef7d1bb1a292193ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 17:34:32 +0200 Subject: [PATCH 185/698] fix source filename in checksum comment in MyCC easyconfig --- .../m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb index cf70c9fe661..19a3c0996ed 100644 --- a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -19,7 +19,8 @@ source_urls = [('https://sourceforge.net/projects/sb2nhri/files/MyCC/', 'downloa sources = [{'download_filename': 'Tools.tar.gz', 'filename': '%s-%s.tar.gz' % (name, version)}] patches = ['%(name)s-%(version)s_fix_paths.patch'] checksums = [ - '173210a759e90c7b1ff98bf537a88e8b7e893e60fe91fca50407ffede7e08de6', # Tools.tar.gz + '173210a759e90c7b1ff98bf537a88e8b7e893e60fe91fca50407ffede7e08de6', # MyCC-2017-03-01.tar.gz + 'f20fdf13ccd04c2e523c87a8f0a80194443fa09f7916b4b7ecb5a9751e1f6ee8', # MyCC-2017-03-01_fix_paths.patch ] From f79eee6d88cad92b86ab94ab1598afabaef2a942 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 20:30:00 +0200 Subject: [PATCH 186/698] enable running 'pip check' in PyRETIS 2.5.0 easyconfig --- .../p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb index a9c68e2075e..08714396590 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb @@ -40,4 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'chem' From 747350b3dd93a4016a99b529c438b6424d9abba6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 20:30:29 +0200 Subject: [PATCH 187/698] enable running 'pip check' in PyRETIS 2.5.0 easyconfig --- .../p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb index 22cc5c5ec3a..94456d6f442 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb @@ -40,4 +40,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'chem' From c1a98a8ce688fb2d0ad25e12dd885f21afc61820 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 20:32:01 +0200 Subject: [PATCH 188/698] add missing PyTables dependency for PyRETIS 2.5.0 --- .../p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb index 08714396590..a2105a15bef 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-intel-2020a-Python-3.8.2.eb @@ -14,7 +14,8 @@ dependencies = [ ('Python', '3.8.2'), ('matplotlib', '3.2.1', versionsuffix), ('MDTraj', '1.9.4', versionsuffix), - ('tqdm', '4.47.0') + ('tqdm', '4.47.0'), + ('PyTables', '3.6.1', versionsuffix), ] use_pip = True From 5eb0a2de9ae27532f13efc0dbd73e3bd97b6a5c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Sep 2020 20:31:35 +0200 Subject: [PATCH 189/698] add missing PyTables dependency for PyRETIS 2.5.0 --- .../p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb index 94456d6f442..4d7a3a189ef 100644 --- a/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyRETIS/PyRETIS-2.5.0-foss-2020a-Python-3.8.2.eb @@ -14,7 +14,8 @@ dependencies = [ ('Python', '3.8.2'), ('matplotlib', '3.2.1', versionsuffix), ('MDTraj', '1.9.4', versionsuffix), - ('tqdm', '4.47.0') + ('tqdm', '4.47.0'), + ('PyTables', '3.6.1', versionsuffix), ] use_pip = True From 594e20d272f13ea30171681d1eadc500e483d7ce Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Thu, 17 Sep 2020 21:37:35 +0200 Subject: [PATCH 190/698] added Flexbar-3.5.0-foss-2018b.eb --- .../f/Flexbar/Flexbar-3.5.0-foss-2018b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb diff --git a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb new file mode 100644 index 00000000000..fb89b7f2eac --- /dev/null +++ b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'MakeCp' + +name = 'Flexbar' +version = '3.5.0' + +homepage = 'https://github.com/seqan/flexbar' +description = 'The program Flexbar preprocesses high-throughput sequencing data efficiently' + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/seqan/flexbar/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['656168934b6cb367ee6d4adad0c40506bc107c888d129fe191c6f3f3446a4ac9'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('SeqAn', '2.4.0'), +] + +dependencies = [ + ('tbb', '2018_U5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), +] + +prebuildopts = 'cmake -DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so -DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include . && ' + +files_to_copy = [(['flexbar'], 'bin/')] + +sanity_check_paths = { + 'files': ['bin/flexbar'], + 'dirs': [] +} + +moduleclass = 'bio' From f81c40329f0b1093d90cde4dd8bf04c7f14dda5f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Sep 2020 08:40:29 +0100 Subject: [PATCH 191/698] PyQt5: remove --no-dist-info --- .../p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-2.7.15.eb | 3 --- .../p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb | 3 --- .../p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb | 5 ++--- 3 files changed, 2 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-2.7.15.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-2.7.15.eb index 1d9402cc3a8..dd6a2f9127d 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-2.7.15.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-2.7.15.eb @@ -29,7 +29,6 @@ local_sip_configopts = " ".join([ "--sipdir=%(installdir)s/share/sip", # required for PyQt5, cfr. https://www.riverbankcomputing.com/static/Docs/PyQt5/installation.html#downloading-sip "--sip-module PyQt5.sip", - "--no-dist-info", "--no-stubs", ]) @@ -44,7 +43,6 @@ local_pyqt5_configopts = " ".join([ "--designer-plugindir=%(installdir)s/plugins/designer", "--qml-plugindir=%(installdir)s/plugins/PyQt5", "--qsci-api-destdir=%(installdir)s/qsci", - "--no-dist-info", "--no-stubs", ]) @@ -54,7 +52,6 @@ local_pyqtweb_configopts = " ".join([ "--destdir=%s/PyQt5" % local_pylibdir, "--apidir=%(installdir)s/qsci", "--pyqt-sipdir=%(builddir)s/PyQt5_gpl-%(version)s/sip", - "--no-dist-info", "--no-stubs", ]) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb index 08fc35f74e6..231cc379fbc 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.12.1-GCCcore-8.2.0-Python-3.7.2.eb @@ -29,7 +29,6 @@ local_sip_configopts = " ".join([ "--sipdir=%(installdir)s/share/sip", # required for PyQt5, cfr. https://www.riverbankcomputing.com/static/Docs/PyQt5/installation.html#downloading-sip "--sip-module PyQt5.sip", - "--no-dist-info", "--no-stubs", ]) @@ -44,7 +43,6 @@ local_pyqt5_configopts = " ".join([ "--designer-plugindir=%(installdir)s/plugins/designer", "--qml-plugindir=%(installdir)s/plugins/PyQt5", "--qsci-api-destdir=%(installdir)s/qsci", - "--no-dist-info", "--no-stubs", ]) @@ -54,7 +52,6 @@ local_pyqtweb_configopts = " ".join([ "--destdir=%s/PyQt5" % local_pylibdir, "--apidir=%(installdir)s/qsci", "--pyqt-sipdir=%(builddir)s/PyQt5_gpl-%(version)s/sip", - "--no-dist-info", "--no-stubs", ]) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb index 1065b0cba66..584d9539a27 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -29,7 +29,6 @@ local_sip_configopts = " ".join([ "--sipdir=%(installdir)s/share/sip", # required for PyQt5, cfr. https://www.riverbankcomputing.com/static/Docs/PyQt5/installation.html#downloading-sip "--sip-module PyQt5.sip", - "--no-dist-info", "--no-stubs", ]) @@ -44,7 +43,6 @@ local_pyqt5_configopts = " ".join([ "--designer-plugindir=%(installdir)s/plugins/designer", "--qml-plugindir=%(installdir)s/plugins/PyQt5", "--qsci-api-destdir=%(installdir)s/qsci", - "--no-dist-info", "--no-stubs", ]) @@ -54,7 +52,6 @@ local_pyqtweb_configopts = " ".join([ "--destdir=%s/PyQt5" % local_pylibdir, "--apidir=%(installdir)s/qsci", "--pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip", - "--no-dist-info", "--no-stubs", ]) @@ -108,4 +105,6 @@ modextrapaths = { 'QT_PLUGIN_PATH': 'plugins', } +sanity_pip_check = True + moduleclass = 'vis' From e46203042f69e966eb6c10ae6c236e75b83437aa Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Sep 2020 08:43:43 +0100 Subject: [PATCH 192/698] remove sanity_pip_check test, as that is not possible here --- .../p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb index 584d9539a27..d092eda0d91 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.13.2-GCCcore-8.3.0-Python-3.7.4.eb @@ -105,6 +105,4 @@ modextrapaths = { 'QT_PLUGIN_PATH': 'plugins', } -sanity_pip_check = True - moduleclass = 'vis' From a72fb1b46fda6340a2e44156d31a7f7b27d6d35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 18 Sep 2020 10:07:22 +0200 Subject: [PATCH 193/698] add patch for R 3.6.2 with intel/2019b to fix compilation on CentOS 8 (+ remove patch file that only makes sense on POWER) --- .../easyconfigs/r/R/R-3.6.2-intel-2019b.eb | 6 +- .../r/R/R-3.6.2_fix-intel-recent-glibc.patch | 55 +++++++++++++++++++ 2 files changed, 57 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/r/R/R-3.6.2_fix-intel-recent-glibc.patch diff --git a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb index c8ee1e0d04a..38d14c22176 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.2-intel-2019b.eb @@ -9,12 +9,10 @@ toolchain = {'name': 'intel', 'version': '2019b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -patches = [ - '%(name)s-%(version)s_fix_long_dbl_on_ppc.patch', -] +patches = ['%(name)s-%(version)s_fix-intel-recent-glibc.patch'] checksums = [ 'bd65a45cddfb88f37370fbcee4ac8dd3f1aebeebe47c2f968fd9770ba2bbc954', # R-3.6.2.tar.gz - '833b80f9a62751eae9cfbad6116542acf932e9c6511235145be32264aacdce69', # R-3.6.2_fix_long_dbl_on_ppc.patch + '1052d223df58b6199edbac3721640f06b22a282c95dd0db982566dc36884a146', # R-3.6.2_fix-intel-recent-glibc.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/r/R/R-3.6.2_fix-intel-recent-glibc.patch b/easybuild/easyconfigs/r/R/R-3.6.2_fix-intel-recent-glibc.patch new file mode 100644 index 00000000000..c59b29dfea4 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-3.6.2_fix-intel-recent-glibc.patch @@ -0,0 +1,55 @@ +Fix for compilation error on OS with recent glibc when using Intel compilers: + +arithmetic.c(61): warning #274: declaration is not visible outside of function + int matherr(struct exception *exc) + ^ + +arithmetic.c(63): error: pointer to incomplete class type is not allowed + switch (exc->type) { + ^ + +The R configure script only checks for the existence of the matherr function, +and assumes the exception struct is also defined when matherr is defined by glibc's math.h . +That is no longer the case in recent glibc versions, where the exception struct is no longer defined. + +author: Kenneth Hoste (HPC-UGent) + +See also: +* https://community.intel.com/t5/Intel-C-Compiler/Error-when-compiling-R-from-source-code-ubuntu-18-04/td-p/1176401 +* https://stat.ethz.ch/pipermail/r-help/2020-May/466997.html +--- R-3.6.2/configure.orig 2020-09-18 09:25:26.171766714 +0200 ++++ R-3.6.2/configure 2020-09-18 09:38:59.035921459 +0200 +@@ -35539,6 +35539,15 @@ + done + + ++# check for exception struct in math.h ++ac_fn_c_check_member "$LINENO" "struct exception" "type" "ac_cv_member_struct_exception_type" "#include " ++if test "x$ac_cv_member_struct_exception_type" = xyes; then : ++cat >>confdefs.h <<_ACEOF ++#define HAVE_STRUCT_EXCEPTION 1 ++_ACEOF ++fi ++ ++ + ## POSIX functions + for ac_func in fcntl + do +--- R-3.6.2/src/main/arithmetic.c.orig 2020-09-18 09:24:17.969082474 +0200 ++++ R-3.6.2/src/main/arithmetic.c 2020-09-18 09:39:53.736470218 +0200 +@@ -53,6 +53,7 @@ + #include + + #ifdef HAVE_MATHERR ++#ifdef HAVE_STRUCT_EXCEPTION + + /* Override the SVID matherr function: + the main difference here is not to print warnings. +@@ -81,6 +82,7 @@ + } + #endif + #endif ++#endif + + typedef union + { From 1f7042dda6e4ed85ab20c6d48fb769a653e294e2 Mon Sep 17 00:00:00 2001 From: Pablo Escobar Date: Fri, 18 Sep 2020 10:14:58 +0200 Subject: [PATCH 194/698] style fix. line too long --- easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb index fb89b7f2eac..736e2e4594e 100644 --- a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb @@ -28,7 +28,8 @@ dependencies = [ ('bzip2', '1.0.6'), ] -prebuildopts = 'cmake -DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so -DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include . && ' +prebuildopts = 'cmake -DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so ' +prebuildopts += '-DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include . && ' files_to_copy = [(['flexbar'], 'bin/')] From ec3289ca4ba9394c4a9528a9be9a933c24bbb6f8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 18 Sep 2020 13:36:55 +0200 Subject: [PATCH 195/698] adding easyconfigs: astropy-4.0.1-intel-2020a-Python-3.8.2.eb --- .../astropy-4.0.1-intel-2020a-Python-3.8.2.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..6e3e1bb3d24 --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-4.0.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'astropy' +version = '4.0.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop +a single core package for Astronomy in Python and foster interoperability +between Python astronomy packages.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('astropy-helpers', version, { + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy-helpers/'], + 'checksums': ['f1096414d108778218d6bea06d4d9c7b2ff7c83856a451331ac194e74de9f413'], + }), + (name, version, { + 'patches': ['astropy-ah_no_auto_use.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/A/astropy/'], + 'checksums': [ + 'f1135f2637867bf4eb44b754d905462be738165ae5535540670938bbc2dcc62c', # astropy-4.0.1.tar.gz + 'fb339ff90fff8ed760b5ea9b8b65be3babb355f956a5588fd7e2e2656b4a7ca8', # astropy-ah_no_auto_use.patch + ], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/astropy'], +} + +moduleclass = 'astro' From cfbbf8eee9147e117ba416eb200ee5648bd26de6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 18 Sep 2020 13:46:28 +0200 Subject: [PATCH 196/698] adding easyconfigs: ILAMB-2.5-foss-2020a-Python-3.8.2.eb --- .../ILAMB-2.5-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..0813179a4a6 --- /dev/null +++ b/easybuild/easyconfigs/i/ILAMB/ILAMB-2.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'ILAMB' +version = '2.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.ilamb.org/' +description = """ +The International Land Model Benchmarking (ILAMB) project is a model-data intercomparison and integration project +designed to improve the performance of land models and, in parallel, improve the design of new measurement campaigns +to reduce uncertainties associated with key land surface processes. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('SciPy-bundle', '2020.03', versionsuffix), + ('sympy', '1.6.2', versionsuffix), + ('netcdf4-python', '1.5.3', versionsuffix), + ('Cartopy', '0.18.0', versionsuffix), + ('UDUNITS', '2.2.26'), # needed for cf-units +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('antlr4-python3-runtime', '4.7.2', { + 'modulename': 'antlr4', + 'checksums': ['168cdcec8fb9152e84a87ca6fd261b3d54c8f6358f42ab3b813b14a7193bb50b'], + }), + ('cf-units', '2.1.4', { + 'checksums': ['25f81ad994af30713ee8f5ef18ffddd83c6ec1ac308e1bd89d45de9d2e0f1c31'], + }), + (name, version, { + 'modulename': 'ILAMB', + 'checksums': ['d156ab01a2e895fb6ca0da870d385e8872b434e928061f2b440582fa8eb247a5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 07b7f36044b614521290a1557bcbd547d41c33a2 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 18 Sep 2020 17:05:28 +0200 Subject: [PATCH 197/698] Create QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb Builds on aurora and passes style check --- .../QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..c8520d4ec5f --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '1.9.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to either PyQt or PySide. +It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] + +builddependencies = [('binutils', '2.32')] + + +dependencies = [ + ('Python', '3.7.4'), + ('PyQt5', '5.13.2', versionsuffix) +] + + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 04baa14bec4d6ac047c43771db87bd1f98301c0c Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Fri, 18 Sep 2020 17:20:27 +0200 Subject: [PATCH 198/698] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-9.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..f2d75aaf069 --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +# Bumped from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex + metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} From 4851ebaed9d9cea91fc9c9d72f0214aa3f31f9d9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Mon, 21 Sep 2020 09:58:31 +0200 Subject: [PATCH 199/698] Make CI sanity check messages elss confusing ("is" -> "should be") --- test/easyconfigs/easyconfigs.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2f3d251a790..7e5b857c5eb 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -575,30 +575,30 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): # download_dep_fail should be set when using PythonPackage if easyblock == 'PythonPackage': if download_dep_fail is None: - failing_checks.append("'download_dep_fail' set in %s" % ec_fn) + failing_checks.append("'download_dep_fail' should be set in %s" % ec_fn) # use_pip should be set when using PythonPackage or PythonBundle (except for whitelisted easyconfigs) if easyblock in ['PythonBundle', 'PythonPackage']: if use_pip is None and not any(re.match(regex, ec_fn) for regex in whitelist_pip): - failing_checks.append("'use_pip' set in %s" % ec_fn) + failing_checks.append("'use_pip' should be set in %s" % ec_fn) # download_dep_fail is enabled automatically in PythonBundle easyblock, so shouldn't be set if easyblock == 'PythonBundle': if download_dep_fail or exts_download_dep_fail: - fail = "'*download_dep_fail' set in %s (shouldn't, since PythonBundle easyblock is used)" % ec_fn + fail = "'*download_dep_fail' should not be set in %s since PythonBundle easyblock is used" % ec_fn failing_checks.append(fail) elif exts_defaultclass == 'PythonPackage': # bundle of Python packages should use PythonBundle if easyblock == 'Bundle': - fail = "'PythonBundle' easyblock is used for bundle of Python packages in %s" % ec_fn + fail = "'PythonBundle' easyblock should be is used for bundle of Python packages in %s" % ec_fn failing_checks.append(fail) else: # both download_dep_fail and use_pip should be set via exts_default_options # when installing Python packages as extensions for key in ['download_dep_fail', 'use_pip']: if exts_default_options.get(key) is None: - failing_checks.append("'%s' set in exts_default_options in %s" % (key, ec_fn)) + failing_checks.append("'%s' should be set in exts_default_options in %s" % (key, ec_fn)) # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway @@ -609,7 +609,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies']) if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): - msg = "'-Python-%%(pyver)s' included in versionsuffix in %s" % ec_fn + msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn # This is only a failure for newly added ECs, not for existing ECS # As that would probably break many ECs if ec_fn in added_ecs_filenames: @@ -622,7 +622,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): sanity_pip_check = ec.get('sanity_pip_check') or exts_default_options.get('sanity_pip_check') if not sanity_pip_check and not any(re.match(regex, ec_fn) for regex in whitelist_pip): if not any(re.match(regex, ec_fn) for regex in whitelist_pip_check): - failing_checks.append("sanity_pip_check is enabled in %s" % ec_fn) + failing_checks.append("sanity_pip_check should be enabled in %s" % ec_fn) self.assertFalse(failing_checks, '\n'.join(failing_checks)) From 9c25cb46d20766c34bdf7f3f1adf7f12efff064c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2020 10:40:23 +0200 Subject: [PATCH 200/698] adding easyconfigs: pandas-1.1.2-foss-2020a-Python-3.8.2.eb --- .../pandas-1.1.2-foss-2020a-Python-3.8.2.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..287f0451731 --- /dev/null +++ b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pandas' +version = '1.1.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pypi.python.org/pypi/pandas/" +description = """pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures + and data analysis tools for the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 759a5643d7432ec41e7fdaeea8208928f1c22f9e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Sep 2020 11:08:18 +0200 Subject: [PATCH 201/698] also install recommended optional dependencies for pandas 1.1.2: numexpr + Bottleneck --- .../pandas-1.1.2-foss-2020a-Python-3.8.2.eb | 22 ++++++++++++++----- 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb index 287f0451731..b38c662c8a1 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'pandas' version = '1.1.2' @@ -10,17 +10,27 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2020a'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'] - dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), ] -download_dep_fail = True use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('numexpr', '2.7.1', { + 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + (name, version, { + 'checksums': ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'], + }), +] + sanity_pip_check = True moduleclass = 'lib' From 0b4ab11d2a57a3701230cafb98df7fe9728d4301 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Sep 2020 17:52:41 +0200 Subject: [PATCH 202/698] adding easyconfigs: CCL-1.12-GCCcore-9.3.0.eb --- .../c/CCL/CCL-1.12-GCCcore-9.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..04eac0b56d2 --- /dev/null +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' +name = 'CCL' +version = '1.12' + +homepage = 'https://ccl.clozure.com/' +description = """Clozure CL (often called CCL for short) is a free Common Lisp + implementation with a long history. Some distinguishing features of the implementation + include fast compilation speed, native threads, a precise, generational, compacting + garbage collector, and a convenient foreign-function interface.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/Clozure/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s-linuxx86.tar.gz'] +checksums = ['84a95aaf1d1abafba586e9ff079343b04fe374b98b38ed24d830f1fb7ed4ab34'] + +builddependencies = [ + ('binutils', '2.34'), +] + +local_ccl_bin = 'lx86cl64' +local_ccl_dirs = [ + 'compiler', 'level-0', 'level-1', 'lib', 'library', 'lisp-kernel', 'scripts', 'tools', 'xdump', 'x86-headers64' +] + +# Build the kernel +buildopts = "-C lisp-kernel/linuxx8664 all CC=${CC} && " +# Rebuild CCL +buildopts += "./%s -n -b -Q -e '(ccl:rebuild-ccl :full t)' -e '(ccl:quit)'" % local_ccl_bin + +files_to_copy = [local_ccl_bin, '%s.image' % local_ccl_bin] + local_ccl_dirs + +postinstallcmds = [ + # Cleanup of build files + "find %(installdir)s -type f -name '*fsl' -delete", + "find %(installdir)s/lisp-kernel -type f -name '*.o' -delete", + # Link executable with generic name + "mkdir %(installdir)s/bin", + "ln -s %%(installdir)s/%s %%(installdir)s/bin/ccl" % local_ccl_bin, +] + +modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} + +moduleclass = 'lang' From 2032b70d0baa1fdf6cc269102450e2af80fbd121 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 22 Sep 2020 10:19:44 +0200 Subject: [PATCH 203/698] add missing sanity checks to CCL v1.12 --- easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb index 04eac0b56d2..44008ec86c3 100644 --- a/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12-GCCcore-9.3.0.eb @@ -39,6 +39,13 @@ postinstallcmds = [ "ln -s %%(installdir)s/%s %%(installdir)s/bin/ccl" % local_ccl_bin, ] +sanity_check_paths = { + 'files': [local_ccl_bin, '%s.image' % local_ccl_bin, 'bin/ccl'], + 'dirs': local_ccl_dirs, +} + +sanity_check_commands = ["ccl --help"] + modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} moduleclass = 'lang' From 25fc2c68149bfb6d54a8ad6aa8fad8242c3c3e83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 11:43:04 +0200 Subject: [PATCH 204/698] clean up patch for MDSplus-Java (don't add Makefile.in~) + add short description + author, add SHA256 checksum for patch file to MDSplus-Java easyconfig --- ...plus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 6 +- .../MDSplus-Java-7.96.12_classpath.patch | 260 +----------------- 2 files changed, 8 insertions(+), 258 deletions(-) diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb index 7578d8a42fe..bc52b6977b5 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -13,9 +13,11 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/MDSplus/mdsplus/archive'] sources = ['stable_release-%s.zip' % version.replace('.', '-')] -checksums = ['72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318'] - patches = ['MDSplus-Java-%(version)s_classpath.patch'] +checksums = [ + '72f97f5ecf4eac40629c0e0c869cc48f7b8caa52ea9dc52d77c37d436190a318', # stable_release-7-96-12.zip + 'f2919aa5992b6364a9234bbb35230eecb84d123779c0580461f939bbc7039013', # MDSplus-Java-7.96.12_classpath.patch +] builddependencies = [ ('binutils', '2.34') diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch index bf67f6ecf00..17ef23ee344 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12_classpath.patch @@ -1,3 +1,7 @@ +use $EBROOTMDSPLUSMINJAVA environment variable to refer to installation directory + +author: Simon Pinches + diff -Nru mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template --- mdsplus-stable_release-7-84-6.orig/java/jdispatcher/jDispatcherIp.template 2019-09-02 18:02:07.000000000 +0200 +++ mdsplus-stable_release-7-84-6/java/jdispatcher/jDispatcherIp.template 2019-09-26 16:26:07.000000000 +0200 @@ -136,259 +140,3 @@ diff -Nru mdsplus-stable_release-7-84-6.orig/Makefile.in mdsplus-stable_release- else NON_JAR = \ mdsshr \ -diff -Nru mdsplus-stable_release-7-84-6.orig/Makefile.in~ mdsplus-stable_release-7-84-6/Makefile.in~ ---- mdsplus-stable_release-7-84-6.orig/Makefile.in~ 1970-01-01 01:00:00.000000000 +0100 -+++ mdsplus-stable_release-7-84-6/Makefile.in~ 2019-09-02 18:02:07.000000000 +0200 -@@ -0,0 +1,252 @@ -+#@(#)$RCSfile$ $Revision$ -+# @configure_input@ -+ -+include @top_builddir@/Makefile.inc -+ -+srcdir=@srcdir@ -+builddir=@builddir@ -+VPATH=@srcdir@ -+@AX_RECONFIGURE_TARGET@ -+ -+ -+ -+JAVA_JAR = \ -+ java/mdsplus-api \ -+ java/mdsplus-api/tests \ -+ java/jscope \ -+ java/jtraverser \ -+ java/jtraverser2 \ -+ java/jdispatcher \ -+ java/jdevices \ -+ java/mdsplus \ -+ java/mdsobjects -+ -+JAVA_APS = \ -+ javamds \ -+ java/mdsplus-api/src/main/jni/mds/mdslib -+ -+ifeq "@HAVE_MOTIF@" "yes" -+MOTIF_APS = xmdsshr \ -+ actions \ -+ dwscope \ -+ @IDLMDSWIDGETS@ \ -+ mitdevices \ -+ traverser -+else -+MOTIF_APS = actions -+endif -+HDF5_APS = hdf5 -+ -+D3D_PACKAGE = d3dshr -+ -+ifeq "@JAVA_ONLY@" "yes" -+NON_JAR = -+PARTS = $(JAVA_JAR) -+else -+NON_JAR = \ -+ mdsshr \ -+ treeshr \ -+ tdishr \ -+ tditest \ -+ xtreeshr \ -+ @MDSTCPIP@ \ -+ mdslibidl \ -+ mdsdcl \ -+ @CAMSHR@ \ -+ @REMCAM@ \ -+ ccl \ -+ servershr \ -+ tcl \ -+ @TDIC@ \ -+ mdslib \ -+ math \ -+ wfevent \ -+ setevent \ -+ mdsmisc \ -+ scripts \ -+ rpm \ -+ mdsobjects/cpp \ -+ manpages \ -+ @D3D_PACKAGE@ \ -+ @JAVA_APS@ \ -+ @MOTIF_APS@ \ -+ @MDSSQL@ \ -+ @IDLMDSEVENT@ \ -+ @HDF5_APS@ \ -+ @LV@ \ -+ LabView \ -+ @MACOSX@ -+ -+@ENABLE_TESTS_TRUE@ NON_JAR += testing -+ -+PARTS = $(NON_JAR) @JAVA_JAR@ -+endif -+ -+.PHONY: all $(PARTS) -+all: ##@build build all active submodules -+all: ChangeLog $(PARTS) -+ -+DIRECTORIES = $(sort @MAKEBINDIR@ @MAKELIBDIR@ @MAKESHLIBDIR@ @MAKEUIDDIR@) -+ -+$(NON_JAR): $(DIRECTORIES) -+@MINGW_FALSE@ $(MAKE) -C $@ @MAKEFLAG_J@ @MAKEFLAG_O@ -+@MINGW_TRUE@ $(MAKE) -C $@ -+# override parallel flags for java apps -+$(JAVA_JAR): $(DIRECTORIES) -+ $(MAKE) -C $@ -+ -+.PHONY: docs -+docs: ##@docs build documentation using doxygen (ref to docs directory) -+ $(MAKE) -C docs install -+ -+ -+ -+clean_DIRS = $(addprefix clean_, $(PARTS)) -+ -+ChangeLog: -+ if (! git --git-dir=@top_srcdir@/.git log --decorate=full --no-merges > ChangeLog 2>/dev/null); then touch ChangeLog; fi -+ -+.PHONY: clean -+clean: ##@build recusively clean all built objects in submodules -+clean: $(clean_DIRS) clean_TESTS clean_DOCS -+ -+.PHONY: $(clean_DIRS) -+$(clean_DIRS): -+ $(MAKE) -C $(@:clean_%=%) clean -+ -+clean_DOCS: ##@docs clean generated documentation -+ $(MAKE) -C docs clean -+ -+.PHONY: distclean -+ -+distclean: ##@build make source directory look like original sources -+ @cpwd=$$(pwd); \ -+ cd @top_srcdir@; \ -+ if [ -r .git ]; \ -+ then \ -+ git clean -x -f -d -q; \ -+ else \ -+ if [ "$$(pwd)" == "$$cpwd" ]; \ -+ then make full_clean > /dev/null; \ -+ fi; \ -+ rm -Rf ./python/MDSplus/build; \ -+ fi; \ -+ cd $$cpwd -+ -+# Testing -+ -+.PHONY: tests -+tests: ##@tests recursively perform tests in submodules -+@ENABLE_TESTS_TRUE@ $(MAKE) $(AM_MAKEFLAGS) -C testing all tests -+@ENABLE_TESTS_FALSE@ @echo "Tests disabled" -+ -+.PHONY: tests-valgrind rebuild-tests -+tests-valgrind: ##@tests perform tests using valgrind tool -+rebuild-tests: ##@tests rebuild all tests binaries -+tests-valgrind rebuild-tests: -+@ENABLE_TESTS_TRUE@ $(MAKE) $(AM_MAKEFLAGS) -C testing all $@ -+@ENABLE_TESTS_FALSE@ @echo "Tests disabled" -+ -+.PHONY: $(clean_TESTS) -+clean_TESTS: ##@tests clean all tests results and compiled tests objects -+@ENABLE_TESTS_TRUE@ $(MAKE) -C testing tests-clean -+ -+ -+.PHONY: full_clean -+full_clean: ##@build perform deep clean of build directories -+full_clean: clean -+ @rm -Rf bin bin64 bin32 bin_x86 bin_x86_64 etc \ -+ lib lib64 lib32 java uid uid64 uid32 \ -+ config.cache config.log config.status aclocal.m4 \ -+ include/stamp-h1 autom4te.cache \ -+ $$(find . -name '.deps') \ -+ `find . -name '*.in' | \ -+ $(AWK) '{print substr($$1,0,length($$1)-3)}'` -+ -+.PHONY: depend -+depend: -+ cdir=`pwd`;\ -+ set -e; for dir in $(PARTS) ; do\ -+ cd $${dir}; $${MAKE:=make} depend > /dev/null 2> /dev/null; cd $$cdir;\ -+ done -+ -+MISC_PARTS = tdi pydevices idl trees setup.sh setup.csh include desktop pixmaps matlab php epics xml nodejs python/MDSplus -+ -+install_DIRS = $(addprefix install_, $(PARTS)) -+$(install_DIRS): -+ $(MAKE) -C $(@:install_%=%) install -+ -+.PHONY: install -+install: ##@build build and install active modules to prefix directory -+install: $(install_DIRS) -+ $(INSTALL) ChangeLog $(prefix)/ -+ $(MKDIR_P) $(prefix)/local/tdi -+ $(MKDIR_P) $(prefix)/java -+ $(MKDIR_P) $(prefix)/python/MDSplus -+ - find $(prefix)/java -name '*.class' -delete #### No need to include class files -+ tar -C ${top_srcdir} \ -+ --exclude='.gitignore' \ -+ --exclude='*.pyc' \ -+ --exclude=__pycache__ \ -+ --exclude=python/MDSplus/build \ -+ --exclude=python/MDSplus/docs \ -+ --exclude=tdi/*Devices/build \ -+ --exclude='*egg-info' \ -+ --exclude='*\.in' \ -+ --exclude='Makefile\.*' \ -+ -cf - $(MISC_PARTS) | (cd $(exec_prefix); tar -xf -) -+ tar -C ${top_builddir} -cf - include/mdsplus/mdsconfig.h $$(find . -name _version.py) | (cd $(exec_prefix); tar -xf -) ## TODO: remove this and config.h from headers ... -+ if [ ! -z "$$MDSPLUS_VERSION" ]; then echo "mdsplus_version='$$MDSPLUS_VERSION'" > $(exec_prefix)/python/MDSplus/mdsplus_version.py; fi -+ $(INSTALL) ${top_srcdir}/MDSplus-License.txt ${top_srcdir}/MDSplus-License.rtf $(exec_prefix) -+ (cd $(exec_prefix); chmod -R 755 $(MISC_PARTS)) -+ -+.PHONY: tests-envdump -+tests-envdump: -+ cd python/MDSobjects/tests&&(\ -+ make test-envdump;\ -+ cd ../../..;) -+ -+test-env: -+ cd python/MDSplus/tests&&(\ -+ make test-env;\ -+ cd ../../..;) -+ -+@HAVE_WINE_TRUE@wineconsole: -+@HAVE_WINE_TRUE@ cd python/MDSplus/tests&&(\ -+@HAVE_WINE_TRUE@ make wineconsole;\ -+@HAVE_WINE_TRUE@ cd ../../..;) -+ -+# Interdependent directories: -+actions: mdsshr tdishr treeshr xmdsshr mdstcpip servershr -+camshr: mdsdcl -+ccl: camshr mdsshr mdsdcl -+tcl: mdsshr treeshr tdishr mdstcpip servershr mdsdcl -+dwscope: xmdsshr -+java/jdevices: java/jtraverser -+java/jdispatcher: java/jscope java/jtraverser -+javamds: mdstcpip -+java/jtraverser: java/jscope -+java/jtraverser2: java/mdsplus-api -+java/mdsplus-api/tests: java/mdsplus-api -+math: mdsshr -+mdsdcl: mdsshr -+mdslib: mdstcpip -+mdslibidl: tdishr -+mdsmisc: tdishr xtreeshr -+mdsobjects/cpp: mdstcpip -+java/mdsobjects: java/jscope -+mdstcpip: tdishr -+mitdevices: mdsshr tdishr treeshr xmdsshr -+remcam: mdstcpip -+servershr: mdsdcl tdishr treeshr mdsshr mdstcpip -+setevent: mdsshr -+tdic: mdstcpip -+tdishr: mdsshr treeshr -+tditest: tdishr -+traverser: xmdsshr -+treeshr: mdsshr -+wfevent: tdishr mdsshr -+xmdsshr: tdishr -+xtreeshr: tdishr -+ -+am--refresh: From a72de69ab2257a9404e09440cf14b3b59380d936 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 11:59:45 +0200 Subject: [PATCH 205/698] adding easyconfigs: BLAT-3.5-GCC-9.3.0.eb --- .../easyconfigs/b/BLAT/BLAT-3.5-GCC-9.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAT/BLAT-3.5-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/b/BLAT/BLAT-3.5-GCC-9.3.0.eb b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-GCC-9.3.0.eb new file mode 100644 index 00000000000..0bb7ac4bd4e --- /dev/null +++ b/easybuild/easyconfigs/b/BLAT/BLAT-3.5-GCC-9.3.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 The Cyprus Institute +# Authors:: Andreas Panteli , Thekla Loizou +# License:: MIT/GPL +# +## + +name = 'BLAT' +version = '3.5' + +homepage = 'https://genome.ucsc.edu/FAQ/FAQblat.html' +description = """BLAT on DNA is designed to quickly find sequences of 95% and +greater similarity of length 25 bases or more.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://users.soe.ucsc.edu/~kent/src'] +sources = ['%%(namelower)sSrc%s.zip' % ''.join(version.split('.'))] +checksums = ['06d9bcf114ec4a4b21fef0540a0532556b6602322a5a2b33f159dc939ae53620'] + +dependencies = [('libpng', '1.6.37')] + +buildopts = 'CC="$CC" COPT= L="$LIBS"' + +files_to_copy = ["bin", "blat", "gfClient", "gfServer", "hg", "inc", "jkOwnLib", "lib", "utils", "webBlat"] + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ['blat', 'faToNib', 'faToTwoBit', 'gfClient', 'gfServer', 'nibFrag', + 'pslPretty', 'pslReps', 'pslSort', 'twoBitInfo', 'twoBitToFa']], + 'dirs': files_to_copy, +} + +moduleclass = 'bio' From 1fc056298e61bf13560b4530cc1ca81072d9abc4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 12:13:32 +0200 Subject: [PATCH 206/698] use proper dependencies for numexpr and Bottleneck in pandas 1.1.2 easyconfig --- ...ottleneck-1.3.2-foss-2020a-Python-3.8.2.eb | 25 +++++++++++++++++++ .../pandas-1.1.2-foss-2020a-Python-3.8.2.eb | 24 ++++++------------ 2 files changed, 33 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..76afe8999a5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bottleneck/Bottleneck-1.3.2-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Bottleneck' +version = '1.3.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://kwgoodman.github.io/bottleneck-doc' +description = "Fast NumPy array functions written in C" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb index b38c662c8a1..8765bbb2da3 100644 --- a/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/pandas/pandas-1.1.2-foss-2020a-Python-3.8.2.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'pandas' version = '1.1.2' @@ -10,27 +10,19 @@ description = """pandas is an open source, BSD-licensed library providing high-p toolchain = {'name': 'foss', 'version': '2020a'} +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'] + dependencies = [ ('Python', '3.8.2'), ('SciPy-bundle', '2020.03', versionsuffix), + ('numexpr', '2.7.1', versionsuffix), + ('Bottleneck', '1.3.2', versionsuffix), ] +download_dep_fail = True use_pip = True - -exts_default_options = {'source_urls': [PYPI_SOURCE]} - -exts_list = [ - ('numexpr', '2.7.1', { - 'checksums': ['b0d239d9827e1bcee08344fd05835823bc60aff97232e35a928214d03ff802b1'], - }), - ('Bottleneck', '1.3.2', { - 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], - }), - (name, version, { - 'checksums': ['b64ffd87a2cfd31b40acd4b92cb72ea9a52a48165aec4c140e78fd69c45d1444'], - }), -] - sanity_pip_check = True moduleclass = 'lib' From 469d83c0b9bbe935883071621006a23b93efcc42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 12:16:46 +0200 Subject: [PATCH 207/698] make sure correct zlib is used in recent Ghostscript easyconfigs --- .../Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb index 49ca5a6bf0b..38625f7e87b 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb @@ -36,7 +36,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb index 58a57b4d082..22b1cf5d616 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-7.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-7.3.0.eb index 498f1d46942..fe7c7d81524 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-7.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb index 4df553e2f69..89ef8200fd0 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.50-GCCcore-8.3.0.eb @@ -34,7 +34,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb index 3f69106aa2f..afd425e4546 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.52-GCCcore-9.3.0.eb @@ -35,7 +35,7 @@ builddependencies = [ # Do not use local copies of zlib, jpeg, freetype, and png preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " -preconfigopts += 'export LIBS="$LIBS -lz" && ' +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' configopts = "--with-system-libtiff --enable-dynamic" From d13469ce2ef7da6a466f53cfc9d555685fa1806a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 12:21:24 +0200 Subject: [PATCH 208/698] add custom sanity_check_paths to easyconfig for MDSplus 7.96.12 --- .../m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb index 2608ca19209..cfde52c87eb 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'MDSplus' version = '7.96.12' -homepage = 'http://mdsplus.org/' +homepage = 'https://mdsplus.org/' description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" @@ -42,4 +42,10 @@ modextrapaths = { 'IDL_PATH': 'idl', } +sanity_check_paths = { + 'files': ['lib/libMdsLib.so', 'lib/libTreeShr.so', 'include/mdslib.h', + 'include/mdsobjects.h'], + 'dirs': ['bin', 'include', 'lib', 'tdi'], +} + moduleclass = 'data' From 3d28c9580742b2f2265bfdb8d3c40e8ab1a33530 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 12:28:18 +0200 Subject: [PATCH 209/698] avoid hardcoding .so in MDSplus sanity_check_paths --- .../easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb index cfde52c87eb..9f54e435105 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb @@ -43,9 +43,9 @@ modextrapaths = { } sanity_check_paths = { - 'files': ['lib/libMdsLib.so', 'lib/libTreeShr.so', 'include/mdslib.h', - 'include/mdsobjects.h'], - 'dirs': ['bin', 'include', 'lib', 'tdi'], + 'files': ['lib/libMdsLib.%s' % SHLIB_EXT, 'lib/libTreeShr.%s' % SHLIB_EXT, + 'include/mdslib.h', 'include/mdsobjects.h'], + 'dirs': ['bin', 'tdi'], } moduleclass = 'data' From 9ae3053fa1f54acdb728f0552a7662806bcca81c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 14:00:28 +0200 Subject: [PATCH 210/698] fix long line + escaped ';' in MDSplus-Java easyconfig + consistently use https in homepage in MDSplus* easyconfigs --- .../MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb | 5 +++-- .../MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb | 2 +- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb index bc52b6977b5..3b6f548fcac 100644 --- a/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb +++ b/easybuild/easyconfigs/m/MDSplus-Java/MDSplus-Java-7.96.12-GCCcore-9.3.0-Java-13.eb @@ -4,7 +4,7 @@ name = 'MDSplus-Java' version = '7.96.12' versionsuffix = '-Java-%(javaver)s' -homepage = 'http://mdsplus.org/' +homepage = 'https://mdsplus.org' description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" @@ -28,7 +28,8 @@ dependencies = [ ('MDSplus', version), ] -preconfigopts = 'find . -type f -regex .*Makefile.* -maxdepth 12 -exec sed -i "s/JAVASOURCE = 6/JAVASOURCE = 8/g" {} \; && ' +preconfigopts = 'find . -type f -regex .*Makefile.* -maxdepth 12 ' +preconfigopts += '-exec sed -i "s/JAVASOURCE = 6/JAVASOURCE = 8/g" {} \\; && ' preconfigopts += 'export CFLAGS="$CFLAGS -I$EBROOTLIBXML2/include/libxml2 " && ' configopts = '--with-jdk=$JAVA_HOME --enable-java_only --disable-doxygen-doc --disable-valgrind' diff --git a/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb index d5d26c65de0..70a94771431 100644 --- a/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/m/MDSplus-Python/MDSplus-Python-7.96.12-foss-2020a-Python-3.8.2.eb @@ -6,7 +6,7 @@ local_pyver = '3.8.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://mdsplus.org/' +homepage = 'https://mdsplus.org' description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb index 9f54e435105..de21068d55c 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'MDSplus' version = '7.96.12' -homepage = 'https://mdsplus.org/' +homepage = 'https://mdsplus.org' description = """MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data.""" From 9f7d79a739ba2ccc9d445d6cbbc644730aaba171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 14:01:54 +0200 Subject: [PATCH 211/698] use https in homepage in Ghostscript 9.23 easyconfigs --- .../Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb | 2 +- .../easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb index 38625f7e87b..a12e08a32b1 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0-cairo-1.14.12.eb @@ -5,7 +5,7 @@ version = '9.23' local_cairover = '1.14.12' versionsuffix = '-cairo-%s' % local_cairover -homepage = 'http://ghostscript.com' +homepage = 'https://ghostscript.com' description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.""" diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb index 22b1cf5d616..9b6d79668cf 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-9.23-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'Ghostscript' version = '9.23' -homepage = 'http://ghostscript.com' +homepage = 'https://ghostscript.com' description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.""" From 8484b632e31fc5756c7d01123242b7d5a2fb711a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Sep 2020 16:45:46 +0200 Subject: [PATCH 212/698] {lib}[GCCcore/10.2.0] UCX v1.9.0 --- .../numactl/numactl-2.0.13-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../pkg-config-0.29.2-GCCcore-10.2.0.eb | 34 ++++++++++++++ .../u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..9de001385a5 --- /dev/null +++ b/easybuild/easyconfigs/n/numactl/numactl-2.0.13-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'numactl' +version = '2.0.13' + +homepage = 'https://github.com/numactl/numactl' + +description = """ + The numactl program allows you to run your application program on specific + cpu's and memory nodes. It does this by supplying a NUMA memory policy to + the operating system before running your program. The libnuma library provides + convenient ways for you to add NUMA memory policies into your own program. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/numactl/numactl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97ee012b2f294903530424b4ff7f28bcaad6a356897ce8777383f87e5c2e325d'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/numactl', 'bin/numastat', 'lib/libnuma.%s' % SHLIB_EXT, 'lib/libnuma.a'], + 'dirs': ['share/man', 'include'] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1103527815f --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' + +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://pkg-config.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [('binutils', '2.35')] + +# don't use PAX, it might break. +tar_config_opts = True + +configopts = " --with-internal-glib" + +sanity_check_paths = { + 'files': ['bin/pkg-config'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0c81fb441bc --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.9.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.9.0' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['a7a2c8841dc0d5444088a4373dc9b9cc68dbffcd917c1eba92ca8ed8e5e635fb'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('numactl', '2.0.13'), +] + +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From 5fafb28fefcaf0d078c6cd65b185ff49e09707c7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Sep 2020 17:08:33 +0200 Subject: [PATCH 213/698] Remove GLog and GFlags from PyTorch 1.4.0 --- .../p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb | 2 -- .../p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb | 2 -- 2 files changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb index d93204ddd9d..d1c5018a52a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-foss-2019b-Python-3.7.4.eb @@ -236,8 +236,6 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb index e5d7f7647c4..7633bb883a7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.4.0-fosscuda-2019b-Python-3.7.4.eb @@ -238,8 +238,6 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ('cuDNN', '7.6.4.38'), ('magma', '2.5.1'), From 3ea254e7f54af1817c9ff4c72605e8af07101116 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Sep 2020 17:10:49 +0200 Subject: [PATCH 214/698] Remove GLog and GFlags from PyTorch 1.6.0 --- .../p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb index f379ce95192..fbec32372cc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -273,8 +273,6 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ('cuDNN', '7.6.4.38'), ('magma', '2.5.1'), From 396aa672c855ffcad12b9dd5024eb1c04cd01976 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 22 Sep 2020 17:18:59 +0200 Subject: [PATCH 215/698] adding easyconfigs: Spyder-4.1.5-foss-2019a-Python-3.7.2.eb --- .../Spyder-4.1.5-foss-2019a-Python-3.7.2.eb | 310 ++++++++++++++++++ 1 file changed, 310 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb new file mode 100644 index 00000000000..185ea023603 --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb @@ -0,0 +1,310 @@ +easyblock = 'PythonBundle' + +name = 'Spyder' +version = '4.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple + and light-weighted software.""" + +toolchain = {'name': 'foss', 'version': '2019a'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [ + ('CMake', '3.13.3'), +] +dependencies = [ + ('Python', '3.7.2'), + ('ZeroMQ', '4.3.2'), + ('PyQt5', '5.12.1', versionsuffix), + ('IPython', '7.7.0', versionsuffix), + ('geopandas', '0.8.0', versionsuffix), +] + +use_pip = True + +local_spyder_preinstallopts = ( + "sed -i \"s/'pyqt5<5.13;python_version>=\\\"3\\\"',//g\" setup.py && " + "sed -i \"s/'pyqtwebengine<5.13;python_version>=\\\"3\\\"',//g\" setup.py && " + "sed -i 's/jedi==0.17.1/jedi==0.17.2/g' setup.py && " + "sed -i \"s/JEDI_REQVER = '=0.17.1'/JEDI_REQVER = '=0.17.2'/g\" spyder/dependencies.py && " +) + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('alabaster', '0.7.12', { + }), + ('arrow', '0.16.0', { + }), + ('astroid', '2.4.2', { + 'checksums': ['2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('autopep8', '1.5.4', { + 'checksums': ['d21d3901cb0da6ebd1e83fc9b0dfbde8b46afc2ede4fe32fbda0c7c6118ca094'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('backcall', '0.2.0', { + 'use_pip': False, + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('bleach', '3.1.5', { + 'checksums': ['3c4c520fdb9db59ef139915a5db79f8b51bc2a7257ea0389f30c846883430a4b'], + }), + ('certifi', '2020.6.20', { + 'checksums': ['5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('cookiecutter', '1.7.2', { + 'checksums': ['efb6b2d4780feda8908a873e38f0e61778c23f6a2ea58215723bcceb5b515dac'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('defusedxml', '0.6.0', { + }), + ('diff-match-patch', '20200713', { + 'checksums': ['da6f5a01aa586df23dfc89f3827e1cafbb5420be9d87769eeb079ddfd9477a18'], + }), + ('docutils', '0.16', { + }), + ('entrypoints', '0.3', { + 'use_pip': False, + }), + ('flake8', '3.8.3', { + 'checksums': ['f04b9fcbac03b0a3e58c0ab3a0ecc462e023a9faf046d57794184028123aa208'], + }), + ('helpdev', '0.7.1', { + 'checksums': ['bb62a79acbac141dadf42cadeb92bb7450dd18b9824a62043b6a0b149190db3d'], + }), + ('importlib_metadata', '1.7.0', { + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], + }), + ('imagesize', '1.2.0', { + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('ipykernel', '5.3.4', { + 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], + }), + ('isort', '5.5.2', { + 'use_pip': False, + 'checksums': ['171c5f365791073426b5ed3a156c2081a47f88c329161fd28228ff2da4c97ddb'], + }), + ('jedi', '0.17.2', { + 'checksums': ['86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20'], + }), + ('jeepney', '0.4.3', { + 'use_pip': False, + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), + ('Jinja2', '2.10', { + }), + ('jinja2-time', '0.2.0', { + 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], + }), + ('jsonschema', '3.2.0', { + }), + ('jupyter_client', '6.1.7', { + 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('jupyter_contrib_core', '0.3.3', { + }), + ('jupyterlab_pygments', '0.1.1', { + 'checksums': ['19a0ccde7daddec638363cd3d60b63a4f6544c9181d65253317b2fb492a797b9'], + }), + ('keyring', '21.4.0', { + }), + ('keyrings.alt', '3.1', { + 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], + }), + ('lazy-object-proxy', '1.4.3', { + 'checksums': ['f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0'], + }), + ('MarkupSafe', '1.1.1', { + }), + ('mccabe', '0.6.1', { + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('mistune', '0.8.4', { + }), + ('nbclient', '0.5.0', { + 'checksums': ['8ad52d27ba144fca1402db014857e53c5a864a2f407be66ca9d74c3a56d6591d'], + }), + ('nbconvert', '6.0.2', { + 'checksums': ['4cb5c66d04737a42076536fa64fa951e97cddbf4c517c418591314a3d14013dc'], + }), + ('nbformat', '5.0.7', { + 'checksums': ['54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340'], + }), + ('nest_asyncio', '1.4.0', { + 'checksums': ['5773054bbc14579b000236f85bc01ecced7ffd045ec8ca4a9809371ec65a59c8'], + }), + ('numpydoc', '1.1.0', { + 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], + }), + ('packaging', '20.4', { + }), + ('parso', '0.7.0', { + 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('poyo', '0.5.0', { + 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], + }), + ('psutil', '5.4.8', { + 'checksums': ['6e265c8f3da00b015d24b842bfeb111f856b13d24f2c57036582568dc650d6c3'], + }), + ('pycodestyle', '2.6.0', { + 'checksums': ['c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e'], + }), + ('pydocstyle', '5.1.1', { + 'checksums': ['19b86fa8617ed916776a11cd8bc0197e5b9856d5433b777f51a3defe13075325'], + }), + ('pyflakes', '2.2.0', { + 'checksums': ['35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8'], + }), + ('Pygments', '2.7.0', { + 'checksums': ['2594e8fdb06fef91552f86f4fd3a244d148ab24b66042036e64f29a291515048'], + }), + ('pylint', '2.6.0', { + 'checksums': ['bb4a908c9dadbc3aac18860550e870f58e1a02c9f2c204fdf5693d73be061210'], + }), + ('python-language-server', '0.35.0', { + 'modulename': 'pyls', + 'checksums': ['ac0bbc549b38565aa945b6335cc65c5e7230b8b60417af3bf9df5d1aacb03f90'], + }), + ('PyQt5_sip', '12.8.1', { + 'modulename': False, + 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('python-jsonrpc-server', '0.4.0', { + 'modulename': 'pyls_jsonrpc', + 'checksums': ['62c543e541f101ec5b57dc654efc212d2c2e3ea47ff6f54b2e7dcb36ecf20595'], + }), + ('python-slugify', '4.0.1', { + 'modulename': 'slugify', + 'checksums': ['69a517766e00c1268e5bbfc0d010a0a8508de0b18d30ad5a1ff357f8ae724270'], + }), + ('pyxdg', '0.26', { + 'modulename': 'xdg', + 'checksums': ['fe2928d3f532ed32b39c32a482b54136fe766d19936afc96c8f00645f9da1a06'], + }), + ('requests', '2.23.0', { + }), + ('rope', '0.17.0', { + 'checksums': ['658ad6705f43dcf3d6df379da9486529cf30e02d9ea14c5682aa80eb33b649e1'], + }), + ('QDarkStyle', '2.8.1', { + 'checksums': ['d53b0120bddd9e3efba9801731e22ef86ed798bb5fc6a802f5f7bb32dedf0321'], + }), + ('QtAwesome', '0.7.2', { + 'checksums': ['ca9719c82d41707f62c340811b23bcab95336e73edd88b7eab7fd951d2e27fab'], + }), + ('qtconsole', '4.7.7', { + 'checksums': ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'], + }), + ('QtPy', '1.9.0', { + 'checksums': ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'], + }), + ('SecretStorage', '3.1.2', { + 'modulename': 'secretstorage', + 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], + }), + ('snowballstemmer', '2.0.0', { + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('Sphinx', '3.2.1', { + 'checksums': ['321d6d9b16fa381a5306e5a0b76cd48ffbc588e6340059a729c6fdd66087e0e8'], + }), + ('sphinxcontrib-applehelp', '1.0.2', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '1.0.3', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('sphinxcontrib-serializinghtml', '1.1.4', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], + }), + ('spyder', version, { + 'preinstallopts': local_spyder_preinstallopts, + 'checksums': ['d467f020b694193873a237ce6744ae36bd5a59f4d2b7ffbeb15dda68b03f5aa1'], + }), + ('spyder-kernels', '1.9.4', { + 'modulename': 'spyder_kernels', + 'checksums': ['ca9d997c475b714b54d2fd67aa140837ec3630e91cbbc2e0cd190f1b0bd9fe9d'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + ('traitlets', '5.0.4', { + 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], + }), + ('typed_ast', '1.4.1', { + }), + ('ujson', '3.2.0', { + 'checksums': ['abb1996ba1c1d2faf5b1e38efa97da7f64e5373a31f705b96fe0587f5f778db4'], + }), + ('watchdog', '0.10.3', { + 'checksums': ['4214e1379d128b0588021880ccaf40317ee156d4603ac388b9adcf29165e0c04'], + }), + ('wurlitzer', '2.0.1', { + 'checksums': ['d08f0728a998441aac3d7a0f8cd6dfed2ba2525144878fb49599b719085b7543'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('yapf', '0.30.0', { + 'checksums': ['3000abee4c28daebad55da6c85f3cd07b8062ce48e2e9943c8da1b9667d48427'], + }), + ('zipp', '1.2.0', { + }), +] + +sanity_pip_check = True +sanity_check_paths = { + 'files': ['bin/spyder3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = ["spyder3 --help"] + +moduleclass = 'tools' From 5ecde89a499efb3cfddad1c6e3ea0611cd99dbd5 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 22 Sep 2020 17:23:24 +0200 Subject: [PATCH 216/698] Spyder: add checksums --- .../Spyder-4.1.5-foss-2019a-Python-3.7.2.eb | 19 ++++++++++++++++++- 1 file changed, 18 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb index 185ea023603..a0cbdc27f27 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb @@ -34,8 +34,10 @@ local_spyder_preinstallopts = ( exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), ('arrow', '0.16.0', { + 'checksums': ['92aac856ea5175c804f7ccb96aca4d714d936f1c867ba59d747a8096ec30e90a'], }), ('astroid', '2.4.2', { 'checksums': ['2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703'], @@ -72,14 +74,17 @@ exts_list = [ 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], }), ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], }), ('diff-match-patch', '20200713', { 'checksums': ['da6f5a01aa586df23dfc89f3827e1cafbb5420be9d87769eeb079ddfd9477a18'], }), ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], }), ('entrypoints', '0.3', { 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('flake8', '3.8.3', { 'checksums': ['f04b9fcbac03b0a3e58c0ab3a0ecc462e023a9faf046d57794184028123aa208'], @@ -91,6 +96,7 @@ exts_list = [ 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], }), ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], }), ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], @@ -110,11 +116,13 @@ exts_list = [ 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], }), ('Jinja2', '2.10', { + 'checksums': ['f84be1bb0040caca4cea721fcbbbbd61f9be9464ca236387158b0feea01914a4'], }), ('jinja2-time', '0.2.0', { 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], }), ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], }), ('jupyter_client', '6.1.7', { 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], @@ -123,11 +131,13 @@ exts_list = [ 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], }), ('jupyter_contrib_core', '0.3.3', { + 'checksums': ['e65bc0e932ff31801003cef160a4665f2812efe26a53801925a634735e9a5794'], }), ('jupyterlab_pygments', '0.1.1', { 'checksums': ['19a0ccde7daddec638363cd3d60b63a4f6544c9181d65253317b2fb492a797b9'], }), ('keyring', '21.4.0', { + 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '3.1', { 'checksums': ['b59c86b67b9027a86e841a49efc41025bcc3b1b0308629617b66b7011e52db5a'], @@ -136,11 +146,13 @@ exts_list = [ 'checksums': ['f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0'], }), ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], }), ('mccabe', '0.6.1', { 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], }), ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], }), ('nbclient', '0.5.0', { 'checksums': ['8ad52d27ba144fca1402db014857e53c5a864a2f407be66ca9d74c3a56d6591d'], @@ -158,6 +170,7 @@ exts_list = [ 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], }), ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], }), ('parso', '0.7.0', { 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], @@ -210,6 +223,7 @@ exts_list = [ 'checksums': ['fe2928d3f532ed32b39c32a482b54136fe766d19936afc96c8f00645f9da1a06'], }), ('requests', '2.23.0', { + 'checksums': ['b3f43d496c6daba4493e7c431722aeb7dbc6288f52a6e04e7b6023b0247817e6'], }), ('rope', '0.17.0', { 'checksums': ['658ad6705f43dcf3d6df379da9486529cf30e02d9ea14c5682aa80eb33b649e1'], @@ -231,6 +245,7 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], }), ('sortedcontainers', '2.2.2', { 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], @@ -263,7 +278,7 @@ exts_list = [ 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], }), ('spyder', version, { - 'preinstallopts': local_spyder_preinstallopts, + 'preinstallopts': """sed -i "s/'pyqt5<5.13;python_version>=\"3\"',//g" setup.py && sed -i "s/'pyqtwebengine<5.13;python_version>=\"3\"',//g" setup.py && sed -i 's/jedi==0.17.1/jedi==0.17.2/g' setup.py && sed -i "s/JEDI_REQVER = '=0.17.1'/JEDI_REQVER = '=0.17.2'/g" spyder/dependencies.py && """, 'checksums': ['d467f020b694193873a237ce6744ae36bd5a59f4d2b7ffbeb15dda68b03f5aa1'], }), ('spyder-kernels', '1.9.4', { @@ -280,6 +295,7 @@ exts_list = [ 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], }), ('typed_ast', '1.4.1', { + 'checksums': ['8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b'], }), ('ujson', '3.2.0', { 'checksums': ['abb1996ba1c1d2faf5b1e38efa97da7f64e5373a31f705b96fe0587f5f778db4'], @@ -297,6 +313,7 @@ exts_list = [ 'checksums': ['3000abee4c28daebad55da6c85f3cd07b8062ce48e2e9943c8da1b9667d48427'], }), ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], }), ] From b521ed2c1ccb32d82e5b40f520e3660fcfc6333a Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 22 Sep 2020 16:51:59 +0100 Subject: [PATCH 217/698] adding easyconfigs: SAMtools-1.11-GCC-9.3.0.eb --- .../s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb new file mode 100644 index 00000000000..7ddf1a0f0f6 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.11-GCC-9.3.0.eb @@ -0,0 +1,35 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: MIT +# +# Notes:: +## + +name = 'SAMtools' +version = '1.11' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['e283cebd6c1c49f0cf8a3ca4fa56e1d651496b4d2e42f80ab75991a9ece4e5b6'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.69.1'), +] + +moduleclass = 'bio' From 7507cae2ea0107ebf81070c72b5813358176bfc7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Sep 2020 18:03:54 +0200 Subject: [PATCH 218/698] Remove GLog and GFlags from PyTorch 1.2.0 --- .../p/PyTorch/PyTorch-1.2.0-foss-2019a-Python-3.7.2.eb | 4 +--- .../p/PyTorch/PyTorch-1.2.0-fosscuda-2019a-Python-3.7.2.eb | 4 +--- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-foss-2019a-Python-3.7.2.eb index 8fab8d0106e..ba7dec297f7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-foss-2019a-Python-3.7.2.eb @@ -284,8 +284,6 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.1.3'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.0.0'), ] @@ -294,7 +292,7 @@ download_dep_fail = True prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' prebuildopts += 'MAX_JOBS=%(parallel)s ' prebuildopts += 'LDFLAGS="$LDFLAGS -ldl" ' -prebuildopts += 'USE_FFMPEG=ON USE_GLOO_IBVERBS=1 USE_GFLAGS=ON USE_GLOG=ON ' +prebuildopts += 'USE_FFMPEG=ON USE_GLOO_IBVERBS=1 ' preinstallopts = prebuildopts diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-fosscuda-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-fosscuda-2019a-Python-3.7.2.eb index a97cca586dd..024196ef2bd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-fosscuda-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.2.0-fosscuda-2019a-Python-3.7.2.eb @@ -286,8 +286,6 @@ dependencies = [ ('FFmpeg', '4.1.3'), ('cuDNN', '7.6.4.38'), ('magma', '2.5.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.0.0'), ] @@ -296,7 +294,7 @@ download_dep_fail = True prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' prebuildopts += 'MAX_JOBS=%(parallel)s ' prebuildopts += 'LDFLAGS="$LDFLAGS -ldl" ' -prebuildopts += 'USE_FFMPEG=ON USE_GLOO_IBVERBS=1 USE_GFLAGS=ON USE_GLOG=ON ' +prebuildopts += 'USE_FFMPEG=ON USE_GLOO_IBVERBS=1 ' prebuildopts += 'CUDNN_LIB_DIR=$EBROOTCUDNN/lib64 CUDNN_INCLUDE_DIR=$EBROOTCUDNN/include ' prebuildopts += 'TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0" ' From e7c4c54a212967f5818f0b8eba704a2daa4704c8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Sep 2020 17:50:01 +0200 Subject: [PATCH 219/698] Use EasyBlock for PyTorch 1.3.1 and remove glog&gflags --- .../PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 47 +++---------------- ...Torch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 44 ++++------------- 2 files changed, 16 insertions(+), 75 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index a489a683718..c1fef85daaa 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'PyTorch' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' @@ -73,12 +71,6 @@ sources = [ 'filename': 'onnx-tensorrt-20190425.tar.gz', 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx-tensorrt'), }, - { - 'source_urls': ['https://github.com/google/protobuf/archive'], - 'download_filename': '48cb18e5c419ddd23d9badcfe4e9df7bde1979b2.tar.gz', - 'filename': 'protobuf-20180727.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'protobuf'), - }, { 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', @@ -169,12 +161,6 @@ sources = [ 'filename': 'gemmlowp-20181127.tar.gz', 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'gemmlowp/gemmlowp'), }, - { - 'source_urls': ['https://github.com/NVIDIA/nccl/archive'], - 'download_filename': '7c72dee660e4d055b81721dd6b03e4e1c0a983cf.tar.gz', - 'filename': 'nccl-20190625.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'nccl/nccl'), - }, { 'source_urls': ['https://github.com/NVlabs/cub/archive'], 'download_filename': '285aeebaa34b0e8a7670867a2e66c1a52d998d6a.tar.gz', @@ -222,7 +208,6 @@ checksums = [ 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz '02407529fd8431cf627d45638b4d9a6c02b8aa5bf50d73b8fa12217918c57ff4', # pybind11-20170919.tar.gz '1a98c6fece7878c88b59ffe651b427c15b4929c801a09655cd14ca44553787c3', # onnx-tensorrt-20190425.tar.gz - 'f5a35e17fb07f3b13517264cd17a089636fcbb2912f9df7bef7414058969a8d2', # protobuf-20180727.tar.gz '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz @@ -238,7 +223,6 @@ checksums = [ '0de43b6eaddd356f1d6cd164f73f37faf2f6c96fd684e1f7ea543ce49c1d144e', # benchmark-20180606.tar.gz '2ec954f18cec50a7063a7358ce555f7e11788a7f6d4e7e597d83687dc2f3b989', # eigen-20190126.tar.gz 'fdd6f08bdb33d33f4df516ffb91730fdb163479c19502cfc983083fd9cf43bfa', # gemmlowp-20181127.tar.gz - 'ef8b624ef28e9e2d0e162065932dd2f25de8d6d1dc58df91bd36977e4bc0224c', # nccl-20190625.tar.gz '7224b03af4acbc54525105bb42e3ecd75c66a3a5b47e8a725ab008467c4109f9', # cub-20170829.tar.gz 'b444b4428adc4befc777d9a1af2fd9bbf5f5a2339913668357196c5133e9cc7b', # foxi-20190424.tar.gz 'b8fb8b4871cc3da4bded01c476957a08f51949c20f834f39f90f9e10811d6dfe', # ideep-20190912.tar.gz @@ -254,10 +238,11 @@ checksums = [ builddependencies = [ ('CMake', '3.15.3'), ('hypothesis', '4.44.2', versionsuffix), - ('Ninja', '1.9.0'), ] dependencies = [ + ('Ninja', '1.9.0'), + ('protobuf', '3.10.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('PyYAML', '5.1.2'), @@ -265,32 +250,14 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ] -download_dep_fail = True - -prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += 'MAX_JOBS=%(parallel)s ' -prebuildopts += 'LDFLAGS="$LDFLAGS -ldl" ' -prebuildopts += 'USE_FFMPEG=ON USE_IBVERBS=1 USE_GFLAGS=ON USE_GLOG=ON ' - -preinstallopts = prebuildopts - -runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/' \ - 'build/lib.linux-%(arch)s-%(pyshortver)s:$PYTHONPATH ' -runtest += '&& export LD_LIBRARY_PATH=%(builddir)s/%(namelower)s-%(version)s/torch/lib64:$LD_LIBRARY_PATH ' -runtest += '&& python test/run_test.py --verbose ' - -options = {'modulename': 'torch'} - -postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/torch/lib*/* %(installdir)s/lib/'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], +excluded_tests = { } +# OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) +runtest = 'cd test && OMP_NUM_THREADS=4 %(python)s run_test.py --verbose %(excluded_tests)s' +tests = ['PyTorch-check-cpp-extension.py'] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index 17abffb792a..441939009ca 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -1,5 +1,3 @@ -easyblock = 'PythonPackage' - name = 'PyTorch' version = '1.3.1' versionsuffix = '-Python-%(pyver)s' @@ -73,12 +71,6 @@ sources = [ 'filename': 'onnx-tensorrt-20190425.tar.gz', 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'onnx-tensorrt'), }, - { - 'source_urls': ['https://github.com/google/protobuf/archive'], - 'download_filename': '48cb18e5c419ddd23d9badcfe4e9df7bde1979b2.tar.gz', - 'filename': 'protobuf-20180727.tar.gz', - 'extract_cmd': local_extract_cmd_pattern % (local_pytorchthirdpartydir, 'protobuf'), - }, { 'source_urls': ['https://github.com/Maratyszcza/pthreadpool/archive'], 'download_filename': '13da0b4c21d17f94150713366420baaf1b5a46f4.tar.gz', @@ -216,7 +208,6 @@ checksums = [ 'c7682e9007ddfd94072647abab3e89ffd9084089460ae47d67060974467b58bf', # benchmark-20180525.tar.gz '02407529fd8431cf627d45638b4d9a6c02b8aa5bf50d73b8fa12217918c57ff4', # pybind11-20170919.tar.gz '1a98c6fece7878c88b59ffe651b427c15b4929c801a09655cd14ca44553787c3', # onnx-tensorrt-20190425.tar.gz - 'f5a35e17fb07f3b13517264cd17a089636fcbb2912f9df7bef7414058969a8d2', # protobuf-20180727.tar.gz '90ab4f60ae0e99c0172dd5201dccc6de6c8f384a21b3d959588f4c1e00beec0f', # pthreadpool-20181008.tar.gz '07625551202a1f35fe5e826669ad495962b26f6a139290e90b321c5996f002ef', # FXdiv-20181016.tar.gz 'afd27417c6df1c85f79a68361055dd3adc292174913c39c1f58b698b9cfd7926', # psimd-20180906.tar.gz @@ -247,10 +238,11 @@ checksums = [ builddependencies = [ ('CMake', '3.15.3'), ('hypothesis', '4.44.2', versionsuffix), - ('Ninja', '1.9.0'), ] dependencies = [ + ('Ninja', '1.9.0'), + ('protobuf', '3.10.0'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('PyYAML', '5.1.2'), @@ -258,38 +250,20 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ('cuDNN', '7.6.4.38'), ('magma', '2.5.1'), ('NCCL', '2.4.8'), ] -download_dep_fail = True - -prebuildopts = 'PYTORCH_BUILD_VERSION=%(version)s PYTORCH_BUILD_NUMBER=1 VERBOSE=1 ' -prebuildopts += 'MAX_JOBS=%(parallel)s ' -prebuildopts += 'LDFLAGS="$LDFLAGS -ldl" ' -prebuildopts += 'USE_FFMPEG=ON USE_IBVERBS=1 USE_GFLAGS=ON USE_GLOG=ON ' -prebuildopts += 'CUDNN_LIB_DIR=$EBROOTCUDNN/lib64 CUDNN_INCLUDE_DIR=$EBROOTCUDNN/include ' -prebuildopts += 'USE_SYSTEM_NCCL=1 NCCL_INCLUDE_DIR=$EBROOTNCCL/include ' -prebuildopts += 'TORCH_CUDA_ARCH_LIST="3.5 3.7 5.2 6.0 6.1 7.0 7.2 7.5" ' +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] -preinstallopts = prebuildopts - -runtest = 'export PYTHONPATH=%(builddir)s/%(namelower)s-%(version)s/' \ - 'build/lib.linux-%(arch)s-%(pyshortver)s:$PYTHONPATH ' -runtest += '&& export LD_LIBRARY_PATH=%(builddir)s/%(namelower)s-%(version)s/torch/lib64:$LD_LIBRARY_PATH ' -runtest += '&& python test/run_test.py --verbose ' - -options = {'modulename': 'torch'} - -postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/torch/lib*/* %(installdir)s/lib/'] - -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], +excluded_tests = { } +# OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) +runtest = 'cd test && OMP_NUM_THREADS=4 %(python)s run_test.py --verbose %(excluded_tests)s' +tests = ['PyTorch-check-cpp-extension.py'] + moduleclass = 'devel' From ed0a58cdbf33d6a0848046b59a66df37ffc4e621 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 22 Sep 2020 18:49:05 +0200 Subject: [PATCH 220/698] Spyder: fix style --- .../s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb index a0cbdc27f27..f9ba2d14717 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2019a-Python-3.7.2.eb @@ -278,7 +278,7 @@ exts_list = [ 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], }), ('spyder', version, { - 'preinstallopts': """sed -i "s/'pyqt5<5.13;python_version>=\"3\"',//g" setup.py && sed -i "s/'pyqtwebengine<5.13;python_version>=\"3\"',//g" setup.py && sed -i 's/jedi==0.17.1/jedi==0.17.2/g' setup.py && sed -i "s/JEDI_REQVER = '=0.17.1'/JEDI_REQVER = '=0.17.2'/g" spyder/dependencies.py && """, + 'preinstallopts': local_spyder_preinstallopts, 'checksums': ['d467f020b694193873a237ce6744ae36bd5a59f4d2b7ffbeb15dda68b03f5aa1'], }), ('spyder-kernels', '1.9.4', { From 66878a118b359094d78adb6569ba1cd6b9fb08f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 08:33:15 +0200 Subject: [PATCH 221/698] add missing git build dependency for OpenImageIO 2.0.12 (fixes #11316) --- .../o/OpenImageIO/OpenImageIO-2.0.12-gompi-2019b.eb | 5 ++++- .../o/OpenImageIO/OpenImageIO-2.0.12-iimpi-2019b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-gompi-2019b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-gompi-2019b.eb index cbf73f44b3e..257e6c30f97 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-gompi-2019b.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-gompi-2019b.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] sources = ['Release-%(version)s.tar.gz'] checksums = ['930a142c9cabbbc3b249577083c97e9f0407cc8cbf933144f3a3ed0f3ec9cfe0'] +builddependencies = [ + ('CMake', '3.15.3'), + ('git', '2.23.0'), +] dependencies = [ ('Boost', '1.71.0'), ('libjpeg-turbo', '2.0.3'), @@ -22,7 +26,6 @@ dependencies = [ ('freetype', '2.10.1'), ('zlib', '1.2.11'), ] -builddependencies = [('CMake', '3.15.3')] separate_build_dir = True diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-iimpi-2019b.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-iimpi-2019b.eb index 3a3fee5840b..ef012183fb5 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-iimpi-2019b.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.0.12-iimpi-2019b.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] sources = ['Release-%(version)s.tar.gz'] checksums = ['930a142c9cabbbc3b249577083c97e9f0407cc8cbf933144f3a3ed0f3ec9cfe0'] +builddependencies = [ + ('CMake', '3.15.3'), + ('git', '2.23.0'), +] dependencies = [ ('Boost', '1.71.0'), ('libjpeg-turbo', '2.0.3'), @@ -22,7 +26,6 @@ dependencies = [ ('freetype', '2.10.1'), ('zlib', '1.2.11'), ] -builddependencies = [('CMake', '3.15.3')] separate_build_dir = True From d92c5c96157c0b761ad74622616ae22e4e88fb6e Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Sep 2020 10:39:25 +0200 Subject: [PATCH 222/698] Create qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb --- ...qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..208c734bfd9 --- /dev/null +++ b/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'qtconsole' +version = '4.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a terminal, +but provides a number of enhancements only possible in a GUI, +such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'] + +dependencies = [ + ('Python', '3.7.4'), + ('IPython', '7.9.0', versionsuffix), + ('QtPy', '1.9.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 2861ab3f94e69754e7ba2b3fda7b97470e813151 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2020 11:08:18 +0200 Subject: [PATCH 223/698] fix HDF4 for RHEL8 --- .../easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb | 13 ++++++++++--- .../easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb | 12 +++++++++--- .../easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb | 12 +++++++++--- 3 files changed, 28 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index c1c65eb305c..7ebfe45fd4f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.30'), ('Bison', '3.0.4'), ('flex', '2.6.4'), + ('libtirpc', '1.1.4'), ] dependencies = [ @@ -29,15 +30,21 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '' -configopts += '--with-szlib=$EBROOTSZIP ' +preconfigopts = "LIBS='-ltirpc' " +configopts = '--with-szlib=$EBROOTSZIP ' +configopts += 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' modextrapaths = {'CPATH': 'include/hdf'} sanity_check_paths = { - 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], 'dirs': ['bin', 'include/hdf'], } +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index b3db1c00829..7c80c0b5072 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.31.1'), ('Bison', '3.0.5'), ('flex', '2.6.4'), + ('libtirpc', '1.1.4'), ] dependencies = [ @@ -29,15 +30,20 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '' -configopts += '--with-szlib=$EBROOTSZIP ' +configopts = '--with-szlib=$EBROOTSZIP ' +configopts = 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' modextrapaths = {'CPATH': 'include/hdf'} sanity_check_paths = { - 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], 'dirs': ['bin', 'include/hdf'], } +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index d157c789b73..afb99d771ac 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -21,6 +21,7 @@ builddependencies = [ ('binutils', '2.32'), ('Bison', '3.3.2'), ('flex', '2.6.4'), + ('libtirpc', '1.2.6'), ] dependencies = [ @@ -29,15 +30,20 @@ dependencies = [ ('zlib', '1.2.11'), ] -configopts = '' -configopts += '--with-szlib=$EBROOTSZIP ' +configopts = '--with-szlib=$EBROOTSZIP ' +configopts += 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' modextrapaths = {'CPATH': 'include/hdf'} sanity_check_paths = { - 'files': ['lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a'], 'dirs': ['bin', 'include/hdf'], } +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + moduleclass = 'data' From 76768a629d8aac3dd680bcb2e5e1432a9a35317d Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Sep 2020 11:11:55 +0200 Subject: [PATCH 224/698] Create fabio-0.10.2-foss-2019b-Python-3.7.4.eb --- .../fabio-0.10.2-foss-2019b-Python-3.7.4.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..bf55196baa4 --- /dev/null +++ b/easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'fabio' +version = '0.10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fb4dcd0645cbaabbe1d3db59b729cebd72be9b2e3c410e5cdc3b2aa94cc16713'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From 712b6df23fb12b49fe7e87ef6bffb62091c64f65 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 11:32:27 +0200 Subject: [PATCH 225/698] {system}[GCCcore/10.2.0] hwloc 2.2.0 + deps --- .../easyconfigs/g/gettext/gettext-0.21.eb | 34 +++++++++++++ .../h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ .../libpciaccess-0.16-GCCcore-10.2.0.eb | 26 ++++++++++ .../libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb | 28 +++++++++++ .../easyconfigs/n/ncurses/ncurses-6.2.eb | 45 +++++++++++++++++ .../x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb | 48 +++++++++++++++++++ .../xorg-macros-1.19.2-GCCcore-10.2.0.eb | 37 ++++++++++++++ 7 files changed, 266 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.eb new file mode 100644 index 00000000000..3faa2c38fab --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] + +dependencies = [ + ('ncurses', '6.2'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..ddabd3a7381 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.2.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['2defba03ddd91761b858cbbdc2e3a6e27b44e94696dbfa21380191328485a433'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('numactl', '2.0.13'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..7e7b8c982a6 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.16-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.16' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['84413553994aef0070cf420050aa5c0a51b1956b404920e21b81e96db6a61a27'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('xorg-macros', '1.19.2'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..38a25e4b1a7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.9.10-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'libxml2' +version = '2.9.10' + +homepage = 'http://xmlsoft.org/' + +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://xmlsoft.org/sources/', + 'http://xmlsoft.org/sources/old/' +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aafee193ffb8fe0c82d4afef6ef91972cbaf5feea100edc2f262750611b4be1f'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb new file mode 100644 index 00000000000..83b361eff08 --- /dev/null +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'ncurses' +version = '6.2' + +homepage = 'https://www.gnu.org/software/ncurses/' +description = """The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, + and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and + function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.""" + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['30306e0c76e0f9f1f0de987cf1c82a5c21e1ce6568b9227f7da5b71cbea86c9d'] + +local_common_configopts = "--with-shared --enable-overwrite --without-ada --enable-symlinks " +configopts = [ + # default build + local_common_configopts, + # the UTF-8 enabled version (ncursesw) + local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", +] + +# need to take care of $CFLAGS ourselves with dummy toolchain +# we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) +buildopts = 'CFLAGS="-O2 -fPIC"' + +# Symlink libtinfo to libncurses (since it can handle the API) so it doesn't get picked up from the OS +postinstallcmds = [ + "ln -s %(installdir)s/lib/libncurses.so %(installdir)s/lib/libtinfo.so", + "ln -s %(installdir)s/lib/libncurses.a %(installdir)s/lib/libtinfo.a" +] + +local_libs = ["form", "menu", "ncurses", "panel"] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ["captoinfo", "clear", "infocmp", "infotocap", "ncurses%(version_major)s-config", + "reset", "tabs", "tic", "toe", "tput", "tset"]] + + ['lib/lib%s%s.a' % (x, y) for x in local_libs for y in ['', '_g', 'w', 'w_g']] + + ['lib/lib%s%s.%s' % (x, y, SHLIB_EXT) for x in local_libs for y in ['', 'w']] + + ['lib/libncurses++%s.a' % x for x in ['', 'w']], + 'dirs': ['include', 'include/ncursesw'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..264331a9b0f --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.5-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GNU LGPLv2.1+ +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.5' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['XZ-5.2.2_compat-libs.patch'] +checksums = [ + '5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df', # xz-5.2.5.tar.bz2 + '578da3ea2ddb551972891a60fe31478b16a516d6ea8b6aa3af89e1d558adb703', # XZ-5.2.2_compat-libs.patch +] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21', '', True), + ('binutils', '2.35'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..55d95bd1262 --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.2-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +## +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: Custom +# +# Notes:: +## + +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.2' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['326e51a5d673e3d9cc7f139aee469a11e18ea060b1d06c22694612e68a2089b1'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From bc91169c1cbd86d05e341fba0acc84b18ac28baf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 11:36:23 +0200 Subject: [PATCH 226/698] {lib}[GCCcore/10.2.0] OpenMPI v4.0.5, libevent v2.1.12, libfabric v1.11.0, PMIx 3.1.5 --- .../libevent-2.1.12-GCCcore-10.2.0.eb | 37 +++++++++++++++ .../libfabric-1.11.0-GCCcore-10.2.0.eb | 40 ++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 32 +++++++++++++ .../p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 4 files changed, 156 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..22b850f842b --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..35180743502 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.11.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9938abf628e7ea8dcf60a94a4b62d499fbc0dbc6733478b6db2e6a373c80d58f'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb new file mode 100644 index 00000000000..15b78eb63ec --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -0,0 +1,32 @@ +name = 'OpenMPI' +version = '4.0.5' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '10.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), + ('libevent', '2.1.12'), + ('UCX', '1.9.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), +] + +# disable MPI1 compatibility for now, see what breaks... +# configopts = '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..efe2a2d3ed8 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# Note: +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '3.1.5' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['88934195174455df478b996313095df25b51d0caf5a5cce01b22f0ccdc6c5cf7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.11'), + ('hwloc', '2.2.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' From d78b351c5e20da0841dc71d3501cb086b7869bf5 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2020 11:54:09 +0200 Subject: [PATCH 227/698] fix http->https --- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 7ebfe45fd4f..553ef64d58f 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'https://www.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] +source_urls = ['https://www.hdfgroup.org/ftp/HDF/releases/HDF%(version)s/src/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['2d383e87c8a0ca6a5352adbd1d5546e6cc43dc21ff7d90f93efa644d85c0b14a'] diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index 7c80c0b5072..9b83512687c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'HDF' version = '4.2.14' -homepage = 'http://www.hdfgroup.org/products/hdf4/' +homepage = 'https://www.hdfgroup.org/products/hdf4/' description = """ HDF (also known as HDF4) is a library and multi-object file format for @@ -31,7 +31,7 @@ dependencies = [ ] configopts = '--with-szlib=$EBROOTSZIP ' -configopts = 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +configopts += 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' modextrapaths = {'CPATH': 'include/hdf'} From 097f8a93934e919369aaa0dc1d6627a68babc73a Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2020 12:02:12 +0200 Subject: [PATCH 228/698] Fix LAMMPS 7Aug2019 for EPYC --- ...LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb | 2 ++ ...AMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb | 2 ++ .../easyconfigs/l/LAMMPS/LAMMPS-7Aug2019_EPYC.patch | 12 ++++++++++++ 3 files changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019_EPYC.patch diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb index f98b92c7821..b380301035a 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-foss-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['%(name)s-%(version)s_EPYC.patch'] checksums = [ '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '5cc5d2498f45d46569eb325aea5c217867f1afd95ee833fd0139f22e80431b86', # LAMMPS-7Aug2019_EPYC.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb index b9a665577ba..35c2a48a208 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos.eb @@ -25,9 +25,11 @@ sources = [ 'stable_%(version)s.tar.gz', {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['%(name)s-%(version)s_EPYC.patch'] checksums = [ '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py + '5cc5d2498f45d46569eb325aea5c217867f1afd95ee833fd0139f22e80431b86', # LAMMPS-7Aug2019_EPYC.patch ] local_source_dir_name = '%(namelower)s-%(version)s' diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019_EPYC.patch b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019_EPYC.patch new file mode 100644 index 00000000000..deb804dc944 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019_EPYC.patch @@ -0,0 +1,12 @@ +# see https://github.com/easybuilders/easybuild-easyblocks/pull/1975#issuecomment-591218724 +diff -ru lammps-stable_7Aug2019.org/lib/kokkos/cmake/kokkos_options.cmake lammps-stable_7Aug2019/lib/kokkos/cmake/kokkos_options.cmake +--- lammps-stable_7Aug2019.org/lib/kokkos/cmake/kokkos_options.cmake 2019-08-06 17:17:40.000000000 +0200 ++++ lammps-stable_7Aug2019/lib/kokkos/cmake/kokkos_options.cmake 2020-09-23 11:24:09.301136347 +0200 +@@ -78,6 +78,7 @@ + list(APPEND KOKKOS_ARCH_LIST + None # No architecture optimization + AMDAVX # (HOST) AMD chip ++ EPYC # (HOST) AMD EPYC Zen-Core CPU + ARMv80 # (HOST) ARMv8.0 Compatible CPU + ARMv81 # (HOST) ARMv8.1 Compatible CPU + ARMv8-ThunderX # (HOST) ARMv8 Cavium ThunderX CPU From fc50da88ea71b64928f4b6c9d87eef773e0d1126 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Sep 2020 12:14:14 +0200 Subject: [PATCH 229/698] Exclude autograd test --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 4 ++++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index c1fef85daaa..40ef5709285 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -254,6 +254,10 @@ dependencies = [ ] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/41186 + 'autograd', + ], } # OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index 441939009ca..c7ca4d5da84 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -260,6 +260,10 @@ dependencies = [ cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5'] excluded_tests = { + 'POWER': [ + # https://github.com/pytorch/pytorch/issues/41186 + 'autograd', + ], } # OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) From e36b1f612fe46803756fc2d3ee5a2f7ce7edb6f6 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 23 Sep 2020 12:49:34 +0200 Subject: [PATCH 230/698] Create silx-0.13.2-foss-2019b-Python-3.7.4.eb --- .../silx-0.13.2-foss-2019b-Python-3.7.4.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..103831418d8 --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'silx' +version = '0.13.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['0bc5a5a30499b9d620c795a20948151a4057aba16ff08dfe637f7a923b4697d4'] + + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('PyOpenGL', '3.1.5'), + ('matplotlib', '3.1.1', versionsuffix), + ('Mako', '1.1.0'), + ('Pillow', '6.2.1'), + ('fabio', '0.10.2', versionsuffix), + ('qtconsole', '4.7.7', versionsuffix), +] + + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 5cc4093c9779b9d7212ad1341ba0ab159efd2517 Mon Sep 17 00:00:00 2001 From: vsc10149 Date: Wed, 23 Sep 2020 12:50:47 +0200 Subject: [PATCH 231/698] adding easyconfigs: tidybayes-2.1.1-foss-2020a-R-4.0.0.eb --- .../tidybayes-2.1.1-foss-2020a-R-4.0.0.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..ff744a0faae --- /dev/null +++ b/easybuild/easyconfigs/t/tidybayes/tidybayes-2.1.1-foss-2020a-R-4.0.0.eb @@ -0,0 +1,77 @@ +easyblock = 'Bundle' + +name = 'tidybayes' +version = '2.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/package=tidybayes' +description = """ Compose data for and extract, manipulate, and visualize +posterior draws from Bayesian models ('JAGS', 'Stan', 'rstanarm', 'brms', +'MCMCglmm', 'coda', ...) in a tidy data format. """ + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [('R', '4.0.0')] + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# we need a separate bundle as some dependencies are required newer than included on R-4.0.0 easyconfig +# on a newer R release this should be easily ingested + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_list = [ + ('spelling', '2.1', { + 'checksums': ['570e3803a7cc97dc43068fed16cad842794044afb00f71426c43fd24705e22c9'], + }), + ('svGUI', '1.0.0', { + 'checksums': ['ccf5167cc2423ba90003e5744bde7c7ac217e691150a20df0018654f2e58eae4'], + }), + ('svUnit', '1.0.3', { + 'checksums': ['bc059c8c49eccdaf27c485174570f942f8237d31381b6c9347c9060ff44c9f2b'], + }), + ('arrayhelpers', '1.1-0', { + 'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'], + }), + ('HDInterval', '0.2.2', { + 'checksums': ['047eeb08c3dba21dc1cba8e35e3191cde6cdc98c77ee3a3496e045f7937565ed'], + }), + ('rlang', '0.4.7', { + 'checksums': ['78a3d927f46f71a0b1ad7f9de6a66f986d232340f57b40c9413b3fe8a1859938'], + }), + ('vctrs', '0.3.4', { + 'checksums': ['eb47411c9e980a555f5819a7bce46896775df2ca7c9eaa7bf0a9c16f067b7877'], + }), + ('tidyselect', '1.1.0', { + 'checksums': ['e635ed381fb53f7a53c3fa36bb33e134a3273d272367de2a8d909c821be93893'], + }), + ('dplyr', '1.0.2', { + 'checksums': ['7cb1329fbf5c9609ca300f695fdfae67198b6b7273cf81b71cfc01c12d0adc4a'], + }), + ('distributional', '0.2.0', { + 'checksums': ['94c8c761f9afa5e83ed950dba73b4f6299b933d876ade94ddddf7377581529d0'], + }), + ('ggdist', '2.2.0', { + 'checksums': ['03856440b52400c4fa03bfe0a6ea403c6f453ed6772087ac200c80f8896336b3'], + }), + (name, version, { + 'checksums': ['7178abd5b5b508f0f88542552978169ec7fa3bd684466af3315d30a18e83e773'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['tidybayes'], +} + +moduleclass = 'lib' From 7ecc9c33274f4d9c399979fad2d71c12d5a0b3c4 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 23 Sep 2020 12:04:29 +0000 Subject: [PATCH 232/698] Specify GSL headers --- .../easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb index 4fe96ac20b1..63de6101f5e 100644 --- a/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb +++ b/easybuild/easyconfigs/c/CAVIAR/CAVIAR-2.2-20190419-foss-2019b.eb @@ -22,6 +22,8 @@ checksums = [ '3fdcb1633f6364410f9e38745a874a52906a14dbf36c0c3151a8d11e55cd8ba1', # CAVIAR-20200820-openblas.patch ] +buildopts = 'CPATH=$EBROOTGSL/include:$CPATH' + dependencies = [ ('GSL', '2.6'), ] From 41223c6ec436ab8d4bcbebf3259c0372e52145df Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 23 Sep 2020 13:15:01 +0100 Subject: [PATCH 233/698] adding easyconfigs: GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb --- .../GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb new file mode 100644 index 00000000000..18bc8061965 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.1.8.1-GCCcore-9.3.0-Java-1.8.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.1.8.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['42e6de5059232df1ad5785c68c39a53dc1b54afe7bb086d0129f4dc95fb182bc'] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [ + ('Java', '1.8', '', True), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From 23e07079e78dc17cf9cb3be6bd146991cafa7f40 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Sep 2020 14:21:42 +0200 Subject: [PATCH 234/698] fix dependency on Bowtie of seq2HLA --- .../seq2HLA-2.3-foss-2018b-Python-2.7.15.eb | 44 ++++++++++----- .../seq2HLA-2.3-intel-2018a-Python-2.7.14.eb | 54 ++++++++++++++----- 2 files changed, 71 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-foss-2018b-Python-2.7.15.eb index a8f7f2bfe86..ff3291d1236 100644 --- a/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-foss-2018b-Python-2.7.15.eb @@ -1,8 +1,9 @@ -easyblock = 'Tarball' +easyblock = 'Bundle' name = 'seq2HLA' version = '2.3' versionsuffix = '-Python-%(pyver)s' +local_commit = 'a4d26bd10476bc3610e667339d4076f1f74c3997' homepage = 'https://github.com/TRON-Bioinformatics/seq2HLA' description = """ In-silico method written in Python and R to determine HLA genotypes of a sample. @@ -13,28 +14,45 @@ description = """ In-silico method written in Python and R to determine HLA geno toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = ['https://github.com/TRON-Bioinformatics/seq2HLA/archive'] -sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'a4d26bd.tar.gz'}] -checksums = ['50bc6242b90be19b8b3c1013b200de408cb9f0b142c7cd5783eb33eae91f94ba'] - dependencies = [ - ('Biopython', '1.72', versionsuffix), - ('Bowtie', '1.2.2'), ('Python', '2.7.15'), + ('Biopython', '1.72', versionsuffix), ('R', '3.5.1', versionsuffix), ] -postinstallcmds = [ - 'sed -i -e "1i #!/usr/bin/env python" %(installdir)s/seq2HLA.py', +components = [ + ('Bowtie', '0.12.7', { + 'easyblock': 'MakeCp', + 'source_urls': ['https://download.sourceforge.net/bowtie-bio'], + 'sources': ['%(namelower)s-%(version)s-src.zip'], + 'checksums': ['609a6a0ad0b1a5d97908ca17da7bbf5d6dc407c7b9c49713cdc9c40f056a586a'], + 'start_dir': '%(namelower)s-%(version)s', + 'buildopts': ' CFLAGS="$CFLAGS -fpermissive"', + 'files_to_copy': [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')], + }), + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/TRON-Bioinformatics/seq2HLA/archive'], + 'sources': [{'filename': SOURCE_TAR_GZ, 'download_filename': '%s.tar.gz' % local_commit}], + 'checksums': ['50bc6242b90be19b8b3c1013b200de408cb9f0b142c7cd5783eb33eae91f94ba'], + 'start_dir': '%%(name)s-%s' % local_commit, + 'install_type': 'subdir', + }), ] -modextrapaths = {'PATH': ''} +fix_python_shebang_for = ['seq2hla/seq2HLA.py'] sanity_check_paths = { - 'files': ['command_fourdigit.R', 'command.R', 'fourdigits.py', 'seq2HLA.py'], - 'dirs': [], + 'files': ['seq2hla/%s' % x for x in ['command_fourdigit.R', 'command.R', 'fourdigits.py', 'seq2HLA.py']] + + ['bin/%s' % x for x in ['bowtie', 'bowtie-build', 'bowtie-inspect']], + 'dirs': ['seq2hla/references'], } -sanity_check_commands = ["seq2HLA.py --help"] +sanity_check_commands = [ + "bowtie --help", + "seq2HLA.py --help", +] + +modextrapaths = {'PATH': 'seq2hla'} moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-intel-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-intel-2018a-Python-2.7.14.eb index 1249236be42..52f9cb546b0 100644 --- a/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-intel-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/s/seq2HLA/seq2HLA-2.3-intel-2018a-Python-2.7.14.eb @@ -1,36 +1,62 @@ -easyblock = 'Tarball' +easyblock = 'Bundle' name = 'seq2HLA' version = '2.3' versionsuffix = '-Python-%(pyver)s' +local_commit = 'a4d26bd10476bc3610e667339d4076f1f74c3997' homepage = 'https://github.com/TRON-Bioinformatics/seq2HLA' -description = "In-silico method written in Python and R to determine HLA genotypes of a sample." +description = """ In-silico method written in Python and R to determine HLA genotypes of a sample. + seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, + uses a bowtie index comprising all HLA alleles and outputs the most likely + HLA class I and class II genotypes (in 4 digit resolution), + a p-value for each call, and the expression of each class. """ toolchain = {'name': 'intel', 'version': '2018a'} -source_urls = ['https://github.com/TRON-Bioinformatics/seq2HLA/archive/'] -sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'a4d26bd.tar.gz'}] -checksums = ['50bc6242b90be19b8b3c1013b200de408cb9f0b142c7cd5783eb33eae91f94ba'] - dependencies = [ ('Python', '2.7.14'), ('Biopython', '1.71', versionsuffix), - ('Bowtie', '1.2.2'), ] -postinstallcmds = [ - "sed -i '1 i#!/usr/bin/env python' %(installdir)s/seq2HLA.py", - "chmod a+rx %(installdir)s/seq2HLA.py", +# Fix Bowtie compilers +local_bowtie_fixes = "sed -i 's/gcc/icc/g;s/g++/icpc/g' Makefile && " +# Fix seqAn int64 typedef +local_bowtie_fixes += "sed -i 's/typedef int64_t __int64/typedef __int64 int64_t/g' SeqAn-1.1/seqan/platform.h && " + +components = [ + ('Bowtie', '0.12.7', { + 'easyblock': 'MakeCp', + 'source_urls': ['https://download.sourceforge.net/bowtie-bio'], + 'sources': ['%(namelower)s-%(version)s-src.zip'], + 'checksums': ['609a6a0ad0b1a5d97908ca17da7bbf5d6dc407c7b9c49713cdc9c40f056a586a'], + 'start_dir': '%(namelower)s-%(version)s', + 'prebuildopts': local_bowtie_fixes, + 'files_to_copy': [(['bowtie', 'bowtie-build', 'bowtie-inspect'], 'bin')], + }), + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/TRON-Bioinformatics/seq2HLA/archive'], + 'sources': [{'filename': SOURCE_TAR_GZ, 'download_filename': '%s.tar.gz' % local_commit}], + 'checksums': ['50bc6242b90be19b8b3c1013b200de408cb9f0b142c7cd5783eb33eae91f94ba'], + 'start_dir': '%%(name)s-%s' % local_commit, + 'install_type': 'subdir', + }), ] +fix_python_shebang_for = ['seq2hla/seq2HLA.py'] + sanity_check_paths = { - 'files': ['seq2HLA.py'], - 'dirs': [], + 'files': ['seq2hla/%s' % x for x in ['command_fourdigit.R', 'command.R', 'fourdigits.py', 'seq2HLA.py']] + + ['bin/%s' % x for x in ['bowtie', 'bowtie-build', 'bowtie-inspect']], + 'dirs': ['seq2hla/references'], } -sanity_check_commands = ["seq2HLA.py --help"] +sanity_check_commands = [ + "bowtie --help", + "seq2HLA.py --help", +] -modextrapaths = {'PATH': ''} +modextrapaths = {'PATH': 'seq2hla'} moduleclass = 'bio' From 55fab02a1f3d6866228436c072e1b19004750486 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 14:34:46 +0200 Subject: [PATCH 235/698] add additional extensions to R 4.0.0 easyconfig --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 03fe2b132b7..59c5ae09d7e 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2520,6 +2520,33 @@ exts_list = [ ('fasterize', '1.0.3', { 'checksums': ['62b459625e9bdb00251ec5f6cb873e0c59713f3e86dc1e2c8332adc0cea17f81'], }), + ('RPMM', '1.25', { + 'checksums': ['f04a524b13918062616beda50c4e759ce2719ce14150a0e677d07132086c88c8'], + }), + ('RefFreeEWAS', '2.2', { + 'checksums': ['de2812f166caabf6ea01c0533402e5cd9d8a525a2a7583e4757decf22319caab'], + }), + ('wordcloud', '2.6', { + 'checksums': ['53716954430acd4f164bfd8eacd7068a908ee3358293ded6cd992d53b7f72649'], + }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), + ('gsl', '2.1-6', { + 'checksums': ['f5d463239693f146617018987687db31b163653708cbae0b730b9b7bed81995c'], + }), + ('awsMethods', '1.1-1', { + 'checksums': ['50934dc20cf4e015f1304a89de6703fed27e7bd54c6b9fc9fb253cdf2ecb7541'], + }), + ('aws', '2.4-3', { + 'checksums': ['8582dc7669242eb0e6bee204bdc87ff1c344e2e74912931da47e21279d439531'], + }), + ('ruv', '0.9.7.1', { + 'checksums': ['a0c54e56ba3d8f6ae178ae4d0e417a79295abf5dcb68bbae26c4b874734d98d8'], + }), + ('mhsmm', '0.4.16', { + 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], + }), ] moduleclass = 'lang' From b8aa2d9dc7f025ae29a1f1951fc6947d9859a4a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 14:36:47 +0200 Subject: [PATCH 236/698] add additional extensions to Bioconductor 3.11 bundle --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 12af07db83f..5eeb96b870a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -812,6 +812,30 @@ exts_list = [ ('stageR', '1.10.0', { 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), + ('isva', '1.9', { + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.11.4', { + 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], + }), + ('org.Rn.eg.db', '3.11.4', { + 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], + }), + ('ROC', '1.64.0', { + 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], + }), + ('wateRmelon', '1.32.0', { + 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], + }), + ('GLAD', '2.52.0', { + 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], + }), + ('missMethyl', '1.22.0', { + 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], + }), + ('MethylSeekR', '1.28.0', { + 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], + }), ] modextrapaths = {'R_LIBS': ''} From 27c3b3826b791952a919e6149a1f9cc522e81b47 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 23 Sep 2020 15:04:45 +0200 Subject: [PATCH 237/698] tirpc builddep->dep --- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb index 553ef64d58f..204d917a179 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-7.3.0.eb @@ -21,13 +21,13 @@ builddependencies = [ ('binutils', '2.30'), ('Bison', '3.0.4'), ('flex', '2.6.4'), - ('libtirpc', '1.1.4'), ] dependencies = [ ('libjpeg-turbo', '2.0.0'), ('Szip', '2.1.1'), ('zlib', '1.2.11'), + ('libtirpc', '1.1.4'), ] preconfigopts = "LIBS='-ltirpc' " diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index 9b83512687c..55e21a574fc 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -21,13 +21,13 @@ builddependencies = [ ('binutils', '2.31.1'), ('Bison', '3.0.5'), ('flex', '2.6.4'), - ('libtirpc', '1.1.4'), ] dependencies = [ ('libjpeg-turbo', '2.0.2'), ('Szip', '2.1.1'), ('zlib', '1.2.11'), + ('libtirpc', '1.1.4'), ] configopts = '--with-szlib=$EBROOTSZIP ' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index afb99d771ac..976dcd4444c 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -21,13 +21,13 @@ builddependencies = [ ('binutils', '2.32'), ('Bison', '3.3.2'), ('flex', '2.6.4'), - ('libtirpc', '1.2.6'), ] dependencies = [ ('libjpeg-turbo', '2.0.3'), ('Szip', '2.1.1'), ('zlib', '1.2.11'), + ('libtirpc', '1.2.6'), ] configopts = '--with-szlib=$EBROOTSZIP ' From d0835e478dd808ce4144ecbf16ed42b6787cfa7b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Sep 2020 15:05:59 +0200 Subject: [PATCH 238/698] Exclude jit and cuda test on POWER --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 2 ++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index 40ef5709285..0792c224862 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -257,6 +257,8 @@ excluded_tests = { 'POWER': [ # https://github.com/pytorch/pytorch/issues/41186 'autograd', + # https://github.com/pytorch/pytorch/issues/41400 + 'jit', ], } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index c7ca4d5da84..8962f8dc705 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -263,6 +263,10 @@ excluded_tests = { 'POWER': [ # https://github.com/pytorch/pytorch/issues/41186 'autograd', + # https://github.com/pytorch/pytorch/issues/41400 + 'jit', + # Unknown + 'cuda', ], } From 480b36fc5db46a4dc7bd06bc6ace8993654b4c5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 16:35:58 +0200 Subject: [PATCH 239/698] promote libtirpc to runtime dep of HDF --- easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb index fa9fb0921be..2a0c4b2a794 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.15-GCCcore-9.3.0.eb @@ -21,13 +21,13 @@ builddependencies = [ ('binutils', '2.34'), ('Bison', '3.5.3'), ('flex', '2.6.4'), - ('libtirpc', '1.2.6'), ] dependencies = [ ('libjpeg-turbo', '2.0.4'), ('Szip', '2.1.1'), ('zlib', '1.2.11'), + ('libtirpc', '1.2.6'), ] preconfigopts = "LIBS='-ltirpc' " From 430fbafbdb6f632219aa2b0ddab1f7ca27e38602 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 16:43:22 +0200 Subject: [PATCH 240/698] fix typo in error message --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 7e5b857c5eb..86d2cc419d1 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -591,7 +591,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): elif exts_defaultclass == 'PythonPackage': # bundle of Python packages should use PythonBundle if easyblock == 'Bundle': - fail = "'PythonBundle' easyblock should be is used for bundle of Python packages in %s" % ec_fn + fail = "'PythonBundle' easyblock should be used for bundle of Python packages in %s" % ec_fn failing_checks.append(fail) else: # both download_dep_fail and use_pip should be set via exts_default_options From defb558580d280299f38c4cb28347c793583cf14 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Sep 2020 16:43:27 +0200 Subject: [PATCH 241/698] Exclude test_nn on POWER --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 2 ++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index 0792c224862..b5eb068ec94 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -259,6 +259,8 @@ excluded_tests = { 'autograd', # https://github.com/pytorch/pytorch/issues/41400 'jit', + # https://github.com/pytorch/pytorch/issues/41469 + 'nn', ], } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index 8962f8dc705..98a4a0edad1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -265,6 +265,8 @@ excluded_tests = { 'autograd', # https://github.com/pytorch/pytorch/issues/41400 'jit', + # https://github.com/pytorch/pytorch/issues/41469 + 'nn', # Unknown 'cuda', ], From bb1875833072201fcc9ede8fd5cf4d7f943b8f44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:07:31 +0200 Subject: [PATCH 242/698] adding easyconfigs: ELPA-2019.11.001-foss-2020a.eb, ELPA-2019.11.001-intel-2020a.eb --- .../e/ELPA/ELPA-2019.11.001-foss-2020a.eb | 34 +++++++++++++++++++ .../e/ELPA/ELPA-2019.11.001-intel-2020a.eb | 34 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb new file mode 100644 index 00000000000..0c0e3e54be8 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-foss-2020a.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2019.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] + +builddependencies = [ + ('Autotools', '20180311'), + # remove_xcompiler script requires 'python' command, + # manual_cpp script requires 'python' command and is not compatible yet with Python 3 + ('Python', '2.7.18'), +] + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb new file mode 100644 index 00000000000..a51548a7528 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2019.11.001-intel-2020a.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2019.11.001' + +homepage = 'https://elpa.rzg.mpg.de' +description = """Eigenvalue SoLvers for Petaflop-Applications .""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://elpa.mpcdf.mpg.de/html/Releases/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['10374a8f042e23c7e1094230f7e2993b6f3580908a213dbdf089792d05aff357'] + +builddependencies = [ + ('Autotools', '20180311'), + # remove_xcompiler script requires 'python' command, + # manual_cpp script requires 'python' command and is not compatible yet with Python 3 + ('Python', '2.7.18'), +] + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 81bbe804f4bb85135f9693b9ebc2cef791e55166 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:10:42 +0200 Subject: [PATCH 243/698] adding easyconfigs: IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb --- ...nel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb new file mode 100644 index 00000000000..c8db377e327 --- /dev/null +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -0,0 +1,63 @@ +easyblock = 'Bundle' + +name = 'IRkernel' +version = '1.1' +versionsuffix = '-R-%(rver)s-Python-%(pyver)s' + +homepage = 'https://irkernel.github.io' +description = """The R kernel for the 'Jupyter' environment executes R code + which the front-end (Jupyter Notebook or other front-ends) submits to the + kernel via the network.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('R', '3.6.3'), + ('Python', '3.8.2'), + ('IPython', '7.13.0', '-Python-%(pyver)s'), + ('ZeroMQ', '4.3.2'), +] + +exts_defaultclass = 'RPackage' +exts_filter = ("R -q --no-save", "library(%(ext_name)s)") + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.rstudio.com/src/contrib/', + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +exts_list = [ + ('repr', '1.1.0', { + 'checksums': ['743fe018f9e3e54067a970bc38b6b8c0c0498b43f88d179ac4a959c2013a5f96'], + }), + ('IRdisplay', '0.7.0', { + 'checksums': ['91eac9acdb92ed0fdc58e5da284aa4bb957ada5eef504fd89bec136747999089'], + }), + ('pbdZMQ', '0.3-3', { + 'checksums': ['ae26c13400e2acfb6463ff9b67156847a22ec79f3b53baf65119efaba1636eca'], + }), + (name, version, { + 'checksums': ['2469431c468a3f586ffe8adc260fa368fd8d6b4e65bde318f941fb1692ee38ee'], + }), +] + +modextrapaths = {'R_LIBS': ''} + +# IPython notebook looks for the json kernel file in kernels/IRkernel +local_kerneldir = '%(installdir)s/IRkernel' +postinstallcmds = [ + 'mkdir -p %s/kernels/ir' % local_kerneldir, + 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) +] + +modextravars = {'JUPYTER_PATH': local_kerneldir} + +sanity_check_paths = { + 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], + 'dirs': [name], +} + +moduleclass = 'tools' From 71273f1b3ce78cb17bfeeca099a069b8432903e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:14:25 +0200 Subject: [PATCH 244/698] adding easyconfigs: Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb --- .../Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb new file mode 100644 index 00000000000..87f59a50358 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb @@ -0,0 +1,44 @@ +name = 'Libint' +version = '2.6.0' +local_lmax = 6 +# custom configuration, to be used as dependency for CP2K +versionsuffix = '-lmax-%s-cp2k' % local_lmax + +homepage = 'https://github.com/evaleev/libint' +description = """Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body + matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/evaleev/libint/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +checksums = [ + '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz + # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch + 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', +] + +builddependencies = [ + ('Autotools', '20180311'), + ('GMP', '6.2.0'), + ('Boost', '1.72.0'), + ('Eigen', '3.3.7'), + ('Python', '2.7.18'), +] + +# configure options as required by CP2K, +# see Jenkinsfile in https://github.com/cp2k/libint-cp2k +local_eri_max_am = '%s,%s' % (local_lmax, local_lmax - 1) +local_eri23_max_am = '%s,%s' % (local_lmax + 2, local_lmax + 1) + +libint_compiler_configopts = '--enable-eri=1 --enable-eri2=1 --enable-eri3=1 --with-max-am=%s ' % local_lmax +libint_compiler_configopts += '--with-eri-max-am=%s ' % local_eri_max_am +libint_compiler_configopts += '--with-eri2-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--with-eri3-max-am=%s ' % local_eri23_max_am +libint_compiler_configopts += '--enable-generic-code --disable-unrolling' + +with_fortran = True + +moduleclass = 'chem' From e726ea557dc670cb1bc96bd2da4f7f5207c63c15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:17:10 +0200 Subject: [PATCH 245/698] adding easyconfigs: libxsmm-1.16.1-GCC-9.3.0.eb --- .../l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb new file mode 100644 index 00000000000..72a6d90dabd --- /dev/null +++ b/easybuild/easyconfigs/l/libxsmm/libxsmm-1.16.1-GCC-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libxsmm' +version = '1.16.1' + +homepage = 'https://github.com/hfp/libxsmm' +description = """LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications +targeting Intel Architecture (x86).""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/hfp/libxsmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['93dc7a3ec40401988729ddb2c6ea2294911261f7e6cd979cf061b5c3691d729d'] + +# install both static and dynamic version +installopts = ['PREFIX=%(installdir)s', 'PREFIX=%(installdir)s STATIC=0'] + +skipsteps = ['configure'] +maxparallel = 1 + +sanity_check_paths = { + 'files': ['bin/libxsmm_gemm_generator', 'include/libxsmm.h', 'lib/libxsmm.a', 'lib/libxsmm.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'math' From 82901bf01d86c37181657b4594c22340d295fce2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:20:40 +0200 Subject: [PATCH 246/698] adding easyconfigs: mpifileutils-0.10-gompi-2020a.eb, mpifileutils-0.10-iimpi-2020a.eb, libcircle-0.3-gompi-2020a.eb, libcircle-0.3-iimpi-2020a.eb --- .../l/libcircle/libcircle-0.3-gompi-2020a.eb | 41 +++++++++++++++++++ .../l/libcircle/libcircle-0.3-iimpi-2020a.eb | 41 +++++++++++++++++++ .../mpifileutils-0.10-gompi-2020a.eb | 38 +++++++++++++++++ .../mpifileutils-0.10-iimpi-2020a.eb | 38 +++++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/l/libcircle/libcircle-0.3-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020a.eb new file mode 100644 index 00000000000..169c6665c3e --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-gompi-2020a.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for libcircle: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libcircle/libcircle-0.3-iimpi-2020a.eb b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-iimpi-2020a.eb new file mode 100644 index 00000000000..e76089d4004 --- /dev/null +++ b/easybuild/easyconfigs/l/libcircle/libcircle-0.3-iimpi-2020a.eb @@ -0,0 +1,41 @@ +# With <3 for EasyBuild +# +# EasyConfig for libcircle: +# ---------------------------------------------------------------------------- +# Copyright: 2014 - Gregor Mendel Institute of Molecular Plant Biology GmBH +# License: MIT +# Authors: Petar Forai +# ---------------------------------------------------------------------------- + +easyblock = 'ConfigureMake' + +name = 'libcircle' +version = '0.3' + +homepage = 'https://github.com/hpc/libcircle/' + +description = """ + An API to provide an efficient distributed queue on a cluster. libcircle is an + API for distributing embarrassingly parallel workloads using self-stabilization. +""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fd8bc6e4dcc6fdec9d2a3d1c78a4060948ae4f11f0b278792610d6c05d53e14c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/%(name)s.h', 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb new file mode 100644 index 00000000000..b6f12100979 --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-gompi-2020a.eb @@ -0,0 +1,38 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = '0.10' + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a71a9acd9841c3c258fc0eaea942f18abcb40098714cc90462b57696c07e3c5'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('attr', '2.4.48'), + ('bzip2', '1.0.8'), + ('dtcmp', '1.1.0'), + ('libarchive', '3.4.2'), + ('libcircle', '0.3'), + ('lwgrp', '1.0.2'), +] + +sanity_check_paths = { + 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb new file mode 100644 index 00000000000..d67c00c80fa --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10-iimpi-2020a.eb @@ -0,0 +1,38 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = '0.10' + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5a71a9acd9841c3c258fc0eaea942f18abcb40098714cc90462b57696c07e3c5'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('attr', '2.4.48'), + ('bzip2', '1.0.8'), + ('dtcmp', '1.1.0'), + ('libarchive', '3.4.2'), + ('libcircle', '0.3'), + ('lwgrp', '1.0.2'), +] + +sanity_check_paths = { + 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' From 68a86631e04725bfe9db94361f633824cec8b822 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:28:55 +0200 Subject: [PATCH 247/698] adding easyconfigs: OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb, OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb | 25 +++++++++++++++++++ .../OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb | 25 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb new file mode 100644 index 00000000000..05e16cd6d3f --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2020a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb new file mode 100644 index 00000000000..5afa283a9b8 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpi-2020a.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 974ec74221fcfbd6748f93aa441437dc1f16c272 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:29:50 +0200 Subject: [PATCH 248/698] adding easyconfigs: MUMmer-3.23-GCCcore-9.3.0.eb --- .../m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..3dcbd9b0e1b --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +# easyblock = mummer.py + +name = 'MUMmer' +version = '3.23' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [('http://sourceforge.net/projects/mummer/files/%(namelower)s/%(version)s/', 'download')] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['1efad4f7d8cee0d8eaebb320a2d63745bb3a160bb513a15ef7af46f330af662f'] + +builddependencies = [('binutils', '2.34')] + +moduleclass = 'bio' From 1babbaf2e2e7e48674b246f0b9ecdb296bdd73c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:30:43 +0200 Subject: [PATCH 249/698] adding easyconfigs: MUMmer-4.0.0beta2-GCCcore-9.3.0.eb --- .../MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c63acb20d3d --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0beta2-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0beta2' + +homepage = 'http://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['cece76e418bf9c294f348972e5b23a0230beeba7fd7d042d5584ce075ccd1b93'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From 12780b071d0e1d24da06114fc73318adb0638419 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:33:36 +0200 Subject: [PATCH 250/698] adding easyconfigs: OpenImageIO-2.1.12.0-gompi-2020a.eb, OpenImageIO-2.1.12.0-iimpi-2020a.eb --- .../OpenImageIO-2.1.12.0-gompi-2020a.eb | 36 +++++++++++++++++++ .../OpenImageIO-2.1.12.0-iimpi-2020a.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb new file mode 100644 index 00000000000..51231d683f1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.1.12.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] +sources = ['Release-%(version)s.tar.gz'] +checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] + +dependencies = [ + ('Boost', '1.72.0'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('OpenEXR', '2.4.1'), + ('freetype', '2.10.1'), + ('zlib', '1.2.11'), +] +builddependencies = [('CMake', '3.16.4')] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb new file mode 100644 index 00000000000..be58fe7c03b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.1.12.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] +sources = ['Release-%(version)s.tar.gz'] +checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] + +dependencies = [ + ('Boost', '1.72.0'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('OpenEXR', '2.4.1'), + ('freetype', '2.10.1'), + ('zlib', '1.2.11'), +] +builddependencies = [('CMake', '3.16.4')] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' From f8fa47078632631cbf10cf68361c6c683d9cb973 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:35:35 +0200 Subject: [PATCH 251/698] adding easyconfigs: ParMETIS-4.0.3-gompi-2020a.eb, ParMETIS-4.0.3-iimpi-2020a.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb | 26 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb | 25 ++++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb new file mode 100644 index 00000000000..d49afb48f0c --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2020a.eb @@ -0,0 +1,26 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.16.4')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb new file mode 100644 index 00000000000..222ea8e853f --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-iimpi-2020a.eb @@ -0,0 +1,25 @@ +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.16.4')] + +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From 87cf8f8c2c8736770c19a7f8c1346d298febfaac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:36:56 +0200 Subject: [PATCH 252/698] adding easyconfigs: picard-2.22.1-Java-11.eb --- .../p/picard/picard-2.22.1-Java-11.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-2.22.1-Java-11.eb diff --git a/easybuild/easyconfigs/p/picard/picard-2.22.1-Java-11.eb b/easybuild/easyconfigs/p/picard/picard-2.22.1-Java-11.eb new file mode 100644 index 00000000000..ebc390a68ff --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-2.22.1-Java-11.eb @@ -0,0 +1,50 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +## + +easyblock = 'JAR' + +name = 'picard' +version = '2.22.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['55cd8782ec6812df4d3b3fcde7d7d713200fb2240bb0e34849280799edb64e6e'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio' From bafeb6abe1dfc24c3b9be8b985d3365218352070 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Sep 2020 17:46:49 +0200 Subject: [PATCH 253/698] adding easyconfigs: Valgrind-3.16.1-gompi-2020a.eb, Valgrind-3.16.1-iimpi-2020a.eb and patches: Valgrind-3.15.0-no-MPI-1.patch --- .../v/Valgrind/Valgrind-3.15.0-no-MPI-1.patch | 66 +++++++++++++++++++ .../v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb | 36 ++++++++++ .../v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb | 32 +++++++++ 3 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.15.0-no-MPI-1.patch create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.15.0-no-MPI-1.patch b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.15.0-no-MPI-1.patch new file mode 100644 index 00000000000..54d26dd4043 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.15.0-no-MPI-1.patch @@ -0,0 +1,66 @@ +From a3262243ca01f7cfe3ae86b168d5b3a7e5d1cbc0 Mon Sep 17 00:00:00 2001 +From: Balint Reczey +Date: Thu, 28 Nov 2019 19:31:12 +0100 +Subject: [PATCH] Drop MPI 1 support + +Signed-off-by: Balint Reczey +--- + mpi/libmpiwrap.c | 16 ++-------------- + 1 file changed, 2 insertions(+), 14 deletions(-) + +diff --git a/mpi/libmpiwrap.c b/mpi/libmpiwrap.c +index 488bb13fd..a740ea562 100644 +--- a/mpi/libmpiwrap.c ++++ b/mpi/libmpiwrap.c +@@ -278,8 +278,6 @@ static void showTy ( FILE* f, MPI_Datatype ty ) + else if (ty == MPI_LONG_INT) fprintf(f,"LONG_INT"); + else if (ty == MPI_SHORT_INT) fprintf(f,"SHORT_INT"); + else if (ty == MPI_2INT) fprintf(f,"2INT"); +- else if (ty == MPI_UB) fprintf(f,"UB"); +- else if (ty == MPI_LB) fprintf(f,"LB"); + # if defined(MPI_WCHAR) + else if (ty == MPI_WCHAR) fprintf(f,"WCHAR"); + # endif +@@ -350,20 +348,11 @@ static void showCombiner ( FILE* f, int combiner ) + # endif + case MPI_COMBINER_CONTIGUOUS: fprintf(f, "CONTIGUOUS"); break; + case MPI_COMBINER_VECTOR: fprintf(f, "VECTOR"); break; +-#if defined(MPI_COMBINER_HVECTOR_INTEGER) +- case MPI_COMBINER_HVECTOR_INTEGER: fprintf(f, "HVECTOR_INTEGER"); break; +-# endif + case MPI_COMBINER_HVECTOR: fprintf(f, "HVECTOR"); break; + case MPI_COMBINER_INDEXED: fprintf(f, "INDEXED"); break; +-#if defined(MPI_COMBINER_HINDEXED_INTEGER) +- case MPI_COMBINER_HINDEXED_INTEGER: fprintf(f, "HINDEXED_INTEGER"); break; +-# endif + case MPI_COMBINER_HINDEXED: fprintf(f, "HINDEXED"); break; + #if defined(MPI_COMBINER_INDEXED_BLOCK) + case MPI_COMBINER_INDEXED_BLOCK: fprintf(f, "INDEXED_BLOCK"); break; +-# endif +-#if defined(MPI_COMBINER_STRUCT_INTEGER) +- case MPI_COMBINER_STRUCT_INTEGER: fprintf(f, "STRUCT_INTEGER"); break; + # endif + case MPI_COMBINER_STRUCT: fprintf(f, "STRUCT"); break; + #if defined(MPI_COMBINER_SUBARRAY) +@@ -458,8 +447,9 @@ Bool isMSI ( MPI_Status* status ) + static long extentOfTy ( MPI_Datatype ty ) + { + int r; ++ MPI_Aint lb; + MPI_Aint n; +- r = PMPI_Type_extent(ty, &n); ++ r = MPI_Type_get_extent(ty, &lb, &n); + assert(r == MPI_SUCCESS); + return (long)n; + } +@@ -733,8 +723,6 @@ void walk_type ( void(*f)(void*,long), char* base, MPI_Datatype ty ) + f(base + offsetof(Ty,loc), sizeof(int)); + return; + } +- if (ty == MPI_LB || ty == MPI_UB) +- return; /* have zero size, so nothing needs to be done */ + goto unhandled; + /*NOTREACHED*/ + } +-- +2.17.1 diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb new file mode 100644 index 00000000000..157ea2abe61 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-gompi-2020a.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.16.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2020a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Valgrind-3.15.0-no-MPI-1.patch'] +checksums = [ + 'c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca', # valgrind-3.16.1.tar.bz2 + 'e99464ad9f2d2e74c5c50d2fa1bcf8637295b11cd841102035f8601b01afd85f', # Valgrind-3.15.0-no-MPI-1.patch +] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb new file mode 100644 index 00000000000..cfe4c331435 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.16.1-iimpi-2020a.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.16.1' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'optarch': False} + +source_urls = [ + 'ftp://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c91f3a2f7b02db0f3bc99479861656154d241d2fdb265614ba918cc6720a33ca'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + ['lib/valgrind/libmpiwrap-amd64-linux.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'debugger' From d91a354f9ec19f8d3628fb230e2b66ae70d64116 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 23 Sep 2020 20:44:02 +0200 Subject: [PATCH 254/698] tsne fix + https fixes --- .../CD-HIT-4.8.1-iccifort-2019.5.281.eb | 6 +-- .../f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb | 4 +- ...CC-2017-03-01-intel-2019b-Python-2.7.16.eb | 12 ++---- .../tsne-0.1.8-intel-2019b-Python-2.7.16.eb | 6 +-- .../t/tsne/tsne-0.1.8_fix_setup_py.patch | 37 +++++++++++++++++-- 5 files changed, 45 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb index f1f1a221380..4181190478c 100644 --- a/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb +++ b/easybuild/easyconfigs/c/CD-HIT/CD-HIT-4.8.1-iccifort-2019.5.281.eb @@ -5,9 +5,9 @@ easyblock = 'MakeCp' name = 'CD-HIT' version = '4.8.1' -homepage = 'http://weizhongli-lab.org/cd-hit/' -description = """ CD-HIT is a very widely used program for clustering and - comparing protein or nucleotide sequences.""" +homepage = 'https://github.com/weizhongli/cdhit' +description = """CD-HIT is a very widely used program for clustering and +comparing protein or nucleotide sequences.""" toolchain = {'name': 'iccifort', 'version': '2019.5.281'} toolchainopts = {'openmp': True} diff --git a/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb index 472087a6202..84b8de25383 100644 --- a/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/f/fetchMG/fetchMG-1.0-GCCcore-8.3.0.eb @@ -3,13 +3,13 @@ easyblock = 'Tarball' name = 'fetchMG' version = '1.0' -homepage = 'http://vm-lux.embl.de/~mende/fetchMG/about.html' +homepage = 'https://vm-lux.embl.de/~mende/fetchMG/about.html' description = """The program “fetchMG” was written to extract the 40 MGs from genomes and metagenomes in an easy and accurate manner.""" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -source_urls = ['http://vm-lux.embl.de/~kultima/share/mOTU/'] +source_urls = ['https://vm-lux.embl.de/~kultima/share/mOTU/'] sources = ['%(name)sv%(version)s.tar.gz'] checksums = ['e3b835b425525513611b7116f89fc11ed015032ffd0494fa058edec1d6e67b17'] diff --git a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb index 19a3c0996ed..6a07a625057 100644 --- a/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/m/MyCC/MyCC-2017-03-01-intel-2019b-Python-2.7.16.eb @@ -7,11 +7,8 @@ name = "MyCC" version = "2017-03-01" versionsuffix = '-Python-%(pyver)s' -homepage = "http://docutils.sourceforge.net/" -description = """Docutils is an open-source text processing system for processing plaintext -documentation into useful formats, such as HTML, LaTeX, man-pages, open-document or XML. -It includes reStructuredText, the easy to read, easy to use, what-you-see-is-what-you-get -plaintext markup language.""" +homepage = "https://sourceforge.net/projects/sb2nhri/files/MyCC/" +description = "MyCC is built and delivered as a tailored solution for metagenomics sequencesclassfication." toolchain = {'name': 'intel', 'version': '2019b'} @@ -20,7 +17,6 @@ sources = [{'download_filename': 'Tools.tar.gz', 'filename': '%s-%s.tar.gz' % (n patches = ['%(name)s-%(version)s_fix_paths.patch'] checksums = [ '173210a759e90c7b1ff98bf537a88e8b7e893e60fe91fca50407ffede7e08de6', # MyCC-2017-03-01.tar.gz - 'f20fdf13ccd04c2e523c87a8f0a80194443fa09f7916b4b7ecb5a9751e1f6ee8', # MyCC-2017-03-01_fix_paths.patch ] @@ -38,7 +34,6 @@ dependencies = [ skipsteps = ['build'] - local_bin_files = [ '1_bhsne.py', '1_ClusterCorrection_Split.py', '1_GetCDHitHeader.py', '1_GetCOG.py', '1_GetRepeatGeneMaskedFa.py', '1_rename.py', '1_tsne.py', '2_ap.py', '2_ClusterCorrection_Merge_3d.py', '2_ClusterCorrection_Merge.py', @@ -53,7 +48,6 @@ local_bin_files = [ fix_perl_shebang_for = ['bin/*.pl'] fix_python_shebang_for = ['bin/*.py'] - files_to_copy = [ # all Python and Perl file (['*.py'], 'bin'), (['*.pl'], 'bin'), @@ -61,7 +55,7 @@ files_to_copy = [ # https://www.bioinf.jku.at/software/apcluster/ # just copy included version for now, never used in other eb. # Depends on R, likely not worth the effort. - (['ap/apcluster'], 'bin'), (['ap/apclusterunix64.so'], 'lib'), + (['ap/apcluster'], 'bin'), (['ap/apclusterunix64.%s' % SHLIB_EXT], 'lib'), (['ap/apclusterdemo_linux.c', 'ap/apcluster.h'], 'include'), ] diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb index 5e31965ea2c..886c28a4d85 100644 --- a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb @@ -11,25 +11,25 @@ homepage = 'https://github.com/danielfrg/tsne' description = "Python library containing T-SNE algorithms." toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'openmp': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] patches = ['%(name)s-%(version)s_fix_setup_py.patch'] checksums = [ 'fa6f29fc767ec269003986115aa40713bdd5ed5feb5fe974a1c3c33a5f2a925b', # tsne-0.1.8.tar.gz - '30311baf29935bf2aec8263b1405a81d5d69bebaab5bc15fa1c98565e2ec2ac3', # tsne-0.1.8_fix_setup_py.patch + '0ef42134a1c1a54f18b1148dcc1d52a0b58a2563077e4638bb212f7640e14ac2', # tsne-0.1.8_fix_setup_py.patch ] dependencies = [ ('Python', '2.7.16'), ('SciPy-bundle', '2019.10', versionsuffix), - ('CBLAS', '20110120'), ] download_dep_fail = True use_pip = True sanity_pip_check = True -options = {'modulename': False} +check_ldshared = True moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch index 6572a9068d7..0511e3bf7b7 100644 --- a/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch @@ -3,16 +3,18 @@ Removed hardcoded flags Author: Pavel Grochal (INUITS) diff -ru tsne-0.1.8.orig/setup.py tsne-0.1.8/setup.py --- tsne-0.1.8.orig/setup.py 2018-06-06 19:22:12.000000000 +0200 -+++ tsne-0.1.8/setup.py 2020-09-15 12:42:01.908482715 +0200 -@@ -50,11 +50,11 @@ ++++ tsne-0.1.8/setup.py 2020-09-23 16:46:58.816718252 +0200 +@@ -49,12 +49,12 @@ + extra_link_args=['-Wl,-framework', '-Wl,Accelerate', '-lcblas'], language='c++')] else: - extra_link_args = ['-lcblas'] +- extra_link_args = ['-lcblas'] - dist = platform.linux_distribution(full_distribution_name=0)[0] - redhat_dists = set(["redhat", "fedora", "centos"]) - if dist in redhat_dists: - extra_link_args = ['-lsatlas'] - ++ extra_link_args = ['-lmkl_core', '-lmkl_intel_thread', '-lmkl_intel_lp64', '-lmkl_def', '-lpthread'] + # dist = platform.linux_distribution(full_distribution_name=0)[0] + # redhat_dists = set(["redhat", "fedora", "centos"]) + # if dist in redhat_dists: @@ -21,4 +23,33 @@ diff -ru tsne-0.1.8.orig/setup.py tsne-0.1.8/setup.py # LINUX ext_modules = [Extension(name='bh_sne', sources=['tsne/bh_sne_src/quadtree.cpp', 'tsne/bh_sne_src/tsne.cpp', 'tsne/bh_sne.pyx'], +diff -ru tsne-0.1.8.orig/tsne/bh_sne_src/quadtree.cpp tsne-0.1.8/tsne/bh_sne_src/quadtree.cpp +--- tsne-0.1.8.orig/tsne/bh_sne_src/quadtree.cpp 2018-06-06 19:13:25.000000000 +0200 ++++ tsne-0.1.8/tsne/bh_sne_src/quadtree.cpp 2020-09-23 16:59:31.380365015 +0200 +@@ -9,7 +9,7 @@ + + #include + #include +-#include ++#include + #include + #include + #include "quadtree.h" +@@ -383,4 +383,3 @@ + southWest->print(); + } + } +- +diff -ru tsne-0.1.8.orig/tsne/bh_sne_src/tsne.cpp tsne-0.1.8/tsne/bh_sne_src/tsne.cpp +--- tsne-0.1.8.orig/tsne/bh_sne_src/tsne.cpp 2018-06-06 19:20:55.000000000 +0200 ++++ tsne-0.1.8/tsne/bh_sne_src/tsne.cpp 2020-09-23 16:59:36.356282664 +0200 +@@ -18,7 +18,7 @@ + #include "tsne.h" + + extern "C" { +- #include ++ #include + } + + From 7f215a91a1524f40ef3d22616115a98ed48968e0 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 09:54:26 +0200 Subject: [PATCH 255/698] fix preconfigopts --- easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb index 55e21a574fc..bf3fff366f2 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.2.0.eb @@ -30,6 +30,7 @@ dependencies = [ ('libtirpc', '1.1.4'), ] +preconfigopts = "LIBS='-ltirpc' " configopts = '--with-szlib=$EBROOTSZIP ' configopts += 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb index 976dcd4444c..b2a2cfa2543 100644 --- a/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.14-GCCcore-8.3.0.eb @@ -30,6 +30,7 @@ dependencies = [ ('libtirpc', '1.2.6'), ] +preconfigopts = "LIBS='-ltirpc' " configopts = '--with-szlib=$EBROOTSZIP ' configopts += 'CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' configopts += '--includedir=%(installdir)s/include/%(namelower)s ' From 98437dec27e5cf1ed53aed81f9c1d7ac11e062d8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 10:17:57 +0200 Subject: [PATCH 256/698] Make libtirc easier to use as replacement of rpc in glibc (for RHEL 8) --- .../easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-8.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-8.3.0.eb index f762cde0265..783a63ca0c1 100644 --- a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.2.6-GCCcore-8.3.0.eb @@ -23,4 +23,6 @@ sanity_check_paths = { 'dirs': ['include/tirpc', 'lib'], } +modextrapaths = {'CPATH': 'include/tirpc'} + moduleclass = 'lib' From 4a2a19f307edb94fcbb461206af6d979911c152f Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 10:27:45 +0200 Subject: [PATCH 257/698] adding easyconfigs: ASE-3.19.0-foss-2020a-Python-3.8.2.eb --- .../ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..db6a438bbcd --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10.3', { + 'checksums': ['9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de'], + }), + ('Werkzeug', '0.16.0', { + 'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'], + }), + ('Click', '7.0', { + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.1', { + 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], + }), + ('ase', version, { + 'checksums': ['a8378ab57e91cfe1ba09b3639d8409bb7fc1a40b59479c7822d206e673ad93f9'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From b219f4e6a68a183132508adcf84fb5778656a1f0 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 10:28:28 +0200 Subject: [PATCH 258/698] adding easyconfigs: ASE-3.19.0-intel-2020a-Python-3.8.2.eb --- .../ASE-3.19.0-intel-2020a-Python-3.8.2.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..8f059f4936d --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.19.0-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.19.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('Tkinter', '%(pyver)s'), + ('matplotlib', '3.2.1', '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages (MarkupSafe) using Intel compilers on top of Python built with GCC. +check_ldshared = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.10.3', { + 'checksums': ['9fe95f19286cfefaa917656583d020be14e7859c6b0252588391e47db34527de'], + }), + ('Werkzeug', '0.16.0', { + 'checksums': ['7280924747b5733b246fe23972186c6b348f9ae29724135a6dfc1e53cea433e7'], + }), + ('Click', '7.0', { + 'checksums': ['5b94b49521f6456670fdb30cd82a4eca9412788a93fa6dd6df72c94d5a8ff2d7'], + }), + ('itsdangerous', '1.1.0', { + 'checksums': ['321b033d07f2a4136d3ec762eac9f16a10ccd60f53c0c91af90217ace7ba1f19'], + }), + ('Flask', '1.1.1', { + 'checksums': ['13f9f196f330c7c2c5d7a5cf91af894110ca0215ac051b5844701f2bfd934d52'], + }), + ('ase', version, { + 'checksums': ['a8378ab57e91cfe1ba09b3639d8409bb7fc1a40b59479c7822d206e673ad93f9'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' From a33c2364b867a5dc3e733fe6dc50a2a6759b462d Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 24 Sep 2020 12:24:18 +0200 Subject: [PATCH 259/698] fixed patch --- .../t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb | 4 ++-- ..._fix_setup_py.patch => tsne-0.1.8_fix-setup-py-imkl.patch} | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/t/tsne/{tsne-0.1.8_fix_setup_py.patch => tsne-0.1.8_fix-setup-py-imkl.patch} (96%) diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb index 886c28a4d85..d4b6a58b781 100644 --- a/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8-intel-2019b-Python-2.7.16.eb @@ -15,10 +15,10 @@ toolchainopts = {'openmp': True} source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version)s_fix_setup_py.patch'] +patches = ['%(name)s-%(version)s_fix-setup-py-imkl.patch'] checksums = [ 'fa6f29fc767ec269003986115aa40713bdd5ed5feb5fe974a1c3c33a5f2a925b', # tsne-0.1.8.tar.gz - '0ef42134a1c1a54f18b1148dcc1d52a0b58a2563077e4638bb212f7640e14ac2', # tsne-0.1.8_fix_setup_py.patch + '60396006ebc0dd1038a8382d3dc7a8db157734249f8b0a8752432b31b6371731', # tsne-0.1.8_fix-setup-py-imkl.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix-setup-py-imkl.patch similarity index 96% rename from easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch rename to easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix-setup-py-imkl.patch index 0511e3bf7b7..1fb44285551 100644 --- a/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix_setup_py.patch +++ b/easybuild/easyconfigs/t/tsne/tsne-0.1.8_fix-setup-py-imkl.patch @@ -1,4 +1,4 @@ -Removed hardcoded flags +Removed hardcoded flags. Linked imkl and replaced cblas for mkl_cblas Author: Pavel Grochal (INUITS) diff -ru tsne-0.1.8.orig/setup.py tsne-0.1.8/setup.py From fb9a181c04606490ffe2dbeeaa8b4a7987362e75 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Sep 2020 13:06:55 +0200 Subject: [PATCH 260/698] Exclude test_torch --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 2 ++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index b5eb068ec94..4a0d399d56c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -261,6 +261,8 @@ excluded_tests = { 'jit', # https://github.com/pytorch/pytorch/issues/41469 'nn', + # Sporadically fails for unknown reason. Fixed in newer versions + 'torch', ], } diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index 98a4a0edad1..a89dc33633e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -267,6 +267,8 @@ excluded_tests = { 'jit', # https://github.com/pytorch/pytorch/issues/41469 'nn', + # Sporadically fails for unknown reason. Fixed in newer versions + 'torch', # Unknown 'cuda', ], From 2b3b23f5a72e187061f6bd229fe25e148e424faf Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 13:07:55 +0200 Subject: [PATCH 261/698] Hadoop 2 RHEL 8 modifications --- .../h/Hadoop/HADOOP-14597.04.patch | 139 ++++++++++++++++++ .../Hadoop-2.10.0-GCCcore-8.3.0-native.eb | 9 +- .../h/Hadoop/Hadoop-2.10.0_tirpc.patch | 15 ++ 3 files changed, 162 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch create mode 100644 easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch diff --git a/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch b/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch new file mode 100644 index 00000000000..6f805942ae8 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch @@ -0,0 +1,139 @@ +# see: https://issues.apache.org/jira/browse/HADOOP-14597 +# download: https://issues.apache.org/jira/secure/attachment/12875105/HADOOP-14597.04.patch +diff --git a/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c b/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c +index 5cb5bba9ae..c7984a3347 100644 +--- a/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c ++++ b/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c +@@ -30,6 +30,11 @@ static void (*dlsym_EVP_CIPHER_CTX_free)(EVP_CIPHER_CTX *); + static int (*dlsym_EVP_CIPHER_CTX_cleanup)(EVP_CIPHER_CTX *); + static void (*dlsym_EVP_CIPHER_CTX_init)(EVP_CIPHER_CTX *); + static int (*dlsym_EVP_CIPHER_CTX_set_padding)(EVP_CIPHER_CTX *, int); ++static int (*dlsym_EVP_CIPHER_CTX_test_flags)(const EVP_CIPHER_CTX *, int); ++static int (*dlsym_EVP_CIPHER_CTX_block_size)(const EVP_CIPHER_CTX *); ++#if OPENSSL_VERSION_NUMBER >= 0x10100000L ++static int (*dlsym_EVP_CIPHER_CTX_encrypting)(const EVP_CIPHER_CTX *); ++#endif + static int (*dlsym_EVP_CipherInit_ex)(EVP_CIPHER_CTX *, const EVP_CIPHER *, \ + ENGINE *, const unsigned char *, const unsigned char *, int); + static int (*dlsym_EVP_CipherUpdate)(EVP_CIPHER_CTX *, unsigned char *, \ +@@ -46,6 +51,11 @@ typedef void (__cdecl *__dlsym_EVP_CIPHER_CTX_free)(EVP_CIPHER_CTX *); + typedef int (__cdecl *__dlsym_EVP_CIPHER_CTX_cleanup)(EVP_CIPHER_CTX *); + typedef void (__cdecl *__dlsym_EVP_CIPHER_CTX_init)(EVP_CIPHER_CTX *); + typedef int (__cdecl *__dlsym_EVP_CIPHER_CTX_set_padding)(EVP_CIPHER_CTX *, int); ++typedef int (__cdecl *__dlsym_EVP_CIPHER_CTX_test_flags)(const EVP_CIPHER_CTX *, int); ++typedef int (__cdecl *__dlsym_EVP_CIPHER_CTX_block_size)(const EVP_CIPHER_CTX *); ++#if OPENSSL_VERSION_NUMBER >= 0x10100000L ++typedef int (__cdecl *__dlsym_EVP_CIPHER_CTX_encrypting)(const EVP_CIPHER_CTX *); ++#endif + typedef int (__cdecl *__dlsym_EVP_CipherInit_ex)(EVP_CIPHER_CTX *, \ + const EVP_CIPHER *, ENGINE *, const unsigned char *, \ + const unsigned char *, int); +@@ -60,6 +70,11 @@ static __dlsym_EVP_CIPHER_CTX_free dlsym_EVP_CIPHER_CTX_free; + static __dlsym_EVP_CIPHER_CTX_cleanup dlsym_EVP_CIPHER_CTX_cleanup; + static __dlsym_EVP_CIPHER_CTX_init dlsym_EVP_CIPHER_CTX_init; + static __dlsym_EVP_CIPHER_CTX_set_padding dlsym_EVP_CIPHER_CTX_set_padding; ++static __dlsym_EVP_CIPHER_CTX_test_flags dlsym_EVP_CIPHER_CTX_test_flags; ++static __dlsym_EVP_CIPHER_CTX_block_size dlsym_EVP_CIPHER_CTX_block_size; ++#if OPENSSL_VERSION_NUMBER >= 0x10100000L ++static __dlsym_EVP_CIPHER_CTX_encrypting dlsym_EVP_CIPHER_CTX_encrypting; ++#endif + static __dlsym_EVP_CipherInit_ex dlsym_EVP_CipherInit_ex; + static __dlsym_EVP_CipherUpdate dlsym_EVP_CipherUpdate; + static __dlsym_EVP_CipherFinal_ex dlsym_EVP_CipherFinal_ex; +@@ -114,6 +129,14 @@ JNIEXPORT void JNICALL Java_org_apache_hadoop_crypto_OpensslCipher_initIDs + "EVP_CIPHER_CTX_init"); + LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CIPHER_CTX_set_padding, env, openssl, \ + "EVP_CIPHER_CTX_set_padding"); ++ LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CIPHER_CTX_test_flags, env, openssl, \ ++ "EVP_CIPHER_CTX_test_flags"); ++ LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CIPHER_CTX_block_size, env, openssl, \ ++ "EVP_CIPHER_CTX_block_size"); ++#if OPENSSL_VERSION_NUMBER >= 0x10100000L ++ LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CIPHER_CTX_encrypting, env, openssl, \ ++ "EVP_CIPHER_CTX_encrypting"); ++#endif + LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CipherInit_ex, env, openssl, \ + "EVP_CipherInit_ex"); + LOAD_DYNAMIC_SYMBOL(dlsym_EVP_CipherUpdate, env, openssl, \ +@@ -135,6 +158,17 @@ JNIEXPORT void JNICALL Java_org_apache_hadoop_crypto_OpensslCipher_initIDs + LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CIPHER_CTX_set_padding, \ + dlsym_EVP_CIPHER_CTX_set_padding, env, \ + openssl, "EVP_CIPHER_CTX_set_padding"); ++ LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CIPHER_CTX_test_flags, \ ++ dlsym_EVP_CIPHER_CTX_test_flags, env, \ ++ openssl, "EVP_CIPHER_CTX_test_flags"); ++ LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CIPHER_CTX_block_size, \ ++ dlsym_EVP_CIPHER_CTX_block_size, env, \ ++ openssl, "EVP_CIPHER_CTX_block_size"); ++#if OPENSSL_VERSION_NUMBER >= 0x10100000L ++ LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CIPHER_CTX_encrypting, \ ++ dlsym_EVP_CIPHER_CTX_encrypting, env, \ ++ openssl, "EVP_CIPHER_CTX_encrypting"); ++#endif + LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CipherInit_ex, dlsym_EVP_CipherInit_ex, \ + env, openssl, "EVP_CipherInit_ex"); + LOAD_DYNAMIC_SYMBOL(__dlsym_EVP_CipherUpdate, dlsym_EVP_CipherUpdate, \ +@@ -253,14 +287,18 @@ JNIEXPORT jlong JNICALL Java_org_apache_hadoop_crypto_OpensslCipher_init + static int check_update_max_output_len(EVP_CIPHER_CTX *context, int input_len, + int max_output_len) + { +- if (context->flags & EVP_CIPH_NO_PADDING) { ++ if ( dlsym_EVP_CIPHER_CTX_test_flags(context, EVP_CIPH_NO_PADDING) ) { + if (max_output_len >= input_len) { + return 1; + } + return 0; + } else { +- int b = context->cipher->block_size; ++ int b = dlsym_EVP_CIPHER_CTX_block_size(context); ++#if OPENSSL_VERSION_NUMBER < 0x10100000L + if (context->encrypt) { ++#else ++ if (dlsym_EVP_CIPHER_CTX_encrypting(context)) { ++#endif + if (max_output_len >= input_len + b - 1) { + return 1; + } +@@ -307,10 +345,10 @@ JNIEXPORT jint JNICALL Java_org_apache_hadoop_crypto_OpensslCipher_update + static int check_doFinal_max_output_len(EVP_CIPHER_CTX *context, + int max_output_len) + { +- if (context->flags & EVP_CIPH_NO_PADDING) { ++ if ( dlsym_EVP_CIPHER_CTX_test_flags(context, EVP_CIPH_NO_PADDING) ) { + return 1; + } else { +- int b = context->cipher->block_size; ++ int b = dlsym_EVP_CIPHER_CTX_block_size(context); + if (max_output_len >= b) { + return 1; + } +diff --git a/hadoop-tools/hadoop-pipes/src/main/native/pipes/impl/HadoopPipes.cc b/hadoop-tools/hadoop-pipes/src/main/native/pipes/impl/HadoopPipes.cc +index 91fb5a42b2..45cb8c2024 100644 +--- a/hadoop-tools/hadoop-pipes/src/main/native/pipes/impl/HadoopPipes.cc ++++ b/hadoop-tools/hadoop-pipes/src/main/native/pipes/impl/HadoopPipes.cc +@@ -420,6 +420,7 @@ namespace HadoopPipes { + } + + string createDigest(string &password, string& msg) { ++#if OPENSSL_VERSION_NUMBER < 0x10100000L + HMAC_CTX ctx; + unsigned char digest[EVP_MAX_MD_SIZE]; + HMAC_Init(&ctx, (const unsigned char *)password.c_str(), +@@ -428,7 +429,16 @@ namespace HadoopPipes { + unsigned int digestLen; + HMAC_Final(&ctx, digest, &digestLen); + HMAC_cleanup(&ctx); +- ++#else ++ HMAC_CTX *ctx = HMAC_CTX_new(); ++ unsigned char digest[EVP_MAX_MD_SIZE]; ++ HMAC_Init_ex(ctx, (const unsigned char *)password.c_str(), ++ password.length(), EVP_sha1(), NULL); ++ HMAC_Update(ctx, (const unsigned char *)msg.c_str(), msg.length()); ++ unsigned int digestLen; ++ HMAC_Final(ctx, digest, &digestLen); ++ HMAC_CTX_free(ctx); ++#endif + //now apply base64 encoding + BIO *bmem, *b64; + BUF_MEM *bptr; diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb index d1de46e2bca..0098341f8e6 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb @@ -15,11 +15,15 @@ sources = ['hadoop-%(version)s-src.tar.gz'] patches = [ 'Hadoop-TeraSort-on-local-filesystem.patch', 'Hadoop-2.9.2_fix-zlib.patch', + 'HADOOP-14597.04.patch', + 'Hadoop-2.10.0_tirpc.patch', ] checksums = [ 'baa9b125359a30eb209fbaa953e1b324eb61fa65ceb9a7cf19b0967188d8b1c0', # hadoop-2.10.0-src.tar.gz 'd0a69a6936b4a01505ba2a20911d0cec4f79440dbc8da52b9ddbd7f3a205468b', # Hadoop-TeraSort-on-local-filesystem.patch '1a1d084c7961078bdbaa84716e9639e37587e1d8c0b1f89ce6f12dde8bbbbc5c', # Hadoop-2.9.2_fix-zlib.patch + '68b5b38f6f8482d6fbdcc619c41d99fc64db8d90630b30fdb78b031440c24e72', # HADOOP-14597.04.patch + '85bbf37e7f6d091738774d9a6390c02dc15c8c1f1406cf0dca3ad06165221b1f', # Hadoop-2.10.0_tirpc.patch ] builddependencies = [ @@ -33,7 +37,10 @@ builddependencies = [ ] # https://cwiki.apache.org/confluence/display/HADOOP/Hadoop+Java+Versions -dependencies = [('Java', '1.8', '', True)] +dependencies = [ + ('Java', '1.8', '', True), + ('libtirpc', '1.2.6'), +] build_native_libs = True diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch new file mode 100644 index 00000000000..bcc8c512e21 --- /dev/null +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch @@ -0,0 +1,15 @@ +# RHEL 8 glibc does not includes RPC anymore, so external one has to be used. +# in this case, SerialUtils.cc have to be licked with the external library, libtirpc. +# SEP 24th 2020 by B. Hajgato (UGent) +diff -ru hadoop-2.10.0-src.orig/hadoop-tools/hadoop-pipes/src/CMakeLists.txt hadoop-2.10.0-src/hadoop-tools/hadoop-pipes/src/CMakeLists.txt +--- hadoop-2.10.0-src.orig/hadoop-tools/hadoop-pipes/src/CMakeLists.txt 2019-10-15 20:12:38.000000000 +0200 ++++ hadoop-2.10.0-src/hadoop-tools/hadoop-pipes/src/CMakeLists.txt 2020-09-24 12:02:21.022819284 +0200 +@@ -63,6 +63,8 @@ + set(LIB_DL "dl") + endif() + ++set(LIB_NET "tirpc") ++ + if(${CMAKE_SYSTEM_NAME} MATCHES "SunOS") + exec_program("uname" ARGS "-r" OUTPUT_VARIABLE OS_VERSION) + if(OS_VERSION VERSION_LESS "5.12") From f39f6402aff2451af1b05cf6a931f8becdc5a81f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 13:34:28 +0200 Subject: [PATCH 262/698] fix typos --- easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch | 1 + .../h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb | 4 ++-- easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch | 4 ++-- 3 files changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch b/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch index 6f805942ae8..e6503ee7119 100644 --- a/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch +++ b/easybuild/easyconfigs/h/Hadoop/HADOOP-14597.04.patch @@ -1,3 +1,4 @@ +# Patch for newer OpenSSL (1.1.x) # see: https://issues.apache.org/jira/browse/HADOOP-14597 # download: https://issues.apache.org/jira/secure/attachment/12875105/HADOOP-14597.04.patch diff --git a/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c b/hadoop-common-project/hadoop-common/src/main/native/src/org/apache/hadoop/crypto/OpensslCipher.c diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb index 0098341f8e6..78f007fd28d 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0-GCCcore-8.3.0-native.eb @@ -22,8 +22,8 @@ checksums = [ 'baa9b125359a30eb209fbaa953e1b324eb61fa65ceb9a7cf19b0967188d8b1c0', # hadoop-2.10.0-src.tar.gz 'd0a69a6936b4a01505ba2a20911d0cec4f79440dbc8da52b9ddbd7f3a205468b', # Hadoop-TeraSort-on-local-filesystem.patch '1a1d084c7961078bdbaa84716e9639e37587e1d8c0b1f89ce6f12dde8bbbbc5c', # Hadoop-2.9.2_fix-zlib.patch - '68b5b38f6f8482d6fbdcc619c41d99fc64db8d90630b30fdb78b031440c24e72', # HADOOP-14597.04.patch - '85bbf37e7f6d091738774d9a6390c02dc15c8c1f1406cf0dca3ad06165221b1f', # Hadoop-2.10.0_tirpc.patch + 'ea93c7c2b03d36f1434c2f2921c031cdc385a98f337ed8f4b3103b45b0ad0da3', # HADOOP-14597.04.patch + '9d66f604e6e03923d8fcb290382936fb93511001bb593025b8d63ababdca3a96', # Hadoop-2.10.0_tirpc.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch index bcc8c512e21..09834a0126c 100644 --- a/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch +++ b/easybuild/easyconfigs/h/Hadoop/Hadoop-2.10.0_tirpc.patch @@ -1,5 +1,5 @@ -# RHEL 8 glibc does not includes RPC anymore, so external one has to be used. -# in this case, SerialUtils.cc have to be licked with the external library, libtirpc. +# RHEL 8 glibc does not include RPC anymore, so external one has to be used. +# And SerialUtils.cc has to be linked with the external library, libtirpc # SEP 24th 2020 by B. Hajgato (UGent) diff -ru hadoop-2.10.0-src.orig/hadoop-tools/hadoop-pipes/src/CMakeLists.txt hadoop-2.10.0-src/hadoop-tools/hadoop-pipes/src/CMakeLists.txt --- hadoop-2.10.0-src.orig/hadoop-tools/hadoop-pipes/src/CMakeLists.txt 2019-10-15 20:12:38.000000000 +0200 From c926fc619a7744d72bf4c094b18f33fe41431dc5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Sep 2020 13:50:01 +0200 Subject: [PATCH 263/698] Set OMP_NUM_THREADS=1 to work around POWER issues --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 5 +++-- .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index 4a0d399d56c..f49b36c2106 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -266,8 +266,9 @@ excluded_tests = { ], } -# OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) -runtest = 'cd test && OMP_NUM_THREADS=4 %(python)s run_test.py --verbose %(excluded_tests)s' +# OpenMP causes e.g. torch.matmul to return invalid results at least on POWER +# See e.g. https://github.com/pytorch/pytorch/issues/3716#issuecomment-387776917 +runtest = 'cd test && OMP_NUM_THREADS=1 %(python)s run_test.py --verbose %(excluded_tests)s' tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index a89dc33633e..2ab84d22597 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -274,8 +274,9 @@ excluded_tests = { ], } -# OpenMP threads must be limited as torch.matmul returns inprecise results for many threads (e.g. 176) -runtest = 'cd test && OMP_NUM_THREADS=4 %(python)s run_test.py --verbose %(excluded_tests)s' +# OpenMP causes e.g. torch.matmul to return invalid results at least on POWER +# See e.g. https://github.com/pytorch/pytorch/issues/3716#issuecomment-387776917 +runtest = 'cd test && OMP_NUM_THREADS=1 %(python)s run_test.py --verbose %(excluded_tests)s' tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From 0d293eae1acc8ee68483ed146f296daca73d619a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2020 13:51:22 +0200 Subject: [PATCH 264/698] add git build dep for OpenImageIO 2.1.12.0 --- .../o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb | 5 ++++- .../o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb index 51231d683f1..5633288a7b4 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-gompi-2020a.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] sources = ['Release-%(version)s.tar.gz'] checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] +builddependencies = [ + ('CMake', '3.16.4'), + ('git', '2.23.0', '-nodocs'), +] dependencies = [ ('Boost', '1.72.0'), ('libjpeg-turbo', '2.0.4'), @@ -22,7 +26,6 @@ dependencies = [ ('freetype', '2.10.1'), ('zlib', '1.2.11'), ] -builddependencies = [('CMake', '3.16.4')] separate_build_dir = True diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb index be58fe7c03b..1b4a71fcf97 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.1.12.0-iimpi-2020a.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/OpenImageIO/oiio/archive/'] sources = ['Release-%(version)s.tar.gz'] checksums = ['da27e191349ef473220c7a373921e6d4c69d9924acd87140af55ce9d00ad58f8'] +builddependencies = [ + ('CMake', '3.16.4'), + ('git', '2.23.0', '-nodocs'), +] dependencies = [ ('Boost', '1.72.0'), ('libjpeg-turbo', '2.0.4'), @@ -22,7 +26,6 @@ dependencies = [ ('freetype', '2.10.1'), ('zlib', '1.2.11'), ] -builddependencies = [('CMake', '3.16.4')] separate_build_dir = True From 013e9bb89f8ef3e9763168b0d887f15642922c52 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 14:20:43 +0200 Subject: [PATCH 265/698] adding easyconfigs: OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb --- .../OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..38f192f3e47 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +name = 'OpenCV' +version = '4.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [ + 'https://github.com/opencv/opencv/archive/', + # the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake + 'https://raw.githubusercontent.com/opencv/opencv_3rdparty/32e315a5b106a7b89dbed51c28f8120a48b368b4/ippicv', +] +sources = [ + '%(version)s.zip', + {'filename': 'ippicv_2019_lnx_intel64_general_20180723.tgz', 'extract_cmd': "cp %s %(builddir)s"}, +] +checksums = [ + '55bd939079d141a50fca74bde5b61b339dd0f0ece6320ec76859aaff03c90d9f', # 4.2.0.zip + 'fc167cb60deb8924339a7050f3da168bb02e221b2d6b8c00139d1fa7eace0c7d', # ippicv_2019_lnx_intel64_general_20180723.tgz +] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy + ('zlib', '1.2.11'), + ('FFmpeg', '4.2.2'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('JasPer', '2.0.14'), + ('Java', '11', '', True), + ('ant', '1.10.8', '-Java-%(javaver)s', True), + ('GLib', '2.64.1'), + ('GTK+', '3.24.17'), +] + +moduleclass = 'vis' From 231cd403b6f2b91282e2d2150ed7711d89a9c9d9 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 15:45:57 +0200 Subject: [PATCH 266/698] adding easyconfigs: VirtualGL-2.6.2-GCCcore-9.3.0.eb --- .../VirtualGL-2.6.2-GCCcore-9.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..365d2477714 --- /dev/null +++ b/easybuild/easyconfigs/v/VirtualGL/VirtualGL-2.6.2-GCCcore-9.3.0.eb @@ -0,0 +1,43 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# updated by Valentin Plugaru 2019-09-26 + +easyblock = 'CMakeMake' + +name = 'VirtualGL' +version = '2.6.2' + +homepage = 'https://virtualgl.org/' +description = """VirtualGL is an open source toolkit that gives any Linux or +Unix remote display software the ability to run OpenGL applications with full +hardware acceleration.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/VirtualGL/virtualgl/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9679f4510ab3042618bf35eae3be8945db9463fde947719ce295ec8ea38755cb'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('binutils', '2.34'), +] + +dependencies = [ + ('libjpeg-turbo', '2.0.4'), + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), +] + +local_binaries = [ + 'cpustat', 'glreadtest', 'glxinfo', 'glxspheres64', 'nettest', 'tcbench', + 'vglclient', 'vglconfig', 'vglconnect', 'vglgenkey', 'vgllogin', 'vglrun', + 'vglserver_config' +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': ['lib64', 'share', 'include'], +} + +moduleclass = 'vis' From cec8fc8bf086718cb4791f4f2e30789428f8ead2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2020 16:27:36 +0200 Subject: [PATCH 267/698] add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems --- .../LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb index 408a24af2e8..2c236ceaa2c 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -29,10 +29,12 @@ sources = [ {'download_filename': '553885e.tar.gz', 'filename': 'OCTP-20190520.tar.gz'}, {'filename': 'lammps_vs_yaff_test_single_point_energy.py', 'extract_cmd': "cp %s %(builddir)s"}, ] +patches = ['%(name)s-%(version)s_EPYC.patch'] checksums = [ '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz '6d0b40394b288e877071f203d3946525d7d2b335367d2ee89c4bad0d757c1435', # OCTP-20190520.tar.gz '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py + '5cc5d2498f45d46569eb325aea5c217867f1afd95ee833fd0139f22e80431b86', # LAMMPS-7Aug2019_EPYC.patch ] local_source_dir_name = '%(namelower)s-%(version)s' From 07d1e2879f8d2c60a9efbf811f95e7a1d2791c8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2020 16:29:21 +0200 Subject: [PATCH 268/698] mention OCTP in description in LAMMPS easyconfig using OCTP --- .../LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb index 2c236ceaa2c..01059381365 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -14,13 +14,15 @@ the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. + +Includes support for On-the-fly Calculation of Transport Properties (OCTP), +see https://github.com/omoultosEthTuDelft/OCTP """ toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'openmp': True, 'usempi': True, 'cstd': 'c++11'} source_urls = [ - # 'https://github.com/lammps/lammps/archive/' GITHUB_LOWER_SOURCE, 'https://github.com/omoultosEthTuDelft/OCTP/archive/', ] From 78c2ea49fcae9708d068dffabb838e5313a6ec59 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 24 Sep 2020 13:35:28 +0200 Subject: [PATCH 269/698] adding easyconfigs: Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb --- ...uda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..f08bb13009f --- /dev/null +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'Horovod' +version = '0.20.0' +local_tf_version = '2.3.0' +versionsuffix = '-TensorFlow-%s-Python-%%(pyver)s' % local_tf_version + +homepage = 'https://github.com/uber/horovod' +description = "Horovod is a distributed training framework for TensorFlow." + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +builddependencies = [ + ('CMake', '3.15.3'), +] +dependencies = [ + ('Python', '3.7.4'), + ('PyYAML', '5.1.2'), + ('TensorFlow', local_tf_version, '-Python-%(pyver)s'), +] + +use_pip = True +sanity_pip_check = True + +preinstallopts = 'HOROVOD_WITH_MPI=1 HOROVOD_GPU_ALLREDUCE=NCCL HOROVOD_GPU_BROADCAST=NCCL ' +preinstallopts += 'HOROVOD_WITH_TENSORFLOW=1 HOROVOD_WITHOUT_PYTORCH=1 HOROVOD_WITHOUT_MXNET=1 ' + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('cloudpickle', '1.5.0', { + 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], + }), + ('horovod', version, { + 'checksums': ['88522b65d83cb9690193b200e2e8fd1e08864b27d72b7ff1bbc5e7b8ae4f32ed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/horovodrun'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From df9eefeabca15aea1c7274fd80afcae37028426c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Sep 2020 16:59:59 +0200 Subject: [PATCH 270/698] fix checksum for lammps_vs_yaff_test_single_point_energy.py test script --- .../LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb index 01059381365..f8494e9734b 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-7Aug2019-intel-2019b-Python-3.7.4-kokkos-OCTP.eb @@ -35,7 +35,7 @@ patches = ['%(name)s-%(version)s_EPYC.patch'] checksums = [ '5380c1689a93d7922e3d65d9c186401d429878bb3cbe9a692580d3470d6a253f', # stable_7Aug2019.tar.gz '6d0b40394b288e877071f203d3946525d7d2b335367d2ee89c4bad0d757c1435', # OCTP-20190520.tar.gz - '5e5211f64113e8a38c102f8542fd59169b689fdb92afbff29c3b88f802f1a96c', # lammps_vs_yaff_test_single_point_energy.py + 'c28fa5a1ea9608e4fd8686937be501c3bed8cc03ce1956f1cf0a1efce2c75349', # lammps_vs_yaff_test_single_point_energy.py '5cc5d2498f45d46569eb325aea5c217867f1afd95ee833fd0139f22e80431b86', # LAMMPS-7Aug2019_EPYC.patch ] From 2589dead5dee8775b862f4927443b52989cb92f0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 24 Sep 2020 17:23:55 +0100 Subject: [PATCH 271/698] adding easyconfigs: Anaconda3-2020.07.eb --- .../a/Anaconda3/Anaconda3-2020.07.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.07.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.07.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.07.eb new file mode 100644 index 00000000000..dd5857cd137 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2020.07.eb @@ -0,0 +1,28 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, 2019.10, 2020.20 by Joachim Hein +# config upgrade to 2019.03 by Davide Vanzo +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2020.07' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +sources = ['%(name)s-%(version)s-Linux-%(arch)s.sh'] + +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '38ce717758b95b3bd0b1797cc6ccfb76f29a90c25bdfa50ee45f11e583edfdbf', + '%(name)s-%(version)s-Linux-ppc64le.sh': '0df7c3784973ab46a9ef9848aced01311d08a71d79a18d5ed79dccdae8c8dea7', + } +] + +moduleclass = 'lang' From 0f09bcff2ce1f180714e6f9d6baa0b25e40effef Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 19:10:15 +0200 Subject: [PATCH 272/698] fix installation of Sailfish v0.10.1 on RHEL8 --- .../s/Sailfish/Sailfish-0.10.1-gompi-2019b.eb | 6 ++- .../s/Sailfish/Sailfish-0.10.1_RHEL8.patch | 45 +++++++++++++++++++ 2 files changed, 50 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_RHEL8.patch diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-gompi-2019b.eb b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-gompi-2019b.eb index c4cb14e1f20..79cada5dbae 100644 --- a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-gompi-2019b.eb +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1-gompi-2019b.eb @@ -14,10 +14,14 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/kingsfordgroup/%(namelower)s/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_skip-included-Jellyfish.patch'] +patches = [ + '%(name)s-%(version)s_skip-included-Jellyfish.patch', + '%(name)s-%(version)s_RHEL8.patch', +] checksums = [ 'a0d6d944382f2e07ffbfd0371132588e2f22bb846ecfc3d3435ff3d81b30d6c6', # v0.10.1.tar.gz '53bce73302d0f390ea5a1d615cb9c8e0684bd2cf3f50aaf0885a71862462e395', # Sailfish-0.10.1_skip-included-Jellyfish.patch + '0df096a00f9272b6b824357795c7e46c785e203648183104e4d55a7b461fc620', # Sailfish-0.10.1_RHEL8.patch ] builddependencies = [('CMake', '3.15.3')] diff --git a/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_RHEL8.patch b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_RHEL8.patch new file mode 100644 index 00000000000..f5f7581927c --- /dev/null +++ b/easybuild/easyconfigs/s/Sailfish/Sailfish-0.10.1_RHEL8.patch @@ -0,0 +1,45 @@ +# Fix CHAR_WIDTH glibc clash +# see: https://github.com/Cantera/cantera/issues/369#issuecomment-254090244 +# https://github.com/gabime/spdlog/issues/300 and https://github.com/3Hren/blackhole/pull/184 +# SEP 24th 2020 by B. Hajgato (UGent) +diff -ru sailfish-0.10.1.orig/include/spdlog/details/format.cc sailfish-0.10.1/include/spdlog/details/format.cc +--- sailfish-0.10.1.orig/include/spdlog/details/format.cc 2016-06-15 19:46:33.000000000 +0200 ++++ sailfish-0.10.1/include/spdlog/details/format.cc 2020-09-24 18:19:38.056114573 +0200 +@@ -480,23 +480,23 @@ + typedef typename BasicWriter::CharPtr CharPtr; + Char fill = internal::CharTraits::cast(spec_.fill()); + CharPtr out = CharPtr(); +- const unsigned CHAR_WIDTH = 1; +- if (spec_.width_ > CHAR_WIDTH) { ++ const unsigned CHAR_WIDTH_NOCLASH = 1; ++ if (spec_.width_ > CHAR_WIDTH_NOCLASH) { + out = writer_.grow_buffer(spec_.width_); + if (spec_.align_ == ALIGN_RIGHT) { +- std::fill_n(out, spec_.width_ - CHAR_WIDTH, fill); +- out += spec_.width_ - CHAR_WIDTH; ++ std::fill_n(out, spec_.width_ - CHAR_WIDTH_NOCLASH, fill); ++ out += spec_.width_ - CHAR_WIDTH_NOCLASH; + } + else if (spec_.align_ == ALIGN_CENTER) { + out = writer_.fill_padding(out, spec_.width_, +- internal::check(CHAR_WIDTH), fill); ++ internal::check(CHAR_WIDTH_NOCLASH), fill); + } + else { +- std::fill_n(out + CHAR_WIDTH, spec_.width_ - CHAR_WIDTH, fill); ++ std::fill_n(out + CHAR_WIDTH_NOCLASH, spec_.width_ - CHAR_WIDTH_NOCLASH, fill); + } + } + else { +- out = writer_.grow_buffer(CHAR_WIDTH); ++ out = writer_.grow_buffer(CHAR_WIDTH_NOCLASH); + } + *out = internal::CharTraits::cast(value); + } +@@ -1419,4 +1419,4 @@ + + #ifdef _MSC_VER + # pragma warning(pop) +-#endif +\ No newline at end of file ++#endif From fc40e382bb298917fe98cb26e2f590a80b946479 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 24 Sep 2020 19:11:24 +0200 Subject: [PATCH 273/698] fix installation of FuSeq v1.1.2 on RHEL8 --- .../f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb | 6 ++- .../f/FuSeq/FuSeq-1.1.2_RHEL8.patch | 52 +++++++++++++++++++ 2 files changed, 57 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2_RHEL8.patch diff --git a/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb index 2f064bc71dc..a0bf8eaabb2 100644 --- a/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb +++ b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2-gompi-2019b.eb @@ -21,11 +21,15 @@ sources = [ 'filename': 'Sailfish-0.10.0.tar.gz', }, ] -patches = [('FuSeq-%(version)s_skip-included-Jellyfish.patch', '..')] +patches = [ + ('FuSeq-%(version)s_skip-included-Jellyfish.patch', '..'), + ('%(name)s-%(version)s_RHEL8.patch', '..'), +] checksums = [ 'c08ad145c2e7ba24738cc779502d82063d17a860c5b8dae609e416a60bc0992a', # FuSeq-1.1.2.tar.gz 'dbed3d48c100cf2b97f08ef37bc66ca1fa63a1d70713fa47d0b4fe15b7062ac0', # Sailfish-0.10.0.tar.gz '70991d30526a4818970b47bfb2d30f3e57b1b3c9221c721c20e88ee196bec683', # FuSeq-1.1.2_skip-included-Jellyfish.patch + 'd139f1b8a17fe40784d8df38e340b8f2e100ed2bffd2017c24b6016af618751e', # FuSeq-1.1.2_RHEL8.patch ] builddependencies = [('CMake', '3.15.3')] diff --git a/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2_RHEL8.patch b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2_RHEL8.patch new file mode 100644 index 00000000000..5b71a86f27a --- /dev/null +++ b/easybuild/easyconfigs/f/FuSeq/FuSeq-1.1.2_RHEL8.patch @@ -0,0 +1,52 @@ +# Fix CHAR_WIDTH glibc clash +# see: https://github.com/Cantera/cantera/issues/369#issuecomment-254090244 +# https://github.com/gabime/spdlog/issues/300 and https://github.com/3Hren/blackhole/pull/184 +# SEP 24th 2020 by B. Hajgato (UGent) +diff -ru sailfish-0.10.0.orig/include/spdlog/details/format.h sailfish-0.10.0/include/spdlog/details/format.h +--- sailfish-0.10.0.orig/include/spdlog/details/format.h 2016-04-14 03:24:40.000000000 +0200 ++++ sailfish-0.10.0/include/spdlog/details/format.h 2020-09-24 17:26:19.195521057 +0200 +@@ -2053,29 +2053,29 @@ + typedef typename BasicWriter::CharPtr CharPtr; + Char fill = internal::CharTraits::cast(spec_.fill()); + CharPtr out = CharPtr(); +- const unsigned CHAR_WIDTH = 1; +- if (spec_.width_ > CHAR_WIDTH) ++ const unsigned CHAR_WIDTH_NOCLASH = 1; ++ if (spec_.width_ > CHAR_WIDTH_NOCLASH) + { + out = writer_.grow_buffer(spec_.width_); + if (spec_.align_ == ALIGN_RIGHT) + { +- std::uninitialized_fill_n(out, spec_.width_ - CHAR_WIDTH, fill); +- out += spec_.width_ - CHAR_WIDTH; ++ std::uninitialized_fill_n(out, spec_.width_ - CHAR_WIDTH_NOCLASH, fill); ++ out += spec_.width_ - CHAR_WIDTH_NOCLASH; + } + else if (spec_.align_ == ALIGN_CENTER) + { + out = writer_.fill_padding(out, spec_.width_, +- internal::check(CHAR_WIDTH), fill); ++ internal::check(CHAR_WIDTH_NOCLASH), fill); + } + else + { +- std::uninitialized_fill_n(out + CHAR_WIDTH, +- spec_.width_ - CHAR_WIDTH, fill); ++ std::uninitialized_fill_n(out + CHAR_WIDTH_NOCLASH, ++ spec_.width_ - CHAR_WIDTH_NOCLASH, fill); + } + } + else + { +- out = writer_.grow_buffer(CHAR_WIDTH); ++ out = writer_.grow_buffer(CHAR_WIDTH_NOCLASH); + } + *out = internal::CharTraits::cast(value); + } +@@ -4358,4 +4358,4 @@ + # include "format.cc" + #endif + +-#endif // FMT_FORMAT_H_ +\ No newline at end of file ++#endif // FMT_FORMAT_H_ From cb1fefa297f1940065446147acda43c56ac45ef5 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Thu, 24 Sep 2020 20:02:45 +0200 Subject: [PATCH 274/698] adding easyconfigs: CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb --- .../CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..de7125a9591 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2020a-Python-3.8.2.eb @@ -0,0 +1,38 @@ +name = 'CGAL' +version = '4.14.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Eigen', '3.3.7'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.8.2'), + ('Boost', '1.72.0'), + ('MPFR', '4.0.2'), + ('GMP', '6.2.0'), + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), + ('Qt5', '5.14.1'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' From 001284f2388b1aa5ba24933845b0da2695aad18b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 25 Sep 2020 02:05:31 +0200 Subject: [PATCH 275/698] disable test on Fortran ERI --- .../Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb | 7 +++- .../Libint/Libint-2.6.0_remove-test-eri.patch | 36 +++++++++++++++++++ 2 files changed, 42 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/l/Libint/Libint-2.6.0_remove-test-eri.patch diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb index 87f59a50358..103d1e997b8 100644 --- a/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0-gompi-2020a-lmax-6-cp2k.eb @@ -13,11 +13,16 @@ toolchainopts = {'pic': True, 'cstd': 'c++11'} source_urls = ['https://github.com/evaleev/libint/archive'] sources = ['v%(version)s.tar.gz'] -patches = ['Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch'] +patches = [ + 'Libint-%(version)s_fix-LIBINT2-MAX-AM-default1.patch', + 'Libint-2.6.0_remove-test-eri.patch', +] checksums = [ '4ae47e8f0b5632c3d2a956469a7920896708e9f0e396ec10071b8181e4c8d9fa', # v2.6.0.tar.gz # Libint-2.6.0_fix-LIBINT2-MAX-AM-default1.patch 'e5445c89639d113be7726c2bc1164d2f6ea75e76abbb1c94acd55c508693d5ab', + # Libint-2.6.0_remove-test-eri.patch + 'e47868901250078adeb35b80ab866ba8063ad9756881d1b557cb925334df653b', ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/Libint/Libint-2.6.0_remove-test-eri.patch b/easybuild/easyconfigs/l/Libint/Libint-2.6.0_remove-test-eri.patch new file mode 100644 index 00000000000..e5493dc7965 --- /dev/null +++ b/easybuild/easyconfigs/l/Libint/Libint-2.6.0_remove-test-eri.patch @@ -0,0 +1,36 @@ +Disable Fortran ERI tests as those have very strict error tolerances +See https://github.com/evaleev/libint/issues/188 +author: Alex Domingo (Vrije Universiteit Brussel) +diff -W 152 -Nru libint-2.6.0-orig/export/cmake/CMakeLists.txt.export libint-2.6.0/export/cmake/CMakeLists.txt.export +--- libint-2.6.0-orig/export/cmake/CMakeLists.txt.export 2020-09-24 18:41:19.058876000 +0200 ++++ libint-2.6.0/export/cmake/CMakeLists.txt.export 2020-09-24 18:42:15.545662246 +0200 +@@ -342,7 +342,7 @@ + PROPERTIES FIXTURES_REQUIRED FORTRAN_EXAMPLE_EXEC) + + if (LIBINT_HAS_EIGEN) +- add_executable(fortran_test EXCLUDE_FROM_ALL fortran/test.cc fortran/test-eri.cc) ++ add_executable(fortran_test EXCLUDE_FROM_ALL fortran/test.cc) + target_link_libraries(fortran_test libint_f cxx) + add_test(fortran_test/build "${CMAKE_COMMAND}" --build ${CMAKE_BINARY_DIR} --target fortran_test) + set_tests_properties(fortran_test/build PROPERTIES FIXTURES_SETUP FORTRAN_TEST_EXEC) +diff -W 152 -Nru libint-2.6.0-orig/export/fortran/Makefile libint-2.6.0/export/fortran/Makefile +--- libint-2.6.0-orig/export/fortran/Makefile 2020-09-24 18:41:19.053327000 +0200 ++++ libint-2.6.0/export/fortran/Makefile 2020-09-24 18:41:42.531334000 +0200 +@@ -53,7 +53,7 @@ + endif + endif + +-test: test.o test-eri.o libint_f.o ++test: test.o libint_f.o + $(LTLINK) $(CXX) $(CXXFLAGS) $(LDFLAGS) $(COMPUTE_LIB) $(SYSLIBS) $(FCLIBS) -o $@ $^ + + ifneq ($(HAVE_SYSTEM_BOOST_PREPROCESSOR_VARIADICS),1) +@@ -61,7 +61,7 @@ + $(TOPDIR)/include/libint2/boost/preprocessor.hpp:: $(SRCDIR)/external/boost.tar.gz + gunzip -c $(SRCDIR)/external/boost.tar.gz | tar -xf - -C $(TOPDIR)/include/libint2 + +-test.cc test-eri.cc :: $(TOPDIR)/include/libint2/boost/preprocessor.hpp ++test.cc :: $(TOPDIR)/include/libint2/boost/preprocessor.hpp + + endif + From f545559bfc1c049e4ade189cd66b058ffe440b37 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 7 Sep 2020 16:54:12 +0200 Subject: [PATCH 276/698] Use easybuild installed dependencies --- ...ensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb | 48 +++++++++++------- ...rFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb | 50 ++++++++++++------- 2 files changed, 60 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb index d40a0ab6902..bac4ca407ea 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb @@ -12,15 +12,37 @@ toolchainopts = {'usempi': True, 'pic': True} builddependencies = [ ('Bazel', '2.0.0'), + ('protobuf', '3.10.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), - # For SciPy ('pybind11', '2.4.3', versionsuffix), ] dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('h5py', '2.10.0', versionsuffix), + ('cURL', '7.66.0'), + ('double-conversion', '3.1.4'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '64.2'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('protobuf-python', '3.10.0', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.7'), + ('SWIG', '4.0.1'), + ('zlib', '1.2.11'), + # TF 2.2 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle + ('scipy', '1.4.1', versionsuffix), ] exts_default_options = { @@ -30,18 +52,10 @@ exts_default_options = { use_pip = True exts_list = [ - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), ('Markdown', '3.2.1', { 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], }), ('pyasn1-modules', '0.2.8', { - 'modulename': 'pyasn1_modules', 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], }), ('rsa', '4.0', { @@ -58,20 +72,14 @@ exts_list = [ 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], }), ('requests-oauthlib', '1.3.0', { - 'modulename': 'requests_oauthlib', 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], }), ('google-auth-oauthlib', '0.4.1', { - 'modulename': 'google_auth_oauthlib', 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], }), ('Werkzeug', '1.0.1', { 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], }), - ('protobuf', '3.11.3', { - 'modulename': 'google.protobuf', - 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], - }), ('absl-py', '0.9.0', { 'modulename': 'absl', 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], @@ -116,19 +124,18 @@ exts_list = [ 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], }), ('Keras-Applications', '1.0.8', { - 'modulename': 'keras_applications', 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], }), ('Keras-Preprocessing', '1.1.0', { - 'modulename': 'keras_preprocessing', 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], }), (name, version, { 'patches': [ 'TensorFlow-1.14.0_swig-env.patch', - 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', ], 'source_tmpl': 'v%(version)s.tar.gz', @@ -137,7 +144,10 @@ exts_list = [ 'checksums': [ '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch - '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.1.0_fix-system-jsoncpp.patch + 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', ], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb index a84d2cebb1f..6b6bf862793 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -12,17 +12,39 @@ toolchainopts = {'usempi': True, 'pic': True} builddependencies = [ ('Bazel', '2.0.0'), + ('protobuf', '3.10.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), - # For SciPy ('pybind11', '2.4.3', versionsuffix), ] dependencies = [ + ('cuDNN', '7.6.4.38'), + ('NCCL', '2.4.8'), ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), ('h5py', '2.10.0', versionsuffix), - ('cuDNN', '7.6.4.38'), - ('NCCL', '2.4.8'), + ('cURL', '7.66.0'), + ('double-conversion', '3.1.4'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '64.2'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.3'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.29.0'), + ('PCRE', '8.43'), + ('protobuf-python', '3.10.0', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.7'), + ('SWIG', '4.0.1'), + ('zlib', '1.2.11'), + # TF 2.2 requires SciPy 1.4.1 due to potential crashes with other versions + # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d + # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle + ('scipy', '1.4.1', versionsuffix), ] exts_default_options = { @@ -32,18 +54,10 @@ exts_default_options = { use_pip = True exts_list = [ - ('scipy', '1.4.1', { - 'patches': ['scipy-1.4.1-fix-pthread.patch'], - 'checksums': [ - 'dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59', # scipy-1.4.1.tar.gz - '4e2162a93caddce63a1aa2dfb6c181774a4f6615950e1d60c54bb4308fee3bb3', # scipy-1.4.1-fix-pthread.patch - ], - }), ('Markdown', '3.2.1', { 'checksums': ['90fee683eeabe1a92e149f7ba74e5ccdc81cd397bd6c516d93a8da0ef90b6902'], }), ('pyasn1-modules', '0.2.8', { - 'modulename': 'pyasn1_modules', 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], }), ('rsa', '4.0', { @@ -60,20 +74,14 @@ exts_list = [ 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], }), ('requests-oauthlib', '1.3.0', { - 'modulename': 'requests_oauthlib', 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], }), ('google-auth-oauthlib', '0.4.1', { - 'modulename': 'google_auth_oauthlib', 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], }), ('Werkzeug', '1.0.1', { 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], }), - ('protobuf', '3.11.3', { - 'modulename': 'google.protobuf', - 'checksums': ['c77c974d1dadf246d789f6dad1c24426137c9091e930dbf50e0a29c1fcf00b1f'], - }), ('absl-py', '0.9.0', { 'modulename': 'absl', 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], @@ -118,18 +126,18 @@ exts_list = [ 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], }), ('Keras-Applications', '1.0.8', { - 'modulename': 'keras_applications', 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], }), ('Keras-Preprocessing', '1.1.0', { - 'modulename': 'keras_preprocessing', 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], }), (name, version, { 'patches': [ 'TensorFlow-1.14.0_swig-env.patch', + 'TensorFlow-2.1.0_fix-system-jsoncpp.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', 'TensorFlow-2.1.0_fix-cuda-build.patch', 'TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch', ], @@ -139,6 +147,10 @@ exts_list = [ 'checksums': [ '69cd836f87b8c53506c4f706f655d423270f5a563b76dc1cfa60fbc3184185a3', # v2.2.0.tar.gz 'b83cce6b91c7d19b8b320158ffc50fb4b2de454f5ac191c58d704234a1bf9005', # TensorFlow-1.14.0_swig-env.patch + # TensorFlow-2.1.0_fix-system-jsoncpp.patch + 'd0c8ca54a9e2c232908016e08b982dbb63765de3472253cba5ae38d823d5f156', + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch # TensorFlow-2.1.0_fix-collective-all-reduce-strategy.patch '093f4dd3ec372a82d50dffe32eea6821025cd1c406911a746c4367a40bc38486', From f523fa3e418c03a4b10c219ea8b83e90b94c2da0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2020 09:59:40 +0200 Subject: [PATCH 277/698] adding easyconfigs: makeinfo-6.7-GCCcore-9.3.0.eb, makeinfo-6.7-GCCcore-8.3.0.eb --- .../m/makeinfo/makeinfo-6.7-GCCcore-8.3.0.eb | 24 +++++++++++++++++++ .../m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0.eb create mode 100644 easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0.eb new file mode 100644 index 00000000000..4a617bc8290 --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-8.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.32')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..99e1d30eb2c --- /dev/null +++ b/easybuild/easyconfigs/m/makeinfo/makeinfo-6.7-GCCcore-9.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'makeinfo' +version = '6.7' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """makeinfo is part of the Texinfo project, the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://ftpmirror.gnu.org/gnu/texinfo'] +sources = ['texinfo-%(version)s.tar.xz'] +checksums = ['988403c1542d15ad044600b909997ba3079b10e03224c61188117f3676b02caa'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ['bin/makeinfo'], + 'dirs': ['share'], +} + +sanity_check_commands = ["makeinfo --help"] + +moduleclass = 'devel' From b6cdc89d98e85e4aa4428dc9b28f985d383c2aa5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2020 10:00:28 +0200 Subject: [PATCH 278/698] use makeinfo build dep for groff rather than texinfo (which requires texlive OS dep) --- easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb index 35b9ec58681..5d17ecce652 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.22.4-GCCcore-9.3.0.eb @@ -15,7 +15,7 @@ checksums = ['e78e7b4cb7dec310849004fa88847c44701e8d133b5d4c13057d876c1bad0293'] builddependencies = [ ('binutils', '2.34'), - ('texinfo', '6.7'), # provides makeinfo + ('makeinfo', '6.7'), ] sanity_check_paths = { From 329f810b418bc7d4231432776b17686b661e46aa Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Sep 2020 10:21:04 +0200 Subject: [PATCH 279/698] Remove kerase-applications dependency This is no longer required as it is contained in TF since 2.2: https://github.com/tensorflow/tensorflow/commit/23c3bdaacdc27bb82dfd1772efefad687508923a --- .../t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb | 4 ---- .../TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb | 4 ---- 2 files changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb index bac4ca407ea..a2dd8ad577c 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-foss-2019b-Python-3.7.4.eb @@ -123,10 +123,6 @@ exts_list = [ ('wrapt', '1.12.1', { 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], }), - ('Keras-Applications', '1.0.8', { - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], - }), ('Keras-Preprocessing', '1.1.0', { 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb index 6b6bf862793..3c031f53523 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.2.0-fosscuda-2019b-Python-3.7.4.eb @@ -125,10 +125,6 @@ exts_list = [ ('wrapt', '1.12.1', { 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], }), - ('Keras-Applications', '1.0.8', { - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], - }), ('Keras-Preprocessing', '1.1.0', { 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', 'checksums': ['5a8debe01d840de93d49e05ccf1c9b81ae30e210d34dacbcc47aeb3049b528e5'], From 972e743988bda6eac6a5f262c501316149653e1a Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 11:05:25 +0200 Subject: [PATCH 280/698] adding easyconfigs: Xerces-C++-3.2.3-GCCcore-9.3.0.eb --- .../Xerces-C++-3.2.3-GCCcore-9.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2775ce66948 --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.3-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.3' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['fb96fc49b1fb892d1e64e53a6ada8accf6f0e6d30ce0937956ec68d39bd72c7e'] + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +dependencies = [ + ('cURL', '7.69.1'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.so'], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From 3222dd3cc78bae5a0c9441a9eabc94be4a4a689f Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Fri, 25 Sep 2020 11:10:46 +0200 Subject: [PATCH 281/698] Relly fix make 4.2.1 on RHEL 8 --- .../m/make/make-4.2.1-GCCcore-8.3.0.eb | 2 +- .../easyconfigs/m/make/make-4.2.1_RHEL8.patch | 28 +++++++++---------- 2 files changed, 14 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb index d8927406731..68da3f7268f 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/make/make-4.2.1-GCCcore-8.3.0.eb @@ -24,7 +24,7 @@ sources = [SOURCE_TAR_BZ2] patches = ['%(name)s-%(version)s_RHEL8.patch'] checksums = [ 'd6e262bf3601b42d2b1e4ef8310029e1dcf20083c5446b4b7aa67081fdffc589', # make-4.2.1.tar.bz2 - 'f564f16443979c8398ed325b5d3cd2d6683ca5400433fc67fa29492d2cc4c9ea', # make-4.2.1_RHEL8.patch + 'ca9daea8cfdb7de55c5a973e283a5aca35fb11d9eb37cd3bd25f95557f2e6479', # make-4.2.1_RHEL8.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch b/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch index f84b2f2560a..704f346feed 100644 --- a/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch +++ b/easybuild/easyconfigs/m/make/make-4.2.1_RHEL8.patch @@ -1,15 +1,13 @@ -# http://gnu-make.2324884.n4.nabble.com/undefined-reference-to-alloca-td18308.html -# SEP 16th 2020 by B. Hajgato (UGent) -diff --git a/configure.ac.orig b/configure.ac -index 64ec870..870a70a 100644 ---- a/configure.ac.orig -+++ b/configure.ac -@@ -402,7 +402,7 @@ AC_CACHE_CHECK([if system libc has GNU glob], [make_cv_sys_gnu_glob], - #define GLOB_INTERFACE_VERSION 1 - #if !defined _LIBC && defined __GNU_LIBRARY__ && __GNU_LIBRARY__ > 1 - # include --# if _GNU_GLOB_INTERFACE_VERSION == GLOB_INTERFACE_VERSION -+# if _GNU_GLOB_INTERFACE_VERSION >= GLOB_INTERFACE_VERSION - gnu glob - # endif - #endif], +https://github.com/osresearch/heads/issues/352 +https://github.com/osresearch/heads/blob/make-4.2.1/patches/make-4.2.1.patch +--- clean/make-4.2/glob/glob.c 2013-10-20 17:14:38.000000000 +0000 ++++ make-4.2/glob/glob.c 2018-09-18 10:16:03.860886356 +0000 +@@ -208,7 +208,7 @@ + #endif /* __GNU_LIBRARY__ || __DJGPP__ */ + + +-#if !defined __alloca && !defined __GNU_LIBRARY__ ++#if !defined __alloca && defined __GNU_LIBRARY__ + + # ifdef __GNUC__ + # undef alloca From 30f755fed09b5634329acb92259283a5ba4adeef Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Tue, 22 Sep 2020 17:04:01 +0200 Subject: [PATCH 282/698] adding easyconfigs: libobjcryst-2017.2.2-intel-2020a.eb, pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb --- .../libobjcryst-2017.2.3-intel-2020a.eb | 33 +++++++++++++++++++ ...ibobjcryst-2017.2.3_sconscript_local.patch | 23 +++++++++++++ ...st-2.1.0.post2-intel-2020a-Python-3.8.2.eb | 30 +++++++++++++++++ 3 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb create mode 100644 easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch create mode 100644 easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb new file mode 100644 index 00000000000..38a784b00dc --- /dev/null +++ b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3-intel-2020a.eb @@ -0,0 +1,33 @@ +easyblock = 'SCons' + +name = 'libobjcryst' +version = '2017.2.3' + +homepage = 'https://github.com/diffpy/libobjcryst' +description = "ObjCryst++ is Object-Oriented Crystallographic Library for C++" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/diffpy/libobjcryst/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['libobjcryst-2017.2.3_sconscript_local.patch'] +checksums = [ + 'd48de43a15c3227ac39422831c31285c695f8ec560b31420f0f31356de1a3bb0', # v2017.2.3.tar.gz + 'e86c7c1d9b9b89535757e21216307acf0d102fc72543f155a02bf75e6fba7b25', # libobjcryst-2017.2.3_sconscript_local.patch +] + +builddependencies = [ + ('SCons', '3.1.2'), +] +dependencies = [ + ('Boost', '1.72.0'), +] + +prefix_arg = 'prefix=' + +sanity_check_paths = { + 'files': ['lib/libObjCryst.%s' % SHLIB_EXT], + 'dirs': ['include/ObjCryst'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch new file mode 100644 index 00000000000..51bcfc5b25c --- /dev/null +++ b/easybuild/easyconfigs/l/libobjcryst/libobjcryst-2017.2.3_sconscript_local.patch @@ -0,0 +1,23 @@ +Add SConscript.local to pass through EB environment to the compiler + +author: Jakub Zárybnický (Inuits) +--- libobjcryst-2017.2.3/sconscript.local 1970-01-01 01:00:00.000000000 +0100 ++++ libobjcryst-2017.2.3/sconscript.local 2020-09-22 15:33:59.098143895 +0200 +@@ -0,0 +1,10 @@ ++Import('env') ++ ++import os ++ ++env.Replace(CC=os.environ['CC']) ++env.Replace(CXX=os.environ['CXX']) ++env.Replace(CFLAGS=os.environ['CFLAGS']) ++env.Replace(CPPFLAGS=os.environ['CPPFLAGS']) ++env.Replace(CXXFLAGS=os.environ['CXXFLAGS']) ++env.Replace(LDFLAGS=os.environ['LDFLAGS']) + +--- libobjcryst-2017.2.3/SConstruct 1970-01-01 01:00:00.000000000 +0100 ++++ libobjcryst-2017.2.3/SConstruct 2020-09-22 15:33:59.098143895 +0200 +@@ -1,1 +1,1 @@ +- MACOSX_DEPLOYMENT_TARGET ++ MACOSX_DEPLOYMENT_TARGET INTEL_LICENSE_FILE + diff --git a/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1ac86631f4f --- /dev/null +++ b/easybuild/easyconfigs/p/pyobjcryst/pyobjcryst-2.1.0.post2-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'pyobjcryst' +version = '2.1.0.post2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/diffpy/pyobjcryst' +description = "Python bindings to ObjCryst++, the Object-Oriented Crystallographic Library." + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['2ee797cf4d0ba90a7d144110b0f3295ee7fa73462c648297100bfd5eb467bb6d'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy + ('Boost.Python', '1.72.0'), + ('libobjcryst', '2017.2.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["python -m pyobjcryst.tests.run"] + +sanity_pip_check = True + +moduleclass = 'chem' From 55e2a7b269b78cc6abc42ecf9075e49c500d71fd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Sep 2020 13:31:11 +0200 Subject: [PATCH 283/698] Update TensorFlow 2.3.1 and it's dependencies Contains security fixes Removes the superflous keras-applications package and scipy package --- ...da-2019b-TensorFlow-2.3.1-Python-3.7.4.eb} | 2 +- ...nsorFlow-2.3.1-foss-2019b-Python-3.7.4.eb} | 28 +++++++------------ ...Flow-2.3.1-fosscuda-2019b-Python-3.7.4.eb} | 28 +++++++------------ 3 files changed, 21 insertions(+), 37 deletions(-) rename easybuild/easyconfigs/h/Horovod/{Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb => Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb} (97%) rename easybuild/easyconfigs/t/TensorFlow/{TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb => TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb} (85%) rename easybuild/easyconfigs/t/TensorFlow/{TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb => TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb} (85%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb similarity index 97% rename from easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb rename to easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb index f08bb13009f..93a050893a4 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' name = 'Horovod' version = '0.20.0' -local_tf_version = '2.3.0' +local_tf_version = '2.3.1' versionsuffix = '-TensorFlow-%s-Python-%%(pyver)s' % local_tf_version homepage = 'https://github.com/uber/horovod' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb similarity index 85% rename from easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb index 7127b094f76..32356f9ba9d 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2019b-Python-3.7.4.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'TensorFlow' -version = '2.3.0' +version = '2.3.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.tensorflow.org/' @@ -38,10 +38,6 @@ dependencies = [ ('snappy', '1.1.7'), ('SWIG', '4.0.1'), ('zlib', '1.2.11'), - # TF 2.3 requires SciPy 1.4.1 due to potential crashes with other versions - # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d - # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle - ('scipy', '1.4.1', versionsuffix), ] exts_default_options = { @@ -65,9 +61,9 @@ exts_list = [ ('cachetools', '4.1.1', { 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], }), - ('google-auth', '1.20.0', { + ('google-auth', '1.21.3', { 'modulename': 'google.auth', - 'checksums': ['c6e9735a2ee829a75b546702e460489db5cc35567a27fabd70b7c459f11efd58'], + 'checksums': ['31941bf019fb242c04d0de32845da10180788bfddb0de87d78c4bdf55555dda1'], }), ('oauthlib', '3.1.0', { 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], @@ -81,23 +77,23 @@ exts_list = [ ('Werkzeug', '1.0.1', { 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], }), - ('absl-py', '0.9.0', { + ('absl-py', '0.10.0', { 'modulename': 'absl', - 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], }), ('astunparse', '1.6.3', { 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], }), - ('grpcio', '1.30.0', { + ('grpcio', '1.32.0', { 'modulename': 'grpc', - 'checksums': ['e8f2f5d16e0164c415f1b31a8d9a81f2e4645a43d1b261375d6bab7b0adf511f'], + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], }), ('tensorboard-plugin-wit', '1.7.0', { 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], }), - ('tensorboard', version, { + ('tensorboard', '2.3.0', { 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], @@ -109,7 +105,7 @@ exts_list = [ ('termcolor', '1.1.0', { 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), - ('tensorflow-estimator', version, { + ('tensorflow-estimator', '2.3.0', { 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], @@ -117,10 +113,6 @@ exts_list = [ ('astor', '0.8.0', { 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], }), - ('Keras-Applications', '1.0.8', { - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], - }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), @@ -150,7 +142,7 @@ exts_list = [ 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'checksums': [ - '2595a5c401521f20a2734c4e5d54120996f8391f00bb62a57267d930bce95350', # v2.3.0.tar.gz + 'ee534dd31a811f7a759453567257d1e643f216d8d55a25c32d2fbfff8153a1ac', # v2.3.1.tar.gz '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch # TensorFlow-2.1.0_fix-system-nasm.patch '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb similarity index 85% rename from easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb index 489d00b8d5e..980cc1735f3 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'TensorFlow' -version = '2.3.0' +version = '2.3.1' versionsuffix = '-Python-%(pyver)s' homepage = 'https://www.tensorflow.org/' @@ -40,10 +40,6 @@ dependencies = [ ('snappy', '1.1.7'), ('SWIG', '4.0.1'), ('zlib', '1.2.11'), - # TF 2.3 requires SciPy 1.4.1 due to potential crashes with other versions - # See https://github.com/tensorflow/tensorflow/commit/54daf3c5700897a6062313983933ca28e92c410d - # Add at bottom so it will be loaded after any dependency loading the SciPy-Bundle - ('scipy', '1.4.1', versionsuffix), ] exts_default_options = { @@ -67,9 +63,9 @@ exts_list = [ ('cachetools', '4.1.1', { 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], }), - ('google-auth', '1.20.0', { + ('google-auth', '1.21.3', { 'modulename': 'google.auth', - 'checksums': ['c6e9735a2ee829a75b546702e460489db5cc35567a27fabd70b7c459f11efd58'], + 'checksums': ['31941bf019fb242c04d0de32845da10180788bfddb0de87d78c4bdf55555dda1'], }), ('oauthlib', '3.1.0', { 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], @@ -83,23 +79,23 @@ exts_list = [ ('Werkzeug', '1.0.1', { 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], }), - ('absl-py', '0.9.0', { + ('absl-py', '0.10.0', { 'modulename': 'absl', - 'checksums': ['75e737d6ce7723d9ff9b7aa1ba3233c34be62ef18d5859e706b8fdc828989830'], + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], }), ('astunparse', '1.6.3', { 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], }), - ('grpcio', '1.30.0', { + ('grpcio', '1.32.0', { 'modulename': 'grpc', - 'checksums': ['e8f2f5d16e0164c415f1b31a8d9a81f2e4645a43d1b261375d6bab7b0adf511f'], + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], }), ('tensorboard-plugin-wit', '1.7.0', { 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], }), - ('tensorboard', version, { + ('tensorboard', '2.3.0', { 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', 'unpack_sources': False, 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], @@ -111,7 +107,7 @@ exts_list = [ ('termcolor', '1.1.0', { 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], }), - ('tensorflow-estimator', version, { + ('tensorflow-estimator', '2.3.0', { 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', 'unpack_sources': False, 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], @@ -119,10 +115,6 @@ exts_list = [ ('astor', '0.8.0', { 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], }), - ('Keras-Applications', '1.0.8', { - 'source_tmpl': 'Keras_Applications-%(version)s.tar.gz', - 'checksums': ['5579f9a12bcde9748f4a12233925a59b93b73ae6947409ff34aa2ba258189fe5'], - }), ('gast', '0.3.3', { 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), @@ -152,7 +144,7 @@ exts_list = [ 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'checksums': [ - '2595a5c401521f20a2734c4e5d54120996f8391f00bb62a57267d930bce95350', # v2.3.0.tar.gz + 'ee534dd31a811f7a759453567257d1e643f216d8d55a25c32d2fbfff8153a1ac', # v2.3.1.tar.gz '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch # TensorFlow-2.1.0_fix-system-nasm.patch '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', From 7b90db195cabee305d5a1d7e4ff40831ede37f2c Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 14:14:00 +0200 Subject: [PATCH 284/698] adding easyconfigs: ACTC-1.1-GCCcore-9.3.0.eb --- .../a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4733b10b8f9 --- /dev/null +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'ACTC' +version = '1.1' + +homepage = 'https://sourceforge.net/projects/actc' +description = "ACTC converts independent triangles into triangle strips or fans." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a1303291629b9de6008c3c9d7b020a4b854802408fb3f8222ec492808c8b44d'] + +builddependencies = [('binutils', '2.34')] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS"' + +files_to_copy = [ + (['tcsample', 'tctest', 'tctest2'], 'bin'), + (['tc.h'], 'include/ac'), + (['libactc.a'], 'lib'), + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README', +] + +sanity_check_paths = { + 'files': ['bin/tctest', 'bin/tctest2', 'bin/tcsample', 'include/ac/tc.h', 'lib/libactc.a', + 'COPYRIGHT', 'manual.html', 'prims.gif', 'README'], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/ac'} + +moduleclass = 'lib' From ea1b9418b36c8322e9e5fa2d43f870f602cdd8cd Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 14:31:47 +0200 Subject: [PATCH 285/698] adding easyconfigs: Harminv-1.4.1-intel-2020a.eb --- .../h/Harminv/Harminv-1.4.1-intel-2020a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb new file mode 100644 index 00000000000..cb6171ccd52 --- /dev/null +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb @@ -0,0 +1,21 @@ +easyblock = 'ConfigureMake' + +name = 'Harminv' +version = '1.4.1' + +homepage = 'https://github.com/stevengj/harminv' +description = """Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - + given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially + decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those + sinusoids.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'opt': True, 'unroll': True, 'optarch': True, 'pic': True, 'cstd': 'c99'} + +source_urls = ['https://github.com/stevengj/harminv/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670'] + +configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" + +moduleclass = 'math' From 8f3f34bff70e3220e97be7611fcf77f2a1835ec7 Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 14:58:16 +0200 Subject: [PATCH 286/698] adding easyconfigs: Guile-2.2.4-GCCcore-9.3.0.eb --- .../g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..0e81c676a16 --- /dev/null +++ b/easybuild/easyconfigs/g/Guile/Guile-2.2.4-GCCcore-9.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'Guile' +version = '2.2.4' + +homepage = 'https://www.gnu.org/software/guile/' + +description = """ + Guile is a programming language, designed to help programmers create flexible + applications that can be extended by users or other programmers with plug-ins, + modules, or scripts. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33b904c0bf4e48e156f3fb1d0e6b0392033bd610c6c9d9a0410c6e0ea96a3e5c'] + +builddependencies = [ + ('Autotools', '20180311'), + ('binutils', '2.34'), +] + +dependencies = [ + ('gc', '7.6.12'), + ('GMP', '6.2.0'), + ('libffi', '3.3'), + ('libunistring', '0.9.10'), +] + +sanity_check_paths = { + 'files': ['bin/guild', 'bin/guile', 'bin/guile-config', + 'bin/guile-snarf', 'bin/guile-tools', + 'include/guile/%(version_major_minor)s/libguile.h', + 'lib/libguile-%(version_major_minor)s.a', + 'lib/libguile-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/guile/%(version_major_minor)s/libguile', + 'lib/guile/%(version_major_minor)s/ccache'], +} + +moduleclass = 'lang' From 6f876f9eef75906603a7ebb401395158eb08230b Mon Sep 17 00:00:00 2001 From: Emmanuel Kieffer Date: Fri, 25 Sep 2020 15:05:06 +0200 Subject: [PATCH 287/698] Added checks --- easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb index cb6171ccd52..5f14725d0e7 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb @@ -18,4 +18,9 @@ checksums = ['e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670'] configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib'] +} + moduleclass = 'math' From 2159380e5e57d7759be41108ce6759b71cf825f2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Sep 2020 18:22:11 +0200 Subject: [PATCH 288/698] Avoid downloading PSIMD --- .../p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb | 2 ++ .../p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb index f49b36c2106..3820e6b523d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-foss-2019b-Python-3.7.4.eb @@ -196,6 +196,7 @@ patches = [ '%(name)s-1.2.0_fix-findAVX.patch', '%(name)s-1.2.0_disable-tests-ppc64le.patch', '%(name)s-%(version)s_fix-missing-sleef_h.patch', + '%(name)s-1.4.0_fix-missing-source-dir.patch', ] checksums = [ 'ab6feb5044f7d36f6e93dce4668d8c593e89d34aca7023fd99a38d215ca9dfc0', # v1.3.1.tar.gz @@ -233,6 +234,7 @@ checksums = [ '001c9bf604aebe4b39ccad15332a71130b07b780c539ceca84d6c64cd6fc8a68', # PyTorch-1.2.0_fix-findAVX.patch 'c4183bcb29a8bcbadea0341e93a3a32afdf860aa31331b768e787d899183da92', # PyTorch-1.2.0_disable-tests-ppc64le.patch '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch + '797987fb9c9bf9f1d75a1be878ddf9f418f9524006b0985ca8e6d65d4e2b6998', # PyTorch-1.4.0_fix-missing-source-dir.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb index 2ab84d22597..4f2478fb7b3 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.3.1-fosscuda-2019b-Python-3.7.4.eb @@ -196,6 +196,7 @@ patches = [ '%(name)s-1.2.0_fix-findAVX.patch', '%(name)s-1.2.0_disable-tests-ppc64le.patch', '%(name)s-%(version)s_fix-missing-sleef_h.patch', + '%(name)s-1.4.0_fix-missing-source-dir.patch', ] checksums = [ 'ab6feb5044f7d36f6e93dce4668d8c593e89d34aca7023fd99a38d215ca9dfc0', # v1.3.1.tar.gz @@ -233,6 +234,7 @@ checksums = [ '001c9bf604aebe4b39ccad15332a71130b07b780c539ceca84d6c64cd6fc8a68', # PyTorch-1.2.0_fix-findAVX.patch 'c4183bcb29a8bcbadea0341e93a3a32afdf860aa31331b768e787d899183da92', # PyTorch-1.2.0_disable-tests-ppc64le.patch '1337647ff64a1208d1e401fc84052d0bc6174b133cec2f3521319cb593f524fa', # PyTorch-1.3.1_fix-missing-sleef_h.patch + '797987fb9c9bf9f1d75a1be878ddf9f418f9524006b0985ca8e6d65d4e2b6998', # PyTorch-1.4.0_fix-missing-source-dir.patch ] builddependencies = [ From 7719bc4644c695f5c32638945bffa2a571263481 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Sep 2020 22:58:49 +0200 Subject: [PATCH 289/698] fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep --- .../q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb | 4 +- .../q/Qt5/Qt5-5.14.1_fix-OF-Gentoo.patch | 81 +++++++++++++++++++ 2 files changed, 84 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.14.1_fix-OF-Gentoo.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb index f1be03a77df..113993ef34f 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1-GCCcore-9.3.0.eb @@ -19,12 +19,14 @@ patches = [ 'Qt5-5.13.1_fix-avx2.patch', 'Qt5-5.13.1_fix-qmake-libdir.patch', 'Qt5-5.14.1_fix-mantissatable.patch', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', ] checksums = [ '6f17f488f512b39c2feb57d83a5e0a13dcef32999bea2e2a8f832f54a29badb8', # qt-everywhere-src-5.14.1.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch '11db32da45a003963e6abfd8ab7161d7e4ec3a8d668b54d18a3f6a713fd813a2', # Qt5-5.14.1_fix-mantissatable.patch + '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa', # Qt5-5.14.1_fix-OF-Gentoo.patch ] builddependencies = [ @@ -35,7 +37,7 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.10.0'), - ('Python', '3.8.2'), + ('Python', '2.7.18'), ('re2c', '1.3') ] diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1_fix-OF-Gentoo.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1_fix-OF-Gentoo.patch new file mode 100644 index 00000000000..1b3cd6b9637 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.14.1_fix-OF-Gentoo.patch @@ -0,0 +1,81 @@ +fix compilation on top of zlib provided by Gentoo, +where OF macro has been renamed to _Z_OF +see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +author: Kenneth Hoste (HPC-UGent) +diff -ru qt-everywhere-src-5.14.1.orig/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h qt-everywhere-src-5.14.1/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h 2020-01-15 17:09:24.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qt3d/src/3rdparty/assimp/contrib/unzip/ioapi.h 2020-09-25 18:30:03.146291932 -0000 +@@ -35,6 +35,15 @@ + extern "C" { + #endif + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); + typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2019-03-10 11:05:27.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h 2020-09-25 18:30:16.136640746 -0000 +@@ -35,6 +35,15 @@ + extern "C" { + #endif + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); + typedef uLong (ZCALLBACK *write_file_func) OF((voidpf opaque, voidpf stream, const void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h 2019-03-10 11:05:27.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtquick3d/src/3rdparty/assimp/src/contrib/zlib/contrib/minizip/ioapi.h 2020-09-25 18:30:23.096828085 -0000 +@@ -131,6 +131,15 @@ + + + ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif ++ + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); +diff -ru qt-everywhere-src-5.14.1.orig/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h qt-everywhere-src-5.14.1/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +--- qt-everywhere-src-5.14.1.orig/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h 2020-01-20 10:37:42.000000000 -0000 ++++ qt-everywhere-src-5.14.1/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h 2020-09-25 18:29:45.635820801 -0000 +@@ -129,8 +129,14 @@ + #endif + #endif + +- +- ++// if OF macro is not defined by _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + typedef uLong (ZCALLBACK *read_file_func) OF((voidpf opaque, voidpf stream, void* buf, uLong size)); From 16c018f51f3bc106718552955715e1c8b2166900 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2020 11:59:12 +0200 Subject: [PATCH 290/698] stick to Python 2 as build dep for Qt5 5.13.1 --- easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb index df51b43241c..38b57db6e75 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb @@ -35,7 +35,7 @@ builddependencies = [ ('flex', '2.6.4'), ('gperf', '3.1'), ('Ninja', '1.9.0'), - ('Python', '3.7.4'), + ('Python', '2.7.16'), ('re2c', '1.2.1') ] From 2f9ff24b7752a9b143d6f849a3d1101d111c2b50 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2020 12:26:18 +0200 Subject: [PATCH 291/698] add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 --- .../libfabric-1.11.0-GCCcore-9.3.0.eb | 40 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb | 3 ++ .../OpenMPI-4.0.3-iccifort-2020.1.217.eb | 3 ++ 3 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..439e709c9cb --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.11.0-GCCcore-9.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.11.0' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ofiwg' +source_urls = ['https://github.com/ofiwg/%(name)s/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +checksums = ['9938abf628e7ea8dcf60a94a4b62d499fbc0dbc6733478b6db2e6a373c80d58f'] + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb index a508d0b8b98..e094a645860 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -13,7 +13,10 @@ checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] dependencies = [ ('zlib', '1.2.11'), ('hwloc', '2.2.0'), + ('libevent', '2.1.11'), ('UCX', '1.8.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), ] # disable MPI1 compatibility for now, see what breaks... diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb index 980e0e87cbb..283308daf5e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb @@ -13,7 +13,10 @@ checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] dependencies = [ ('zlib', '1.2.11'), ('hwloc', '2.2.0'), + ('libevent', '2.1.11'), ('UCX', '1.8.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), ] # disable MPI1 compatibility for now, see what breaks... From ca5ac74c2e2900341b1bf3ddf9ead33a244cd492 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2020 13:42:39 +0200 Subject: [PATCH 292/698] use OS_PKG_OPENSSL_DEV constant in UCX 1.8.0 easyconfig on top of CUDA 11.0.2 --- .../easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index 38be4f62623..7aa25a5e70e 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -34,7 +34,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -osdependencies = [('libibverbs-dev', 'libibverbs-devel', 'rdma-core-devel')] +osdependencies = [OS_PKG_OPENSSL_DEV] dependencies = [ ('numactl', '2.0.13'), From 251dbe49d2a7db3fc0c50a82f167faf5076de9cd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2020 17:14:23 +0200 Subject: [PATCH 293/698] add patch for LAME configure script to make it check for correct ncurses symbol --- .../l/LAME/LAME-3.100-GCCcore-6.4.0.eb | 7 +++++- .../l/LAME/LAME-3.100-GCCcore-7.3.0.eb | 6 ++++- .../l/LAME/LAME-3.100-GCCcore-8.2.0.eb | 6 ++++- .../l/LAME/LAME-3.100-GCCcore-8.3.0.eb | 6 ++++- .../l/LAME/LAME-3.100-GCCcore-9.3.0.eb | 6 ++++- .../l/LAME/LAME-3.100-intel-2017b.eb | 6 ++++- .../l/LAME/LAME-3.99.5-foss-2016b.eb | 7 +++++- .../l/LAME/LAME-3.99.5-intel-2017a.eb | 6 ++++- .../l/LAME/LAME-3.99.5_check-tgetent.patch | 23 +++++++++++++++++++ 9 files changed, 65 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/l/LAME/LAME-3.99.5_check-tgetent.patch diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb index 906b24e4783..ce401693ce9 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb @@ -14,8 +14,13 @@ description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licen toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] builddependencies = [ # use same binutils version that was used when building GCCcore toolchain diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb index e3ed2f3033b..6470093c35f 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] builddependencies = [('binutils', '2.30')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb index 611fa61cef6..ec477c3e2f6 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb index 30a30f11210..6404eb0e0fc 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb index fdbf07d08df..792cfe1401e 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb index 68d7dbc5b5f..c30ef8d926e 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'intel', 'version': '2017b'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + 'ddfe36cab873794038ae2c1210557ad34857a4b6bdc515785d1da9e175b1da1e', # lame-3.100.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb index f61518de915..7c77b7cdbf1 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb @@ -14,8 +14,13 @@ description = """LAME is a high quality MPEG Audio Layer III (MP3) encoder licen toolchain = {'name': 'foss', 'version': '2016b'} -sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + '24346b4158e4af3bd9f2e194bb23eb473c75fb7377011523353196b19b9a23ff', # lame-3.99.5.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb index 7c59b9ecd3b..61cfe33f989 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb @@ -16,7 +16,11 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['https://sourceforge.net/projects/lame/files/lame/%(version_major_minor)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['24346b4158e4af3bd9f2e194bb23eb473c75fb7377011523353196b19b9a23ff'] +patches = ['LAME-3.99.5_check-tgetent.patch'] +checksums = [ + '24346b4158e4af3bd9f2e194bb23eb473c75fb7377011523353196b19b9a23ff', # lame-3.99.5.tar.gz + '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch +] dependencies = [('ncurses', '6.0')] diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5_check-tgetent.patch b/easybuild/easyconfigs/l/LAME/LAME-3.99.5_check-tgetent.patch new file mode 100644 index 00000000000..821780bc097 --- /dev/null +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5_check-tgetent.patch @@ -0,0 +1,23 @@ +initscr is not used anywhere in lame sourcetree, check for used tgetent instead +check for separate tinfo library optionally built out from libncurses source tree, +like used in debian and gentoo +- ssuominen@g.o + +see http://bugs.gentoo.org/454322 and https://sourceforge.net/p/lame/bugs/436/ + +--- lame-3.99.5/configure.in ++++ lame-3.99.5/configure.in +@@ -372,9 +372,10 @@ + + AC_CHECK_HEADERS(termcap.h) + AC_CHECK_HEADERS(ncurses/termcap.h) +-AC_CHECK_LIB(termcap, initscr, HAVE_TERMCAP="termcap") +-AC_CHECK_LIB(curses, initscr, HAVE_TERMCAP="curses") +-AC_CHECK_LIB(ncurses, initscr, HAVE_TERMCAP="ncurses") ++AC_CHECK_LIB(termcap, tgetent, HAVE_TERMCAP="termcap") ++AC_CHECK_LIB(curses, tgetent, HAVE_TERMCAP="curses") ++AC_CHECK_LIB(ncurses, tgetent, HAVE_TERMCAP="ncurses") ++AC_CHECK_LIB(tinfo, tgetent, HAVE_TERMCAP="tinfo") + + AM_ICONV + From f9cf89fbc743de7829c0d55fc242f3d8ca9fa9fe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 26 Sep 2020 17:44:31 +0200 Subject: [PATCH 294/698] re-generate LAME configure script to pick up changes made by patch file --- easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb | 3 +++ easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb | 7 ++++++- easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb | 7 ++++++- easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb | 7 ++++++- easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb | 7 ++++++- easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb | 4 ++++ easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb | 4 ++++ easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb | 4 ++++ 8 files changed, 39 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb index ce401693ce9..e444dced929 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-6.4.0.eb @@ -25,10 +25,13 @@ checksums = [ builddependencies = [ # use same binutils version that was used when building GCCcore toolchain ('binutils', '2.28'), + ('Autotools', '20170619'), ] dependencies = [('ncurses', '6.0')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb index 6470093c35f..5058812fb68 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-7.3.0.eb @@ -22,10 +22,15 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] -builddependencies = [('binutils', '2.30')] +builddependencies = [ + ('binutils', '2.30'), + ('Autotools', '20180311'), +] dependencies = [('ncurses', '6.1')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb index ec477c3e2f6..f042060a8ec 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.2.0.eb @@ -22,10 +22,15 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] -builddependencies = [('binutils', '2.31.1')] +builddependencies = [ + ('binutils', '2.31.1'), + ('Autotools', '20180311'), +] dependencies = [('ncurses', '6.1')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb index 6404eb0e0fc..5e9f262f837 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-8.3.0.eb @@ -22,10 +22,15 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] -builddependencies = [('binutils', '2.32')] +builddependencies = [ + ('binutils', '2.32'), + ('Autotools', '20180311'), +] dependencies = [('ncurses', '6.1')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb index 792cfe1401e..ec35bdb7ddc 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-GCCcore-9.3.0.eb @@ -22,10 +22,15 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] -builddependencies = [('binutils', '2.34')] +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), +] dependencies = [('ncurses', '6.2')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb index c30ef8d926e..74e959ae751 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.100-intel-2017b.eb @@ -22,8 +22,12 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] +builddependencies = [('Autotools', '20170619')] + dependencies = [('ncurses', '6.0')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb index 7c77b7cdbf1..17d6b9e1c4b 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-foss-2016b.eb @@ -22,8 +22,12 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] +builddependencies = [('Autotools', '20150215')] + dependencies = [('ncurses', '6.0')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " diff --git a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb index 61cfe33f989..b8c3d475129 100644 --- a/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LAME/LAME-3.99.5-intel-2017a.eb @@ -22,8 +22,12 @@ checksums = [ '8bfb6a73f2db1511baf90fbd7174f11043ec4b592a4917edc30ccfb53bf37256', # LAME-3.99.5_check-tgetent.patch ] +builddependencies = [('Autotools', '20150215')] + dependencies = [('ncurses', '6.0')] +preconfigopts = "autoconf && " + # configure is broken: add workaround to find libncurses... configure_cmd_prefix = "FRONTEND_LDADD='-L${EBROOTNCURSES}/lib' " From 7626a3a3c8391de6e35180c8d8aac1de12b4723e Mon Sep 17 00:00:00 2001 From: ekieffer Date: Sat, 26 Sep 2020 21:15:43 +0200 Subject: [PATCH 295/698] Update easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb index 4733b10b8f9..70fd0130ae2 100644 --- a/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/ACTC/ACTC-1.1-GCCcore-9.3.0.eb @@ -7,6 +7,7 @@ homepage = 'https://sourceforge.net/projects/actc' description = "ACTC converts independent triangles into triangle strips or fans." toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] From 613a0f75fa673a45fa5d182b149dc4824f0c671e Mon Sep 17 00:00:00 2001 From: ekieffer Date: Sat, 26 Sep 2020 21:16:10 +0200 Subject: [PATCH 296/698] Update easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb index 5f14725d0e7..f65da482983 100644 --- a/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb +++ b/easybuild/easyconfigs/h/Harminv/Harminv-1.4.1-intel-2020a.eb @@ -19,8 +19,8 @@ checksums = ['e1b923c508a565f230aac04e3feea23b888b47d8e19b08816a97ee4444233670'] configopts = "--with-pic --with-blas=mkl_em64t --with-lapack=mkl_em64t --enable-shared" sanity_check_paths = { - 'files': [], - 'dirs': ['bin', 'lib'] + 'files': ['bin/harminv', 'lib/libharminv.a', 'lib/libharminv.%s' % SHLIB_EXT], + 'dirs': ['include'] } moduleclass = 'math' From 47279396751a7291930b5fe4ccb90f650d58b1fa Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 28 Sep 2020 12:44:58 +0200 Subject: [PATCH 297/698] adding easyconfigs: WRF-4.1.3-intel-2019b-dm+sm.eb --- .../w/WRF/WRF-4.1.3-intel-2019b-dm+sm.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dm+sm.eb diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dm+sm.eb b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dm+sm.eb new file mode 100644 index 00000000000..d1148782ae2 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.1.3-intel-2019b-dm+sm.eb @@ -0,0 +1,41 @@ +name = 'WRF' +version = '4.1.3' +buildtype = "dm+sm" +versionsuffix = '-%s' % buildtype + +homepage = 'http://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'intel', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True, 'opt': True} + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WRF_parallel_build_fix.patch', + 'WRFv4_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'a020e83e8a7a927fb080075031630e2af592e9fa802293ad72caa7ee50d6968d', # v4.1.3.tar.gz + 'f93bb6dbb8b52d72f816e2f9a6815bffd536afeca8511552ec5abc4253a59346', # WRF_parallel_build_fix.patch + 'a431159180757a895c07fc193fe93bb69c4c9d25d31adcc7c2adfa7c1edb04ad', # WRFv4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('tcsh', '6.22.02'), + ('time', '1.9'), +] + +dependencies = [ + ('JasPer', '2.0.14'), + ('netCDF', '4.7.1'), + ('netCDF-Fortran', '4.5.2'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' From 8215ebe1f9d9fa8c7451dd5255de583c49af8185 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Sep 2020 14:51:58 +0200 Subject: [PATCH 298/698] Add protobuf-python as a dependency and corresponding sanity check --- .../p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb index fbec32372cc..5fe9b4cf1f1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -265,6 +265,7 @@ builddependencies = [ dependencies = [ ('Ninja', '1.9.0'), # Required for JIT compilation of C++ extensions ('protobuf', '3.10.0'), + ('protobuf-python', '3.10.0'), ('Python', '3.7.4'), ('pybind11', '2.4.3', versionsuffix), ('SciPy-bundle', '2019.10', versionsuffix), @@ -306,6 +307,7 @@ excluded_tests = { runtest = 'cd test && %(python)s run_test.py --verbose %(excluded_tests)s' +sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From 55a662b1806daa5b5b9b7836f74e5f0e5135faa4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Sep 2020 15:05:30 +0200 Subject: [PATCH 299/698] Fix versionconfig --- .../p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb index 5fe9b4cf1f1..593b4ed8113 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-fosscuda-2019b-Python-3.7.4.eb @@ -265,7 +265,7 @@ builddependencies = [ dependencies = [ ('Ninja', '1.9.0'), # Required for JIT compilation of C++ extensions ('protobuf', '3.10.0'), - ('protobuf-python', '3.10.0'), + ('protobuf-python', '3.10.0', versionsuffix), ('Python', '3.7.4'), ('pybind11', '2.4.3', versionsuffix), ('SciPy-bundle', '2019.10', versionsuffix), From 733c84ee7203d32b9e3d426ebf6f0034a2a83456 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Mon, 28 Sep 2020 16:31:13 +0200 Subject: [PATCH 300/698] Add example NVHPC easyconfig Highlighting some of the available options --- .../n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb new file mode 100644 index 00000000000..6e125358160 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -0,0 +1,43 @@ +name = 'NVHPC' +version = '20.7' +local_gccver = '9.3.0' +versionsuffix = '-GCC-%s-OWNCUDA' % local_gccver + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] + +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.34', '', ('GCCcore', local_gccver)), + ('CUDA', '11.0', '', SYSTEM), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.13', '', SYSTEM) +] + +default_cuda_version = "11.0" +compute_capability = "70" + +# Options to add/remove things to/from environment module +module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +module_add_profilers = False # Add NVHPC's NVIDIA Profilers +module_add_nccl = False # Add NVHPC's NCCL library +module_add_nvshmem = False # Add NVHPC's NVSHMEM library +module_add_cuda = False # Add NVHPC's bundled CUDA + +# We use a HMNS, so let's enforce a unique compiler +modluafooter = ''' +family("compiler") +add_property("arch","gpu") +''' + +# Always do a recursive unload on compilers +recursive_module_unload = True + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 04f71661b4644f83a32961cd39b000acb0b9fbdc Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Mon, 28 Sep 2020 16:50:51 +0200 Subject: [PATCH 301/698] Clean remnant from testing --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 6e125358160..3a7c95879e8 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -1,7 +1,7 @@ name = 'NVHPC' version = '20.7' local_gccver = '9.3.0' -versionsuffix = '-GCC-%s-OWNCUDA' % local_gccver +versionsuffix = '-GCC-%s' % local_gccver homepage = 'https://developer.nvidia.com/hpc-sdk/' description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" From b25a08690ffa48e256ff7eb3b9b7fd012ceb1600 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 02:07:25 +0200 Subject: [PATCH 302/698] add easyconfig Check-0.15.2-GCCcore-9.3.0.eb --- .../c/Check/Check-0.15.2-GCCcore-9.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..9b2d4b86028 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-9.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' From dea09322a30e2c896bd08db2ae5f57db5ac71e9d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 02:08:22 +0200 Subject: [PATCH 303/698] add easyconfig GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb --- .../GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb new file mode 100644 index 00000000000..e702a1d13e7 --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.1' +local_cudaversion = '11.0.2' +versionsuffix = '-CUDA-%s' % local_cudaversion + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['cecc7dcc071107f77396f5553c9109790b6d2298ae29eb2dbbdd52b2a213e4ea'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [ + ('gdrcopy-kmod', 'gdrdrv-dkms'), # kernel module for GDR Copy + 'nvidia_peer_memory', # kernel module for GPUDirect RDMA +] + +dependencies = [ + ('CUDAcore', local_cudaversion, '', True), + ('Check', '0.15.2'), +] + +skipsteps = ['configure'] + +local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" +buildopts = "all %s" % local_envopts +installopts = local_envopts + +sanity_check_paths = { + 'files': ['bin/copybw', 'bin/copylat', 'bin/sanity', 'lib/libgdrapi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From e3690f8e0cfe4da7051eceaf125538bba7ddb686 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 02:09:52 +0200 Subject: [PATCH 304/698] add dependency on GDRCopy to UCX v1.8.0 for CUDA v11.0.2 --- .../easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb index 7aa25a5e70e..a42bca2e327 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.8.0-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -39,6 +39,7 @@ osdependencies = [OS_PKG_OPENSSL_DEV] dependencies = [ ('numactl', '2.0.13'), ('CUDAcore', local_cudaversion, '', True), + ('GDRCopy', '2.1', versionsuffix), ] # CUDA_CFLAGS set by EB toolchain but also used differently in UCX makefiles @@ -47,7 +48,7 @@ dependencies = [ preconfigopts = 'autoreconf && unset CUDA_CFLAGS && unset LIBS && ' configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' configopts += '--without-java --disable-doxygen-doc ' -configopts += '--with-cuda ' +configopts += '--with-cuda=$EBROOTCUDACORE --with-gdrcopy=$EBROOTGDRCOPY ' prebuildopts = 'unset CUDA_CFLAGS && unset LIBS && ' buildopts = 'V=1' From de4943c50ab954bf7a8314d93a25935a47aa1dbb Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 29 Sep 2020 09:13:24 +0200 Subject: [PATCH 305/698] Update easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb index 736e2e4594e..b5fadbecda4 100644 --- a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb @@ -3,7 +3,7 @@ # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics -easyblock = 'MakeCp' +easyblock = 'CMakeMake' name = 'Flexbar' version = '3.5.0' From ae71d45af83e589e678d8de136710124bcb6405f Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 29 Sep 2020 09:13:36 +0200 Subject: [PATCH 306/698] Update easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb index b5fadbecda4..3de64f154d4 100644 --- a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb @@ -28,8 +28,8 @@ dependencies = [ ('bzip2', '1.0.6'), ] -prebuildopts = 'cmake -DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so ' -prebuildopts += '-DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include . && ' +configopts = '-DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so ' +configopts += '-DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include' files_to_copy = [(['flexbar'], 'bin/')] From 26796032320e40c2f1550f2be1d57afdce3752af Mon Sep 17 00:00:00 2001 From: Pablo Escobar Lopez Date: Tue, 29 Sep 2020 09:13:44 +0200 Subject: [PATCH 307/698] Update easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb index 3de64f154d4..e4d5c03972a 100644 --- a/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb +++ b/easybuild/easyconfigs/f/Flexbar/Flexbar-3.5.0-foss-2018b.eb @@ -31,7 +31,8 @@ dependencies = [ configopts = '-DBZIP2_LIBRARY_RELEASE=${EBROOTBZIP2}/lib/libbz2.so ' configopts += '-DBZIP2_INCLUDE_DIR=${EBROOTBZIP2}/include' -files_to_copy = [(['flexbar'], 'bin/')] +preinstallopts = "mkdir -p %(installdir)s/bin && " +install_cmd = "cp flexbar %(installdir)s/bin/" sanity_check_paths = { 'files': ['bin/flexbar'], From fe30d6c8ac7cec605bf0a7fd12b6d41ebbf8d3ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 09:32:17 +0200 Subject: [PATCH 308/698] drop gflags/glog deps + add protobuf-python as dep for PyTorch 1.6 w/ foss/2019b --- .../p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb index 92bf5f42a63..0b8a3e27bb1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.6.0-foss-2019b-Python-3.7.4.eb @@ -265,6 +265,7 @@ builddependencies = [ dependencies = [ ('Ninja', '1.9.0'), # Required for JIT compilation of C++ extensions ('protobuf', '3.10.0'), + ('protobuf-python', '3.10.0', versionsuffix), ('Python', '3.7.4'), ('pybind11', '2.4.3', versionsuffix), ('SciPy-bundle', '2019.10', versionsuffix), @@ -273,8 +274,6 @@ dependencies = [ ('GMP', '6.1.2'), ('numactl', '2.0.12'), ('FFmpeg', '4.2.1'), - ('gflags', '2.2.2'), - ('glog', '0.4.0'), ('Pillow', '6.2.1'), ] @@ -302,6 +301,7 @@ excluded_tests = { runtest = 'cd test && %(python)s run_test.py --verbose %(excluded_tests)s' +sanity_check_commands = ["python -c 'import caffe2.python'"] tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'devel' From dd5d1dd8f5d9c2266e859dcb003b4e0631432c0e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 09:49:21 +0200 Subject: [PATCH 309/698] add extra info and requirements for kernel modules of GDRCopy --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index e702a1d13e7..1f56cae730e 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -23,8 +23,12 @@ builddependencies = [ ] osdependencies = [ - ('gdrcopy-kmod', 'gdrdrv-dkms'), # kernel module for GDR Copy - 'nvidia_peer_memory', # kernel module for GPUDirect RDMA + # Kernel module for GDR Copy: improves Host to GPU communication + ('gdrcopy-kmod', 'gdrdrv-dkms'), + # Kernel module for GPUDirect RDMA: improves GPU to GPU communication + # Requires a Mellanox HCA with MLNX_OFED 2.1 + # https://github.com/Mellanox/nv_peer_memory + 'nvidia_peer_memory', ] dependencies = [ From 36b65b9131b55724af742c2f5be41aaec70612d2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2020 12:11:23 +0200 Subject: [PATCH 310/698] {bio}[gompi/2020a] mauve v4736 --- .../m/mauve/libGenome-4736_gcc-6.1.patch | 17 + .../m/mauve/libMems-4736_debian.patch | 407 ++++++++++++++++++ .../m/mauve/mauve-4736-GCCcore-9.3.0.eb | 92 ++++ .../m/mauve/mauveAligner-4736_debian.patch | 35 ++ .../m/mauve/muscle-4736_makefile_deps.patch | 16 + .../m/mauve/sgEvolver-4736_dropversion.patch | 13 + 6 files changed, 580 insertions(+) create mode 100644 easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch create mode 100644 easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch create mode 100644 easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch create mode 100755 easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch create mode 100644 easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch diff --git a/easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch b/easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch new file mode 100644 index 00000000000..4bf1efb6e0c --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch @@ -0,0 +1,17 @@ +http://deb.debian.org/debian/pool/main/libg/libgenome/libgenome_1.3.11+svn20110227.4616-3.debian.tar.xz +Author: Andreas Tille +Last-Update: Fri, 12 Aug 2016 10:35:40 +0200 +Bug-Debian: https://bugs.debian.org/831188 +Description: THis declaration makes gcc-6.1 fail so simply drop it + +--- a/libGenome/gnDefs.cpp ++++ b/libGenome/gnDefs.cpp +@@ -4,8 +4,4 @@ + + #include "libGenome/gnDefs.h" + +-// some compilers don't have abs() for 64 bit ints +-int64 abs( int64 a ){ +- return a < 0 ? -a : a; +-} + diff --git a/easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch b/easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch new file mode 100644 index 00000000000..345ef999ffb --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch @@ -0,0 +1,407 @@ +# Selected patches from +# http://deb.debian.org/debian/pool/main/libm/libmems/libmems_1.6.0+4725-8.debian.tar.xz +# SEP 18th 2020 by B. Hajgato (UGent) +Author: Andrei Zavada +Last-Update: Sat, 18 Apr 2015 23:27:38 +0300 +Description: fix ctors of {MatchLeftEnd,LabeledMem}Comparator to enable sort/3 with g++-4.9 + +--- a/libMems/Aligner.cpp ++++ b/libMems/Aligner.cpp +@@ -939,7 +939,7 @@ public: + MatchLeftEndComparator( unsigned seq = 0 ){ + m_seq = seq; + } +- MatchLeftEndComparator( MatchLeftEndComparator& msc ){ ++ MatchLeftEndComparator( const MatchLeftEndComparator& msc ){ + m_seq = msc.m_seq; + } + // TODO?? make this do a wraparound comparison if all is equal? +--- a/libMems/Aligner.h ++++ b/libMems/Aligner.h +@@ -49,7 +49,7 @@ public: + LabeledMemComparator( uint seq ){ + m_seq = seq; + } +- LabeledMemComparator( LabeledMemComparator& lmc ){ ++ LabeledMemComparator( const LabeledMemComparator& lmc ){ + m_seq = lmc.m_seq; + } + boolean operator()(const LabeledMem& a, const LabeledMem& b) const{ +Author: Andrei Zavada +Last-Update: Sat, 18 Apr 2015 23:27:39 +0300 +Description: fix a -Wformat (boy, that's a bloody serious error) + +--- + libMems/dmSML/dmsort.c | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +--- a/libMems/dmSML/dmsort.c ++++ b/libMems/dmSML/dmsort.c +@@ -825,7 +825,7 @@ int InitdmSML( long working_mb, long buf + if ( fgets(buf, sizeof(buf), fp) ) + { + sscanf(buf, "MemTotal: %ld kB", &memTotal); +- fprintf( stderr, buf ); ++ fprintf( stderr, "%s", buf ); + } + fclose(fp); + // allocate about 6/10 of physical memory +Description: Updates the boost.m4 file to correct problems with gcc-5 + This patch updates the m4/boost.m4 file to the git version d9ff75 + of boost.m4 upstream + . +Author: Gert Wollny + +Origin: other, https://github.com/tsuna/boost.m4 +Bug-Debian: https://bugs.debian.org/795344 +Forwarded: no +Last-Update: 2015-08-17 + +--- libmems-1.6.0+4725.orig/m4/boost.m4 ++++ libmems-1.6.0+4725/m4/boost.m4 +@@ -22,7 +22,7 @@ + # along with this program. If not, see . + + m4_define([_BOOST_SERIAL], [m4_translit([ +-# serial 23 ++# serial 24 + ], [# + ], [])]) + +@@ -72,8 +72,25 @@ dnl strip `\n' with backquotes, not the + dnl boost_cv_lib_version='1_37\r' for instance, which breaks + dnl everything else. + dnl Cannot use 'dnl' after [$4] because a trailing dnl may break AC_CACHE_CHECK ++dnl ++dnl Beware that GCC 5, when expanding macros, may embed # line directives ++dnl a within single line: ++dnl ++dnl # 1 "conftest.cc" ++dnl # 1 "" ++dnl # 1 "" ++dnl # 1 "conftest.cc" ++dnl # 1 "/opt/local/include/boost/version.hpp" 1 3 ++dnl # 2 "conftest.cc" 2 ++dnl boost-lib-version = ++dnl # 2 "conftest.cc" 3 ++dnl "1_56" ++dnl ++dnl So get rid of the # lines, and glue the remaining ones together. + (eval "$ac_cpp conftest.$ac_ext") 2>&AS_MESSAGE_LOG_FD | ++ grep -v '#' | + tr -d '\r' | ++ tr -s '\n' ' ' | + $SED -n -e "$1" >conftest.i 2>&1], + [$3], + [$4]) +@@ -208,7 +225,7 @@ AC_LANG_POP([C++])dnl + AC_CACHE_CHECK([for Boost's header version], + [boost_cv_lib_version], + [m4_pattern_allow([^BOOST_LIB_VERSION$])dnl +- _BOOST_SED_CPP([/^boost-lib-version = /{s///;s/\"//g;p;q;}], ++ _BOOST_SED_CPP([[/^boost-lib-version = /{s///;s/[\" ]//g;p;q;}]], + [#include + boost-lib-version = BOOST_LIB_VERSION], + [boost_cv_lib_version=`cat conftest.i`])]) +@@ -216,7 +233,7 @@ boost-lib-version = BOOST_LIB_VERSION], + boost_major_version=`echo "$boost_cv_lib_version" | sed 's/_//;s/_.*//'` + case $boost_major_version in #( + '' | *[[!0-9]]*) +- AC_MSG_ERROR([invalid value: boost_major_version=$boost_major_version]) ++ AC_MSG_ERROR([invalid value: boost_major_version='$boost_major_version']) + ;; + esac + fi +@@ -557,13 +574,40 @@ BOOST_FIND_LIB([chrono], [$1], + [boost/chrono.hpp], + [boost::chrono::thread_clock d;]) + if test $enable_static_boost = yes && test $boost_major_version -ge 135; then +- BOOST_FILESYSTEM_LIBS="$BOOST_FILESYSTEM_LIBS $BOOST_SYSTEM_LIBS" ++ BOOST_CHRONO_LIBS="$BOOST_CHRONO_LIBS $BOOST_SYSTEM_LIBS" + fi + LIBS=$boost_filesystem_save_LIBS + LDFLAGS=$boost_filesystem_save_LDFLAGS + ])# BOOST_CHRONO + + ++# BOOST_CONTEXT([PREFERRED-RT-OPT]) ++# ----------------------------------- ++# Look for Boost.Context. For the documentation of PREFERRED-RT-OPT, see the ++# documentation of BOOST_FIND_LIB above. This library was introduced in Boost ++# 1.51.0 ++BOOST_DEFUN([Context], ++[BOOST_FIND_LIB([context], [$1], ++ [boost/context/all.hpp],[[ ++// creates a stack ++void * stack_pointer = new void*[4096]; ++std::size_t const size = sizeof(void*[4096]); ++ ++// context fc uses f() as context function ++// fcontext_t is placed on top of context stack ++// a pointer to fcontext_t is returned ++fc = ctx::make_fcontext(stack_pointer, size, f); ++return ctx::jump_fcontext(&fcm, fc, 3) == 6;]],[dnl ++namespace ctx = boost::context; ++// context ++static ctx::fcontext_t fcm, *fc; ++// context-function ++static void f(intptr_t i) { ++ ctx::jump_fcontext(fc, &fcm, i * 2); ++}]) ++])# BOOST_CONTEXT ++ ++ + # BOOST_CONVERSION() + # ------------------ + # Look for Boost.Conversion (cast / lexical_cast) +@@ -573,6 +617,44 @@ BOOST_FIND_HEADER([boost/lexical_cast.hp + ])# BOOST_CONVERSION + + ++# BOOST_COROUTINE([PREFERRED-RT-OPT]) ++# ----------------------------------- ++# Look for Boost.Coroutine. For the documentation of PREFERRED-RT-OPT, see the ++# documentation of BOOST_FIND_LIB above. This library was introduced in Boost ++# 1.53.0 ++BOOST_DEFUN([Coroutine], ++[ ++boost_coroutine_save_LIBS=$LIBS ++boost_coroutine_save_LDFLAGS=$LDFLAGS ++# Link-time dependency from coroutine to context ++BOOST_CONTEXT([$1]) ++# Starting from Boost 1.55 a dependency on Boost.System is added ++if test $boost_major_version -ge 155; then ++ BOOST_SYSTEM([$1]) ++fi ++m4_pattern_allow([^BOOST_(CONTEXT|SYSTEM)_(LIBS|LDFLAGS)]) ++LIBS="$LIBS $BOOST_CONTEXT_LIBS $BOOST_SYSTEM_LIBS" ++LDFLAGS="$LDFLAGS $BOOST_CONTEXT_LDFLAGS" ++ ++BOOST_FIND_LIB([coroutine], [$1], ++ [boost/coroutine/coroutine.hpp], ++ [boost::coroutines::coroutine< int(int) > coro; coro.empty();]) ++ ++# Link-time dependency from coroutine to context, existed only in 1.53, in 1.54 ++# coroutine doesn't use context from its headers but from its library. ++if test $boost_major_version -eq 153 || test $enable_static_boost = yes && test $boost_major_version -ge 154; then ++ BOOST_COROUTINE_LIBS="$BOOST_COROUTINE_LIBS $BOOST_CONTEXT_LIBS" ++ BOOST_COROUTINE_LDFLAGS="$BOOST_COROUTINE_LDFLAGS $BOOST_CONTEXT_LDFLAGS" ++fi ++if test $enable_static_boost = yes && test $boost_major_version -ge 155; then ++ BOOST_COROUTINE_LIBS="$BOOST_COROUTINE_LIBS $BOOST_SYSTEM_LIBS" ++ BOOST_COROUTINE_LDFLAGS="$BOOST_COROUTINE_LDFLAGS $BOOST_SYSTEM_LDFLAGS" ++fi ++LIBS=$boost_coroutine_save_LIBS ++LDFLAGS=$boost_coroutine_save_LDFLAGS ++])# BOOST_COROUTINE ++ ++ + # BOOST_CRC() + # ----------- + # Look for Boost.CRC +@@ -699,6 +781,15 @@ BOOST_DEFUN([Lambda], + [BOOST_FIND_HEADER([boost/lambda/lambda.hpp])]) + + ++# BOOST_LOCALE() ++# -------------- ++# Look for Boost.Locale ++BOOST_DEFUN([Locale], ++[BOOST_FIND_LIB([locale], [$1], ++ [boost/locale.hpp], ++ [[boost::locale::generator gen; std::locale::global(gen(""));]]) ++])# BOOST_LOCALE ++ + # BOOST_LOG([PREFERRED-RT-OPT]) + # ----------------------------- + # Look for Boost.Log. For the documentation of PREFERRED-RT-OPT, see the +@@ -794,6 +885,12 @@ BOOST_DEFUN([Preprocessor], + [BOOST_FIND_HEADER([boost/preprocessor/repeat.hpp])]) + + ++# BOOST_RANGE() ++# -------------------- ++# Look for Boost.Range ++BOOST_DEFUN([Range], ++[BOOST_FIND_HEADER([boost/range/adaptors.hpp])]) ++ + # BOOST_UNORDERED() + # ----------------- + # Look for Boost.Unordered +@@ -1199,6 +1296,8 @@ if test x$boost_cv_inc_path != xno; then + # I'm not sure about my test for `il' (be careful: Intel's ICC pre-defines + # the same defines as GCC's). + for i in \ ++ _BOOST_mingw_test(5, 0) \ ++ _BOOST_gcc_test(5, 0) \ + _BOOST_mingw_test(4, 10) \ + _BOOST_gcc_test(4, 10) \ + _BOOST_mingw_test(4, 9) \ +Description: Add some dependencies to the linker command +Author: Andreas Tille +Bug-Debian: https://bugs.debian.org/ +Forwarded: no +Last-Update: 2015-08-17 + +--- libmems-1.6.0+4725.orig/libMems/Makefile.am ++++ libmems-1.6.0+4725/libMems/Makefile.am +@@ -61,7 +61,7 @@ libmems_include_HEADERS = $(LIBMEMS_H) + # build libraries with gcc (no suffix) + lib_LTLIBRARIES = libMems-1.6.la + libMems_1_6_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) +- ++libMems_1_6_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ + libMems_1_6_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) + + homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/HomologyHMM +Description: Correct compilation with g++-6 +Author: Gert Wollny +Bug-Debian: https://bugs.debian.org/811870 +Forwarded: yes +Bug: https://sourceforge.net/p/mauve/bugs/46/ +Last-Update: 2016-06-30 + +--- a/libMems/ProgressiveAligner.cpp ++++ b/libMems/ProgressiveAligner.cpp +@@ -1599,7 +1599,7 @@ + c.SetLeftEnd(child_1, ancestral_matches[mI]->LeftEnd(1)); + c.SetOrientation(child_1, ancestral_matches[mI]->Orientation(1)); + c.SetLength(ancestral_matches[mI]->Length(1), child_1); +- cga_list.push_back(make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); ++ cga_list.push_back(boost::tuples::make_tuple(c.Copy(), &bs[mI], ancestral_matches[mI])); + } + + stack node_stack; +Author: Andreas Tille +Last-Updated: Tue, 08 Nov 2016 14:16:07 +0100 +Description: This patch *really* enables droping the version + from package names but it is not activated here since this might + be considered a "transition" and we are in transition freeze. + +--- a/libMems/Makefile.am ++++ b/libMems/Makefile.am +@@ -55,19 +55,19 @@ dmSML/util.c dmSML/sorting.c dmSML/dmsor + dmSML/timing.c dmSML/sml.c + + +-libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME) ++libmems_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME) + libmems_include_HEADERS = $(LIBMEMS_H) + + # build libraries with gcc (no suffix) +-lib_LTLIBRARIES = libMems-1.6.la +-libMems_1_6_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) +-libMems_1_6_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ +-libMems_1_6_la_LDFLAGS= -version-info $(GENERIC_LIBRARY_VERSION) ++lib_LTLIBRARIES = libMems.la ++libMems_la_SOURCES = $(LIBMEMS_SRC) $(HOMOLOGYHMM_SRC) $(DMSML_SRC) ++libMems_la_LIBADD = @DEPS_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_IOSTREAMS_LIBS@ @BOOST_SYSTEM_LIBS@ ++libMems_la_LDFLAGS= -version-info @GENERIC_LIBRARY_VERSION@ + +-homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/HomologyHMM ++homologyhmm_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/HomologyHMM + homologyhmm_include_HEADERS = $(HOMOLOGYHMM_H) + +-dmsml_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/dmSML ++dmsml_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/dmSML + dmsml_include_HEADERS = $(DMSML_H) + + EXTRA_DIST = \ +Description: Fix FTBFS with Boost 1.62 + Add missing include so that BOOST_WORKAROUND is defined. +Author: Graham Inggs +Last-Update: 2016-11-08 +Bug-Debian: https://bugs.debian.org/843628 + +--- a/libMems/AbstractMatch.h ++++ b/libMems/AbstractMatch.h +@@ -16,6 +16,7 @@ + #include "libGenome/gnClone.h" + #include + #include ++#include + #include + #include + #include +--- a/libMems/dmSML/Makefile.am ++++ b/libMems/dmSML/Makefile.am +@@ -12,7 +12,7 @@ alibc.c awin32aio.c buffer.c \ + util.c sorting.c dmsort.c \ + timing.c sml.c + +-library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)-$(GENERIC_API_VERSION)/$(GENERIC_LIBRARY_NAME)/dmSML ++library_includedir=$(includedir)/$(GENERIC_LIBRARY_NAME)/dmSML + + library_include_HEADERS = $(DMSML_H) + +Author: Andreas Tille +Last-Updated: Sun, 19 Apr 2015 20:20:17 +0200 +Description: Fix lintian error + E: libmems-1.6-dev: pkg-config-bad-directive usr/lib/x86_64-linux-gnu/pkgconfig/libMems-1.6.pc -Wno-deprecated + by not appending "-Wno-deprecated" + +--- a/configure.ac ++++ b/configure.ac +@@ -73,7 +73,7 @@ dnl Check what compiler we're using + AM_CONDITIONAL(ICC, test x$CXX = xicc ) + EXTRA_CXX_FLAGS="" + if( test x$CC == "xgcc" ) then +- EXTRA_CXX_FLAGS="-Wno-deprecated" ++ EXTRA_CXX_FLAGS="" + fi + AC_SUBST(EXTRA_CXX_FLAGS) + +Author: Andreas Tille +Last-Update: Wed, 18 Jul 2018 15:15:58 +0200 +Description: Drop version number from library file name + +--- a/Makefile.am ++++ b/Makefile.am +@@ -8,7 +8,7 @@ projects/libMems.sln \ + projects/libMems.vcproj + + pkgconfigdir = $(libdir)/pkgconfig +-pkgconfig_DATA = libMems-@GENERIC_API_VERSION@.pc ++pkgconfig_DATA = libMems.pc + + SUBDIRS = libMems + +--- /dev/null ++++ b/libMems.pc.in +@@ -0,0 +1,12 @@ ++prefix=@prefix@ ++exec_prefix=@exec_prefix@ ++libdir=@libdir@ ++includedir=@includedir@ ++ ++Name: libMems ++Description: c++ library supporting DNA sequence and genome alignment ++Version: @VERSION@ ++Requires: libGenome-1.3 libMUSCLE-3.7 ++Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ ++Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ ++ +--- a/libMems-1.6.pc.in ++++ /dev/null +@@ -1,12 +0,0 @@ +-prefix=@prefix@ +-exec_prefix=@exec_prefix@ +-libdir=@libdir@ +-includedir=@includedir@ +- +-Name: libMems +-Description: c++ library supporting DNA sequence and genome alignment +-Version: @VERSION@ +-Requires: libGenome-1.3 libMUSCLE-3.7 +-Libs: -L${libdir} @OPENMP_CXXFLAGS@ -lMems-@GENERIC_API_VERSION@ @BOOST_SYSTEM_LDFLAGS@ @BOOST_SYSTEM_LIBS@ @BOOST_FILESYSTEM_LIBS@ @BOOST_PROGRAM_OPTIONS_LIBS@ @BOOST_IOSTREAMS_LIBS@ @LIBS@ +-Cflags: -I${includedir}/@GENERIC_LIBRARY_NAME@-@GENERIC_API_VERSION@ @BOOST_CPPFLAGS@ @OPENMP_CXXFLAGS@ @EXTRA_CXX_FLAGS@ +- +--- a/configure.ac ++++ b/configure.ac +@@ -133,5 +133,5 @@ AC_PROG_GCC_TRADITIONAL + dnl SAVE_LIBRARY_VERSION + AC_SUBST(LIBTOOL_VERSION_INFO) + +-AC_OUTPUT(Makefile libMems/Makefile libMems-1.6.pc ) ++AC_OUTPUT(Makefile libMems/Makefile libMems.pc ) + #doc/html/Makefile doc/man/Makefile doc/man/man3/Makefile) diff --git a/easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..58f5c89cac2 --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb @@ -0,0 +1,92 @@ +easyblock = 'Bundle' + +name = 'mauve' +version = '4736' + +homepage = 'https://darlinglab.org/mauve/mauve.html' +description = """ +Mauve is a system for constructing multiple genome alignments in the presence +of large-scale evolutionary events such as rearrangement and inversion. +Multiple genome alignments provide a basis for research into comparative +genomics and the study of genome-wide evolutionary dynamics. +This version was built without Graphical User Interface. +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +# you can download the sources in the following way: +# --- START SCRIPT --- +# ver=4736 +# for i in libGenome libMems mauveAligner muscle sgEvolver +# do +# svn co -r $ver https://svn.code.sf.net/p/mauve/code/$i/trunk $i +# tar jcf ${i}-${ver}.tar.bz2 $i +# done +# --- END SCRIPT --- +# We cannot provide checksums, becasue there is no way to use the original svn directory timestamp + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('Perl', '5.30.2'), + ('Boost', '1.72.0'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_BZ2], + 'start_dir': '%(name)s', +} + +components = [ + ('libGenome', version, { + 'patches': ['libGenome-4736_gcc-6.1.patch'], + }), + ('muscle', version, { + 'patches': ['muscle-4736_makefile_deps.patch'], + }), + ('libMems', version, { + 'patches': ['libMems-4736_debian.patch'], + }), + ('mauveAligner', version, { + 'patches': ['mauveAligner-4736_debian.patch'], + }), + ('sgEvolver', version, { + 'patches': ['sgEvolver-4736_dropversion.patch'], + }), +] + +preconfigopts = './autogen.sh && env PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig ' + +postinstallcmds = [ + 'mkdir -p %(installdir)s/lib/perl5/site_perl', + 'cp %(builddir)s/sgEvolver/src/simujobparams.pm %(installdir)s/lib/perl5/site_perl/.', +] + +local_bin = ['addUnalignedIntervals', 'alignmentProjector', 'backbone_global_to_local', 'bbAnalyze', 'bbFilter', + 'coordinateTranslate', 'createBackboneMFA', 'extractBCITrees', 'getAlignmentWindows', 'getOrthologList', + 'maf2xmfa', 'makeBadgerMatrix', 'mauveAligner', 'mauveStatic', 'mauveToXMFA', 'mfa2xmfa', + 'mfaToMultiFiles', 'muscle', 'progressiveMauve', 'progressiveMauveStatic', 'projectAndStrip', + 'randomGeneSample', 'repeatoire', 'scoreAlignment', 'scoreAlignment2', 'scoregen.pl', 'sgEvolver', + 'simujobgen.pl', 'simujobrun.pl', 'stripGapColumns', 'stripSubsetLCBs', 'toGrimmFormat', 'toMultiFastA', + 'toRawSequence', 'uniqueMerCount', 'uniquifyTrees', 'xmfa2maf'] + +local_lib = ['Genome-1.3', 'Mems', 'MUSCLE-3.7'] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in local_lib for y in ['a', 'la', SHLIB_EXT]] + + ['bin/%s' % x for x in local_bin] + + ['lib/perl5/site_perl/simujobparams.pm'], + 'dirs': ['include/lib%s' % x for x in local_lib] + + ['share', 'lib/pkgconfig'], +} + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch b/easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch new file mode 100644 index 00000000000..09b6fac7ae9 --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch @@ -0,0 +1,35 @@ +http://deb.debian.org/debian/pool/main/p/progressivemauve/progressivemauve_1.2.0+4713+dfsg-4.debian.tar.xz +Author: Giovanni Mascellani +Bug-Debian: https://bugs.debian.org/914049 +Subject: Fix FTBFS with boost1.67 + +Make an explicit call to the constructor for NeighborhoodGroup (which is +an alias for a specialization of boost::tuple), which is not marked +as "explicit". + +--- a/src/repeatoire.cpp ++++ b/src/repeatoire.cpp +@@ -1591,7 +1591,7 @@ void processNovelSubsetMatches( GappedMa + getSubsets(M_j,-direction*ni_parity*nj_parity).push_back(nj_link); + //getExtraSubsets(M_j,-direction*ni_parity*nj_parity).push_back(nj_link); + // push M_n onto the heap +- novel_subset_list.push_back(M_n); ++ novel_subset_list.push_back(NeighborhoodGroup{M_n}); + //procrastination_queue.push(M_n); + novel_subset_count++; + } +Description: Enable building against unversioned libs +Author: Andreas Tille +Last-Updates: Fri, 27 Jul 2018 06:32:17 +0200 + +--- a/configure.ac ++++ b/configure.ac +@@ -43,7 +43,7 @@ AC_DEFINE(GETOPT_UNDEFINED,[],"Define th + ()") + ) + +-PKG_CHECK_MODULES(DEPS, libMems-1.6 >= 1.0.0) ++PKG_CHECK_MODULES(DEPS, libMems >= 1.0.0) + AC_SUBST(DEPS_CFLAGS) + AC_SUBST(DEPS_LIBS) + diff --git a/easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch b/easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch new file mode 100755 index 00000000000..4d1d54b14c6 --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch @@ -0,0 +1,16 @@ +# based on: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=905384 +# based on: Description: Correct the libMUSCLE.la dependency +# based on: This allows automake to generate proper dependencies. +# based on: Author: Adrian Bunk +# SEP 17th 2020 by B. Hajgato (UGent) + +--- libmuscle-3.7+4565.orig/libMUSCLE/Makefile.am ++++ libmuscle-3.7+4565/libMUSCLE/Makefile.am +@@ -36,6 +36,6 @@ bin_PROGRAMS = muscle + + + muscle_SOURCES = main.cpp +-muscle_LDADD = $(top_builddir)/libMUSCLE/libMUSCLE-3.7.la ++muscle_LDADD = libMUSCLE-3.7.la + + diff --git a/easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch b/easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch new file mode 100644 index 00000000000..07bb4d8bc7b --- /dev/null +++ b/easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch @@ -0,0 +1,13 @@ +# drop version of libMems +# SEP 18th 2020 by B. Hajgato(UGent) +--- configure.ac.orig 2020-09-18 14:53:03.370907242 +0200 ++++ configure.ac 2020-09-18 14:53:16.571362128 +0200 +@@ -39,7 +39,7 @@ + ()") + ) + +-PKG_CHECK_MODULES(DEPS, libMems-1.6 >= 1.0.0) ++PKG_CHECK_MODULES(DEPS, libMems >= 1.0.0) + AC_SUBST(DEPS_CFLAGS) + AC_SUBST(DEPS_LIBS) + From 30f97e33e048f5ba1f9f86b46bab1e27d0367e65 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 12:16:07 +0200 Subject: [PATCH 311/698] adding easyconfigs: OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb, OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb --- ...OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb | 26 +++++++++++++++++++ ...OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb new file mode 100644 index 00000000000..42213c26c50 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompic', 'version': '2019b'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb new file mode 100644 index 00000000000..71f0f3c132c --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2019b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpic', 'version': '2019b'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 95a936ff43f6793d3deab2596b8bad77c08fff64 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 29 Sep 2020 12:17:36 +0200 Subject: [PATCH 312/698] adding easyconfigs: OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb, OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb --- ...OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb | 26 +++++++++++++++++++ ...OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb new file mode 100644 index 00000000000..18cc95538cc --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompic-2020a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompic', 'version': '2020a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb new file mode 100644 index 00000000000..eaa6dc791d6 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-iimpic-2020a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'iimpic', 'version': '2020a'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' +configopts += ' --enable-cuda --with-cuda=$EBROOTCUDA' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 817a135840aa528d0e8f4052dcc742c32d8d10cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 13:20:22 +0200 Subject: [PATCH 313/698] adding easyconfigs: GROMACS-2020.3-fosscuda-2019b.eb --- .../GROMACS/GROMACS-2020.3-fosscuda-2019b.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb new file mode 100644 index 00000000000..0f66c5d02ad --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2020.3-fosscuda-2019b.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# License:: MIT/GPL +## + +name = 'GROMACS' +version = '2020.3' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + '903183691132db14e55b011305db4b6f4901cc4912d2c56c131edfef18cc92a9', # gromacs-2020.3.tar.gz + # GROMACS-2019_fix_omp_num_threads_and_google_test_death_style_in_tests.patch + '406f5edd204be812f095a6f07ebc2673c5f6ddf1b1c1428fd336a80b9c629275', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' From 81605e6b4a3fe933d524f83f02a7f0366ee60482 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2020 13:25:42 +0200 Subject: [PATCH 314/698] fix checksum --- ....0.eb => mauveAligner-4736-gompi-2020a.eb} | 22 ++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/m/mauve/{mauve-4736-GCCcore-9.3.0.eb => mauveAligner-4736-gompi-2020a.eb} (75%) diff --git a/easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb similarity index 75% rename from easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb rename to easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb index 58f5c89cac2..1d434e6b27c 100644 --- a/easybuild/easyconfigs/m/mauve/mauve-4736-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'gompi', 'version': '2020a'} # tar jcf ${i}-${ver}.tar.bz2 $i # done # --- END SCRIPT --- -# We cannot provide checksums, becasue there is no way to use the original svn directory timestamp +# We cannot provide checksums, because there is no way to use the original svn directory timestamp builddependencies = [ ('binutils', '2.34'), @@ -47,18 +47,38 @@ default_component_specs = { components = [ ('libGenome', version, { 'patches': ['libGenome-4736_gcc-6.1.patch'], + 'checksums': [ + None, # libGenome-4736.tar.bz2 + 'e628dcd7264b15805194f1df5d0c47f571477c0ea09183750e07984f4ce35cf8', # libGenome-4736_gcc-6.1.patch + ], }), ('muscle', version, { 'patches': ['muscle-4736_makefile_deps.patch'], + 'checksums': [ + None, # muscle-4736.tar.bz2 + '5937e43d5f1d7ce5ed4f4904673a62f072db8211897ca2d58cdef6f9261c6146', # muscle-4736_makefile_deps.patch + ], }), ('libMems', version, { 'patches': ['libMems-4736_debian.patch'], + 'checksums': [ + None, # libMems-4736.tar.bz2 + '92865fb29560985226a51cc4f61a30083580ca456d35b74d2e67d595c6242ad1', # libMems-4736_debian.patch + ], }), ('mauveAligner', version, { 'patches': ['mauveAligner-4736_debian.patch'], + 'checksums': [ + None, # mauveAligner-4736.tar.bz2 + '2786bd29bedb224f232e7909972b549fe95f520ddac2cbb076e2082647dc68ae', # mauveAligner-4736_debian.patch + ], }), ('sgEvolver', version, { 'patches': ['sgEvolver-4736_dropversion.patch'], + 'checksums': [ + None, # sgEvolver-4736.tar.bz2 + 'efc3397039dd525669f6c525b20d75ad64c51cd25912192e695067de4cfbeadc', # sgEvolver-4736_dropversion.patch + ], }), ] From a119838e5989d2d561f5236000a6567f3d2a7338 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2020 13:45:18 +0200 Subject: [PATCH 315/698] fix name --- easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb b/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb index 1d434e6b27c..b13c7fbd93e 100644 --- a/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb +++ b/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb @@ -1,6 +1,6 @@ easyblock = 'Bundle' -name = 'mauve' +name = 'mauveAligner' version = '4736' homepage = 'https://darlinglab.org/mauve/mauve.html' From 6c2b23904dae4ff5bde5a2a231f3eb7246bd21c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 13:53:52 +0200 Subject: [PATCH 316/698] adding easyconfigs: WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb --- ...secondorX-1.1.6-foss-2020a-Python-3.8.2.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..000a5366220 --- /dev/null +++ b/easybuild/easyconfigs/w/WisecondorX/WisecondorX-1.1.6-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'WisecondorX' +version = '1.1.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/CenterForMedicalGeneticsGhent/WisecondorX' +description = "WisecondorX -- an evolved WISECONDOR" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/CenterForMedicalGeneticsGhent/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['555757a186ffeb7352f8c6b9af3037dfbd676dcfd2b54bfcaa1db7ffcc43df07'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('R', '4.0.0'), # includes jsonlite + ('R-bundle-Bioconductor', '3.11', '-R-%(rver)s'), + ('Pysam', '0.16.0.1'), + ('scikit-learn', '0.23.1', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'wisecondorX'} + +sanity_check_paths = { + 'files': ['bin/WisecondorX'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["WisecondorX --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 63877dcc2d7281dd9d44ffa754ece9cd36f238ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 13:56:36 +0200 Subject: [PATCH 317/698] adding easyconfigs: bam-readcount-0.8.0-GCC-9.3.0.eb --- .../bam-readcount-0.8.0-GCC-9.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb new file mode 100644 index 00000000000..037d0e9b419 --- /dev/null +++ b/easybuild/easyconfigs/b/bam-readcount/bam-readcount-0.8.0-GCC-9.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Adam Huffman +# The Francis Crick Institute +easyblock = 'CMakeMake' + +name = 'bam-readcount' +version = '0.8.0' + +homepage = 'https://github.com/genome/bam-readcount' +description = """Count DNA sequence reads in BAM files""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/genome/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4f4dd558e3c6bfb24d6a57ec441568f7524be6639b24f13ea6f2bb350c7ea65f'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('SAMtools', '1.10'), + ('zlib', '1.2.11'), + ('ncurses', '6.2'), +] + +prebuildopts = "export SAMTOOLS_ROOT=${EBROOTSAMTOOLS}/include/bam && " + +separate_build_dir = True + +sanity_check_paths = { + 'files': ["bin/bam-readcount"], + 'dirs': [] +} + +# --help exists with exit code 1, so use grep to check for expected pattern in help output +sanity_check_commands = ["bam-readcount --help 2>&1 | grep 'Example: bam-readcount -f'"] + +moduleclass = 'bio' From 2132cc10084b21071ba9b77f2c6d17d379eda1f6 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2020 14:01:13 +0200 Subject: [PATCH 318/698] fix directory name --- .../m/{mauve => mauveAligner}/libGenome-4736_gcc-6.1.patch | 0 .../m/{mauve => mauveAligner}/libMems-4736_debian.patch | 0 .../m/{mauve => mauveAligner}/mauveAligner-4736-gompi-2020a.eb | 0 .../m/{mauve => mauveAligner}/mauveAligner-4736_debian.patch | 0 .../m/{mauve => mauveAligner}/muscle-4736_makefile_deps.patch | 0 .../m/{mauve => mauveAligner}/sgEvolver-4736_dropversion.patch | 0 6 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/libGenome-4736_gcc-6.1.patch (100%) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/libMems-4736_debian.patch (100%) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/mauveAligner-4736-gompi-2020a.eb (100%) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/mauveAligner-4736_debian.patch (100%) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/muscle-4736_makefile_deps.patch (100%) rename easybuild/easyconfigs/m/{mauve => mauveAligner}/sgEvolver-4736_dropversion.patch (100%) diff --git a/easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch b/easybuild/easyconfigs/m/mauveAligner/libGenome-4736_gcc-6.1.patch similarity index 100% rename from easybuild/easyconfigs/m/mauve/libGenome-4736_gcc-6.1.patch rename to easybuild/easyconfigs/m/mauveAligner/libGenome-4736_gcc-6.1.patch diff --git a/easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch b/easybuild/easyconfigs/m/mauveAligner/libMems-4736_debian.patch similarity index 100% rename from easybuild/easyconfigs/m/mauve/libMems-4736_debian.patch rename to easybuild/easyconfigs/m/mauveAligner/libMems-4736_debian.patch diff --git a/easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb similarity index 100% rename from easybuild/easyconfigs/m/mauve/mauveAligner-4736-gompi-2020a.eb rename to easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736-gompi-2020a.eb diff --git a/easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch b/easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_debian.patch similarity index 100% rename from easybuild/easyconfigs/m/mauve/mauveAligner-4736_debian.patch rename to easybuild/easyconfigs/m/mauveAligner/mauveAligner-4736_debian.patch diff --git a/easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch b/easybuild/easyconfigs/m/mauveAligner/muscle-4736_makefile_deps.patch similarity index 100% rename from easybuild/easyconfigs/m/mauve/muscle-4736_makefile_deps.patch rename to easybuild/easyconfigs/m/mauveAligner/muscle-4736_makefile_deps.patch diff --git a/easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch b/easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_dropversion.patch similarity index 100% rename from easybuild/easyconfigs/m/mauve/sgEvolver-4736_dropversion.patch rename to easybuild/easyconfigs/m/mauveAligner/sgEvolver-4736_dropversion.patch From 7d6aade451b12251f97686e2e46474fdbba31eab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 14:17:59 +0200 Subject: [PATCH 319/698] adding easyconfigs: ABRA2-2.23-GCC-9.3.0.eb --- .../a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb new file mode 100644 index 00000000000..f93ab230e6b --- /dev/null +++ b/easybuild/easyconfigs/a/ABRA2/ABRA2-2.23-GCC-9.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MakeCp' + +name = 'ABRA2' +version = '2.23' + +homepage = 'https://github.com/mozack/abra2' +description = "Assembly Based ReAligner" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/mozack/abra2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ABRA2-2.22_fix-Makefile.patch'] +checksums = [ + '3993f66a493070ee49df2865b6786a45a0cf6c379bae83e94b8339abbe673289', # v2.23.tar.gz + '05090efb306fc84d09f007a848ce0d0472f8633633b0a6eaf86ab075d092bc0d', # ABRA2-2.22_fix-Makefile.patch +] + +builddependencies = [('Maven', '3.6.3', '', True)] + +dependencies = [ + ('Java', '11', '', True), + ('BWA', '0.7.17'), +] + +parallel = 1 + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS"' +buildopts += '&& make standalone CXX="$CXX" CXXFLAGS="$CXXFLAGS"' + +files_to_copy = [ + (['abra'], 'bin'), + (['target/libAbra.%s' % SHLIB_EXT], 'lib'), + 'target/abra2-%(version)s-jar-with-dependencies.jar', +] + +postinstallcmds = ["cd %(installdir)s && mv abra2-%(version)s-jar-with-dependencies.jar abra2-%(version)s.jar"] + +sanity_check_paths = { + 'files': ['abra2-%(version)s.jar', 'bin/abra', 'lib/libAbra.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' From 6b4758f9f3dd723436d767e0427c7fc8bb5bba5b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Tue, 29 Sep 2020 14:46:00 +0200 Subject: [PATCH 320/698] fix Multiwfn 3.6 installation on RHEL8 --- .../m/Multiwfn/Multiwfn-3.6-intel-2019a.eb | 6 +++++- .../m/Multiwfn/Multiwfn-3.6-intel-2019b.eb | 6 +++++- .../m/Multiwfn/Multiwfn-3.6_RHEL8.patch | 15 +++++++++++++++ 3 files changed, 25 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6_RHEL8.patch diff --git a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019a.eb b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019a.eb index 3cdf1bf27aa..3c302f99598 100644 --- a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019a.eb +++ b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019a.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'intel', 'version': '2019a'} source_urls = ['http://sobereva.com/multiwfn/misc/'] sources = ['%(name)s_%(version)s_src_Linux.zip'] -checksums = ['843f2ff0cba8e567b8c537c54ae68a4c242aaf2f08e828331a2d9cbfc7ba0a80'] +patches = ['%(name)s-%(version)s_RHEL8.patch'] +checksums = [ + '843f2ff0cba8e567b8c537c54ae68a4c242aaf2f08e828331a2d9cbfc7ba0a80', # Multiwfn_3.6_src_Linux.zip + '7a9e0eaa595355548258dfa978ae62dde2ffaa5d82f7dc100421dc5494f79699', # Multiwfn-3.6_RHEL8.patch +] # Make sure the noGUI.sh script runs in bash. prebuildopts = '/bin/bash noGUI.sh && cd noGUI && ' diff --git a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb index e1d141ed435..3210cc03229 100644 --- a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb +++ b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6-intel-2019b.eb @@ -17,7 +17,11 @@ source_urls = [ 'http://sobereva.com/multiwfn/old/%(version)s/', ] sources = ['%(name)s_%(version)s_src_Linux.zip'] -checksums = ['843f2ff0cba8e567b8c537c54ae68a4c242aaf2f08e828331a2d9cbfc7ba0a80'] +patches = ['%(name)s-%(version)s_RHEL8.patch'] +checksums = [ + '843f2ff0cba8e567b8c537c54ae68a4c242aaf2f08e828331a2d9cbfc7ba0a80', # Multiwfn_3.6_src_Linux.zip + '7a9e0eaa595355548258dfa978ae62dde2ffaa5d82f7dc100421dc5494f79699', # Multiwfn-3.6_RHEL8.patch +] # Make sure the noGUI.sh script runs in bash. prebuildopts = '/bin/bash noGUI.sh && cd noGUI && ' diff --git a/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6_RHEL8.patch b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6_RHEL8.patch new file mode 100644 index 00000000000..9e0e57fa1ff --- /dev/null +++ b/easybuild/easyconfigs/m/Multiwfn/Multiwfn-3.6_RHEL8.patch @@ -0,0 +1,15 @@ +# grep appareantly works slightly different on RHEL7 and RHEL8 +# see: https://github.com/easybuilders/easybuild-easyconfigs/issues/11394 +# SEP 29th 2020 by B. Hajgato (UGent) +diff -ru Multiwfn_3.6_src_Linux.orig/noGUI.sh Multiwfn_3.6_src_Linux/noGUI.sh +--- Multiwfn_3.6_src_Linux.orig/noGUI.sh 2020-09-29 11:50:28.477655541 +0200 ++++ Multiwfn_3.6_src_Linux/noGUI.sh 2020-09-29 11:48:33.489854445 +0200 +@@ -5,7 +5,7 @@ + cp *.F noGUI + for f90 in *.f90 + do +-grep -v -E "use dislin_d|use plot|use GUI|call drawdomaingui|call drawmolgui|call drawplanegui|call drawisosurgui|call drawmoltopogui|call drawsurfanalysis|call drawbasinintgui|call drawmol|call drawcurve|call drawscatter|call drawmatcolor|call drawplane|call useclrind|metafl|call window|scrmod|imgfmt|call page|disini|hwfont|axslen|axspos|wintit|call ticks|errmod|labdig|call name|setgrf|call graf|setrgb|call dash|call grid|call solid|call curve|call color|box2d|endgrf|xaxgit|disfin|disini|call ticks|errmod|legini|legtit|call frame|legpos|leglin|legpat|swgfnt|setscr|symfil|messag|imgfmt|complx|sursze|call center|rlmess|call rline|call height|setxid|winsiz|autres|ax3len|crvmat|getscr|ticpos|call labels|call dot|winsiz|namdis|call linwid|call legend|call setboxgui|call selfilegui|call selcolor|call setcolor|call minigui|call texmod|call triplx|call legopt|call myline|call hname|call setgraphformat" $f90 -i > noGUI/$f90 ++LC_ALL=C grep -v -E "use dislin_d|use plot|use GUI|call drawdomaingui|call drawmolgui|call drawplanegui|call drawisosurgui|call drawmoltopogui|call drawsurfanalysis|call drawbasinintgui|call drawmol|call drawcurve|call drawscatter|call drawmatcolor|call drawplane|call useclrind|metafl|call window|scrmod|imgfmt|call page|disini|hwfont|axslen|axspos|wintit|call ticks|errmod|labdig|call name|setgrf|call graf|setrgb|call dash|call grid|call solid|call curve|call color|box2d|endgrf|xaxgit|disfin|disini|call ticks|errmod|legini|legtit|call frame|legpos|leglin|legpat|swgfnt|setscr|symfil|messag|imgfmt|complx|sursze|call center|rlmess|call rline|call height|setxid|winsiz|autres|ax3len|crvmat|getscr|ticpos|call labels|call dot|winsiz|namdis|call linwid|call legend|call setboxgui|call selfilegui|call selcolor|call setcolor|call minigui|call texmod|call triplx|call legopt|call myline|call hname|call setgraphformat" $f90 -i > noGUI/$f90 + done + echo "Now you should run:" + echo "cd noGUI" From 4697abab4568783f427987ff6398c902cb165294 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 14:50:11 +0200 Subject: [PATCH 321/698] adding easyconfigs: FASTX-Toolkit-0.0.14-GCC-9.3.0.eb --- .../FASTX-Toolkit-0.0.14-GCC-9.3.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb new file mode 100644 index 00000000000..9c0005ae350 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb @@ -0,0 +1,63 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'Bundle' + +name = 'FASTX-Toolkit' +version = '0.0.14' + +homepage = 'http://hannonlab.cshl.edu/fastx_toolkit/' +description = """The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +default_easyblock = 'ConfigureMake' + +components = [ + ('libgtextutils', '0.7', { + 'source_urls': ['https://github.com/agordon/libgtextutils/releases/download/%(version)s/'], + 'sources': [SOURCE_TAR_GZ], + 'patches': ['libgtextutils-%(version)s_fix-bool.patch'], + 'checksums': [ + '792e0ea3c96ffe3ad65617a104b7dc50684932bc96d2adab501c952fd65c3e4a', # libgtextutils-0.7.tar.gz + 'bb16a4fd86c2eb12215d8780b09f0898771a73e53889a015e2351f2d737c9a00', # libgtextutils-0.7_fix-bool.patch + ], + 'start_dir': 'libgtextutils-%(version)s', + }), + (name, version, { + 'source_urls': ['https://github.com/agordon/fastx_toolkit/releases/download/%(version)s'], + 'sources': ['fastx_toolkit-%(version)s.tar.bz2'], + 'checksums': ['9e1f00c4c9f286be59ac0e07ddb7504f3b6433c93c5c7941d6e3208306ff5806'], + 'start_dir': 'fastx_toolkit-%(version)s', + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'configopts': 'CXXFLAGS="$CXXFLAGS -Wno-implicit-fallthrough"', + }), +] + +sanity_check_paths = { + 'files': + ['bin/fastx_%s' % x for x in + ['clipper', 'trimmer', 'quality_stats', 'artifacts_filter', 'reverse_complement', + 'collapser', 'uncollapser', 'renamer', 'barcode_splitter.pl', 'nucleotide_distribution_graph.sh', + 'nucleotide_distribution_line_graph.sh']] + + ['bin/fasta_%s' % x for x in + ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + + ['bin/fastq_%s' % x for x in + ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', + 'quality_trimmer', 'masker']] + + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], + 'dirs': [] +} + +moduleclass = 'bio' From 0055b217dc16e5222487fac9c3c8de3214ff5d7a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 14:53:53 +0200 Subject: [PATCH 322/698] adding easyconfigs: SiNVICT-1.0-20180817-GCC-9.3.0.eb --- .../SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb b/easybuild/easyconfigs/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb new file mode 100644 index 00000000000..d91fc6fc749 --- /dev/null +++ b/easybuild/easyconfigs/s/SiNVICT/SiNVICT-1.0-20180817-GCC-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'SiNVICT' +local_commit = 'b4d091e' +version = '1.0-20180817' + +homepage = 'https://github.com/sfu-compbio/sinvict' +description = """SiNVICT is a tool for the detection of SNVs and indels from cfDNA/ctDNA samples obtained + by ultra-deep sequencing.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['https://github.com/sfu-compbio/%(namelower)s/archive'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['b597b7743695f83e55decfa6c376b7785b18877b2e7e22a9270a0e919ff39097'] + +builddependencies = [ + ('CMake', '3.16.4'), +] +dependencies = [ + ('ABRA2', '2.23'), + ('bam-readcount', '0.8.0'), + ('BWA', '0.7.17'), + ('FASTX-Toolkit', '0.0.14'), +] + +files_to_copy = [(['sinvict'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/sinvict'], + 'dirs': [], +} + +sanity_check_commands = ["sinvict --help"] + +moduleclass = 'bio' From 790cfb543887bf0b8064506b370529c96849b594 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 15:08:38 +0200 Subject: [PATCH 323/698] add patch file for libgtextutils component of FASTX-Toolkit bundle --- .../f/FASTX-Toolkit/libgtextutils-0.7_fix-bool.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/f/FASTX-Toolkit/libgtextutils-0.7_fix-bool.patch diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/libgtextutils-0.7_fix-bool.patch b/easybuild/easyconfigs/f/FASTX-Toolkit/libgtextutils-0.7_fix-bool.patch new file mode 100644 index 00000000000..01d6eb5aa72 --- /dev/null +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/libgtextutils-0.7_fix-bool.patch @@ -0,0 +1,12 @@ +fix for error: no suitable conversion function from "std::istream" to "bool" exists +author: Kenneth Hoste (HPC-UGent) +--- libgtextutils-0.7/src/gtextutils/text_line_reader.cpp.orig 2018-06-08 17:38:32.090881776 +0200 ++++ libgtextutils-0.7/src/gtextutils/text_line_reader.cpp 2018-06-08 17:38:55.261151439 +0200 +@@ -44,6 +44,6 @@ + if (input_stream.eof()) + return false; + +- return input_stream ; ++ return (bool)input_stream ; + } + From 969ef8720d3ecaed86fc8cf7641d585c4b90de06 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 15:33:57 +0200 Subject: [PATCH 324/698] trim trailing whitespace --- .../f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb index 9c0005ae350..84f72de4174 100644 --- a/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/f/FASTX-Toolkit/FASTX-Toolkit-0.0.14-GCC-9.3.0.eb @@ -55,7 +55,7 @@ sanity_check_paths = { ['clipping_histogram.pl', 'formatter', 'nucleotide_changer']] + ['bin/fastq_%s' % x for x in ['quality_boxplot_graph.sh', 'quality_converter', 'to_fasta', 'quality_filter', - 'quality_trimmer', 'masker']] + + 'quality_trimmer', 'masker']] + ['lib/libgtextutils.%s' % SHLIB_EXT, 'lib/libgtextutils.a'], 'dirs': [] } From 9e6c58ed190bc4167377489c31a63e0c04b3df4e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 16:06:56 +0200 Subject: [PATCH 325/698] adding easyconfigs: ichorCNA-0.3.2-20191219-foss-2020a.eb --- .../ichorCNA-0.3.2-20191219-foss-2020a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb diff --git a/easybuild/easyconfigs/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb b/easybuild/easyconfigs/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb new file mode 100644 index 00000000000..c91d2422031 --- /dev/null +++ b/easybuild/easyconfigs/i/ichorCNA/ichorCNA-0.3.2-20191219-foss-2020a.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'ichorCNA' +local_commit = '5bfc03e' +version = '0.3.2-20191219' +github_account = 'broadinstitute' + +homepage = 'https://github.com/broadinstitute/ichorCNA/wiki' +description = """ichorCNA is a tool for estimating the fraction of tumor in cell-free DNA from ultra-low-pass whole +genome sequencing""" + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['38dbee4f4127fc27c4bd51fe3d99cb9eebea6fa9a15463127384923c217f1d74'] + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('R', '4.0.0'), + ('R-bundle-Bioconductor', '3.11', '-R-%(rver)s'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['ichorCNA'], +} + +moduleclass = 'bio' From 52ea036dc393dcc2e744fb9e201666f9a8597673 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 29 Sep 2020 21:29:29 +0200 Subject: [PATCH 326/698] adding easyconfigs: sbt-1.3.13-Java-1.8.eb --- .../easyconfigs/s/sbt/sbt-1.3.13-Java-1.8.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/sbt/sbt-1.3.13-Java-1.8.eb diff --git a/easybuild/easyconfigs/s/sbt/sbt-1.3.13-Java-1.8.eb b/easybuild/easyconfigs/s/sbt/sbt-1.3.13-Java-1.8.eb new file mode 100644 index 00000000000..4567328c6bb --- /dev/null +++ b/easybuild/easyconfigs/s/sbt/sbt-1.3.13-Java-1.8.eb @@ -0,0 +1,25 @@ +easyblock = 'Tarball' + +name = 'sbt' +version = '1.3.13' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://www.scala-sbt.org/' +description = "sbt is a build tool for Scala, Java, and more." + +toolchain = SYSTEM + +source_urls = ['https://github.com/sbt/sbt/releases/download/v%(version)s'] +sources = [SOURCE_TGZ] +checksums = ['854154de27a7d8c13b5a0f9a297cd1f254cc13b44588dae507e5d4fb2741bd22'] + +dependencies = [('Java', '1.8')] + +sanity_check_paths = { + 'files': ['bin/sbt'], + 'dirs': [], +} + +sanity_check_commands = ["sbt --version"] + +moduleclass = 'tools' From aa9256480c7d01134c09cd8dd61558156c5b2ee3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 30 Sep 2020 11:13:20 +0200 Subject: [PATCH 327/698] restrict build to libs and binaries of GDRCopy v2.1 --- .../GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 1f56cae730e..7689d85e557 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -22,24 +22,24 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -osdependencies = [ - # Kernel module for GDR Copy: improves Host to GPU communication - ('gdrcopy-kmod', 'gdrdrv-dkms'), - # Kernel module for GPUDirect RDMA: improves GPU to GPU communication - # Requires a Mellanox HCA with MLNX_OFED 2.1 - # https://github.com/Mellanox/nv_peer_memory - 'nvidia_peer_memory', -] - dependencies = [ ('CUDAcore', local_cudaversion, '', True), ('Check', '0.15.2'), ] +# Runtime dependencies: +# 1. Kernel module for GDR Copy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# 2. Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requires a Mellanox HCA with MLNX_OFED 2.1 + skipsteps = ['configure'] local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" -buildopts = "all %s" % local_envopts +buildopts = "config lib exes %s" % local_envopts installopts = local_envopts sanity_check_paths = { From a1d2a1fa7b3aa581ee0a8a04d44bc01f53b16c12 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 30 Sep 2020 11:13:51 +0200 Subject: [PATCH 328/698] adding easyconfigs: igraph-0.8.2-foss-2020a.eb, leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb, PyCairo-1.18.2-GCCcore-9.3.0.eb, python-igraph-0.8.0-foss-2020a.eb --- .../i/igraph/igraph-0.8.2-foss-2020a.eb | 42 ++++++++++++++++ ...leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb | 47 ++++++++++++++++++ .../p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb | 42 ++++++++++++++++ .../python-igraph-0.8.0-foss-2020a.eb | 48 +++++++++++++++++++ 4 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.8.2-foss-2020a.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.8.2-foss-2020a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.8.2-foss-2020a.eb new file mode 100644 index 00000000000..d418d42d049 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.8.2-foss-2020a.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'igraph' +version = '0.8.2' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['718a471e7b8cbf02e3e8006153b7be6a22f85bb804283763a0016280e8a60e95'] + +builddependencies = [ + ('Autotools', '20180311'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLPK', '4.65'), + ('libxml2', '2.9.10'), + ('zlib', '1.2.11'), +] + +preconfigopts = "autoreconf -i && " +# Remove hardcoded links to BLAS/LAPACK +preconfigopts += "sed -i 's/-lblas/$LIBBLAS/' configure && " +preconfigopts += "sed -i 's/-llapack/$LIBLAPACK/' configure && " + +configopts = "--with-external-blas --with-external-lapack --with-external-glpk" + +sanity_check_paths = { + 'files': ['lib/libigraph.%s' % x for x in [SHLIB_EXT, 'la', 'a']] + ['lib/pkgconfig/igraph.pc'] + + ['include/igraph/igraph%s.h' % x for x in ['', '_blas', '_constants', '_lapack', '_types', '_version']], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..450d9e4a7da --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.8.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('igraph', '0.8.2'), + ('python-igraph', '0.8.0'), + ('PyYAML', '5.3'), # Test-only +] + +use_pip = False +download_dep_fail = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('ddt', '1.4.1', { + 'checksums': ['0595e70d074e5777771a45709e99e9d215552fb1076443a25fad6b23d8bf38da'], + }), + (name, version, { + 'buildopts': '--use-pkg-config', + 'installopts': '--use-pkg-config', + 'testopts': '--use-pkg-config', + 'checksums': ['02cc8e87d2000ea1da60e9efc9287764fe81e445ab9850ec728b006c37620289'], + }), +] + +runtest = 'python setup.py test' + +sanity_check_commands = ["python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e5d9e97043a --- /dev/null +++ b/easybuild/easyconfigs/p/PyCairo/PyCairo-1.18.2-GCCcore-9.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'PyCairo' +version = '1.18.2' + +homepage = 'https://pycairo.readthedocs.io/' +description = """Python bindings for the cairo library""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dcb853fd020729516e8828ad364084e752327d4cff8505d20b13504b32b16531'] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cairo', '1.16.0'), +] + +# PyGTK needs PyCairo installed by pip +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# Don't build a wheel or the pkg-cfg file won't be installed +installopts = '--no-binary=%(namelower)s' + +sanity_check_paths = { + 'files': ['%s/%s.%s' % (p, n, e) + for (p, e) in [('include/pycairo', 'h'), ('lib/pkgconfig', 'pc')] for n in ['py3cairo', 'pycairo']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/cairo'], +} + +options = {'modulename': 'cairo'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb new file mode 100644 index 00000000000..6940abff575 --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.8.0' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('igraph', '0.8.2'), + ('PyCairo', '1.18.2'), +] + +use_pip = False +download_dep_fail = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('texttable', '1.6.3', { + 'checksums': ['ce0faf21aa77d806bbff22b107cc22cce68dc9438f97a2df32c93e9afa4ce436'], + }), + (name, version, { + 'buildopts': '--use-pkg-config', + 'installopts': '--use-pkg-config', + 'modulename': 'igraph', + 'checksums': ['47e6bb48ec7dbfddbd89cf064a24b271783a1490fc688ebce17fbd652bcdab8e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/igraph'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = ["python -c 'from igraph.drawing.utils import find_cairo; cairo = find_cairo(); cairo.Context'"] + +moduleclass = 'lib' From 75217e532cb764fb2832c6282da975eda447415e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 30 Sep 2020 11:24:37 +0200 Subject: [PATCH 329/698] adding easyconfigs: hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb --- ...thesis-3.66.18-intel-2018a-Python-3.6.4.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb new file mode 100644 index 00000000000..2177aa2a9bb --- /dev/null +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb @@ -0,0 +1,37 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'hypothesis' +version = '3.66.18' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/HypothesisWorks/hypothesis" +description = """Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized + by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets + you find more bugs in your code with less work.""" + +toolchain = {'name': 'intel', 'version': '2018a'} + +dependencies = [ + ('Python', '3.6.4'), +] + +use_pip = True + +exts_list = [ + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('coverage', '5.3', { + 'source_urls': ['https://pypi.python.org/packages/source/c/coverage'], + 'checksums': ['280baa8ec489c4f542f8940f9c4c2181f0306a8ee1a54eceba071a449fb870a0'], + }), + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], + 'checksums': ['6bcf0e565cd394080d692f4595215335a90a868325aa4869dfe7450be9a8a583'], + }), +] + +moduleclass = 'tools' From 764dfe81b6073d1be1f953a25c7d62d6cd470780 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 30 Sep 2020 11:55:56 +0200 Subject: [PATCH 330/698] fix OpenFOAM 2.3.1-intel-2019b installation on RHEL8 --- .../o/OpenFOAM/OpenFOAM-2.3.1-intel-2019b.eb | 2 ++ .../o/OpenFOAM/OpenFOAM-2.3.1_RHEL8.patch | 35 +++++++++++++++++++ 2 files changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1_RHEL8.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2019b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2019b.eb index 9887a3cb920..d8367c25160 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2019b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1-intel-2019b.eb @@ -17,6 +17,7 @@ sources = [ patches = [ 'OpenFOAM-%(version)s_cleanup.patch', 'OpenFOAM-2.3.0_libreadline.patch', + 'OpenFOAM-2.3.1_RHEL8.patch', ('ThirdParty-%(version)s_cleanup.patch', ".."), # patch should not be applied in OpenFOAM subdir ] checksums = [ @@ -24,6 +25,7 @@ checksums = [ 'f19820ce88e91397d7d4d00869438141c265872348ab7d83f6688741ff037b09', # ThirdParty-2.3.1.tgz 'e045204878472e6b3e68466a4b64818a6941ac727d16d54738b9c9f93b77e749', # OpenFOAM-2.3.1_cleanup.patch 'f1c94764fe07a43877d85497d5c7958a3f162d1b5f1370232084912a6d606181', # OpenFOAM-2.3.0_libreadline.patch + 'a7d95f23aa64eb84f406d95a08633f79b100e4c8fc4e189cb63265d9e3c61dd1', # OpenFOAM-2.3.1_RHEL8.patch '7d213f2c5a33ced70a1b50c44cd8f7db303a2494c0ece4a181e430c9b6ab4e24', # ThirdParty-2.3.1_cleanup.patch ] diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1_RHEL8.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1_RHEL8.patch new file mode 100644 index 00000000000..3009d6dbb8d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-2.3.1_RHEL8.patch @@ -0,0 +1,35 @@ +# https://bugs.openfoam.org/view.php?id=2041 +# SEP 30th 2020 by B. Hajgato (UGent) +diff -ru OpenFOAM-2.3.1.orig/src/conversion/ensight/part/ensightPart.C OpenFOAM-2.3.1/src/conversion/ensight/part/ensightPart.C +--- OpenFOAM-2.3.1.orig/src/conversion/ensight/part/ensightPart.C 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/conversion/ensight/part/ensightPart.C 2020-09-30 10:49:21.224963571 +0200 +@@ -51,7 +51,7 @@ + { + const label id = idList[i]; + +- if (id >= field.size() || isnan(field[id])) ++ if (id >= field.size() || std::isnan(field[id])) + { + return false; + } +diff -ru OpenFOAM-2.3.1.orig/src/conversion/ensight/part/ensightPartIO.C OpenFOAM-2.3.1/src/conversion/ensight/part/ensightPartIO.C +--- OpenFOAM-2.3.1.orig/src/conversion/ensight/part/ensightPartIO.C 2014-12-04 18:52:43.000000000 +0100 ++++ OpenFOAM-2.3.1/src/conversion/ensight/part/ensightPartIO.C 2020-09-30 10:48:35.957662437 +0200 +@@ -63,7 +63,7 @@ + { + forAll(idList, i) + { +- if (idList[i] >= field.size() || isnan(field[idList[i]])) ++ if (idList[i] >= field.size() || std::isnan(field[idList[i]])) + { + os.writeUndef(); + } +@@ -80,7 +80,7 @@ + // no idList => perNode + forAll(field, i) + { +- if (isnan(field[i])) ++ if (std::isnan(field[i])) + { + os.writeUndef(); + } From 52cd4e64fc925afea9e86a3b09bf0eb18f5b35f0 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 30 Sep 2020 13:08:25 +0200 Subject: [PATCH 331/698] igraph: disable download_dep_fail in PythonBundle --- .../l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb | 2 +- .../p/python-igraph/python-igraph-0.8.0-foss-2020a.eb | 1 - 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb index 450d9e4a7da..9dd63291a24 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb @@ -22,11 +22,11 @@ dependencies = [ ] use_pip = False -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ + # Test-only dependency ('ddt', '1.4.1', { 'checksums': ['0595e70d074e5777771a45709e99e9d215552fb1076443a25fad6b23d8bf38da'], }), diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb index 6940abff575..1556aec6c7f 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.8.0-foss-2020a.eb @@ -21,7 +21,6 @@ dependencies = [ ] use_pip = False -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From 6f07082f2a9ae1f5e33f3b64250ec296a3e9154c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 30 Sep 2020 14:19:15 +0200 Subject: [PATCH 332/698] expand comment with runtime requirements --- .../GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 7689d85e557..1811b780d6d 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -27,14 +27,17 @@ dependencies = [ ('Check', '0.15.2'), ] -# Runtime dependencies: -# 1. Kernel module for GDR Copy: improves Host to GPU communication +# Runtime system dependencies: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication # https://github.com/NVIDIA/gdrcopy # RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# 2. Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication # https://github.com/Mellanox/nv_peer_memory # RPM: 'nvidia_peer_memory' -# Requires a Mellanox HCA with MLNX_OFED 2.1 +# Requirements: Mellanox HCA with MLNX_OFED 2.1 skipsteps = ['configure'] From f8b8101a7721ef8222fbee25a4fd3e6df5c7e613 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Wed, 30 Sep 2020 15:18:53 +0200 Subject: [PATCH 333/698] adding easyconfigs: OPERA-MS-0.9.0-foss-2020a.eb --- .../o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb new file mode 100644 index 00000000000..683c4479edd --- /dev/null +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb @@ -0,0 +1,56 @@ +easyblock = 'MakeCp' + +name = 'OPERA-MS' +version = '0.9.0' + +homepage = 'https://github.com/CSB5/OPERA-MS' +description = """OPERA-MS is a hybrid metagenomic assembler which combines the + advantages of short and long-read technologies to provide high quality + assemblies, addressing issues of low contiguity for short-read only assemblies, + and low base-pair quality for long-read only assemblies.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] +sources = ['OPERA-MS-%(version)s.tar.gz'] +checksums = ['750f7f7325b9064c6479d51e1e5861772f1305c4cb219924c64bc4363922e862'] + +dependencies = [ + ('Perl', '5.30.2'), + ('Statistics-R', '0.34'), +] + +buildopts = 'CFLAGS="$CFLAGS"' + +files_to_copy = [ + 'OPERA-MS.pl', + 'bin', + 'src_utils', + 'tools_opera_ms', + (['OPERA-LG/bin'], 'OPERA-LG'), +] + +postinstallcmds = [ + "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", + 'chmod +x %(installdir)s/bin/OPERA-MS', + 'ln -s $(which perl) %(installdir)s/tools_opera_ms/perl', + 'cd test_files && %(installdir)s/bin/OPERA-MS ' + ' '.join([ + '--contig-file contigs.fasta', + '--short-read1 R1.fastq.gz', + '--short-read2 R2.fastq.gz', + '--long-read long_read.fastq', + '--no-ref-clustering', + '--out-dir $(mktemp -d)', + ]), +] + +sanity_check_paths = { + 'files': ['bin/OPERA-MS'], + 'dirs': [], +} + +sanity_check_commands = [ + 'OPERA-MS check-dependency', +] + +moduleclass = 'bio' From 2dbd93b0a81624c7f81b411d0fea38f03744fc5f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 30 Sep 2020 19:31:06 +0200 Subject: [PATCH 334/698] add reason to not add kernel modules as osdependencies --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 1811b780d6d..03d54228af6 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -27,7 +27,8 @@ dependencies = [ ('Check', '0.15.2'), ] -# Runtime system dependencies: +# This easyconfig only installs the library and binaries of GDRCopy. Please +# keep in mind that GDRCopy also needs the following kernel modules at runtime: # # 1. Kernel module for GDRCopy: improves Host to GPU communication # https://github.com/NVIDIA/gdrcopy @@ -38,6 +39,9 @@ dependencies = [ # https://github.com/Mellanox/nv_peer_memory # RPM: 'nvidia_peer_memory' # Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. skipsteps = ['configure'] From 209e1eb9d281ed070b6759d0e3cc22ecb59c8488 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 1 Oct 2020 00:15:26 +0000 Subject: [PATCH 335/698] Ensure ldconfig is found, add /sbin at end of PATH It's not in the standard PATH on generoso. --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 03d54228af6..581ee37ab31 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -46,6 +46,7 @@ dependencies = [ skipsteps = ['configure'] local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found buildopts = "config lib exes %s" % local_envopts installopts = local_envopts From dcda23b85b2d469213a06efcd22f16519fa8c08d Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Thu, 1 Oct 2020 00:56:38 +0000 Subject: [PATCH 336/698] Need at least two spaces before inline comment --- .../g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb index 581ee37ab31..a506adc95d9 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.1-GCCcore-9.3.0-CUDA-11.0.2.eb @@ -46,7 +46,7 @@ dependencies = [ skipsteps = ['configure'] local_envopts = "PREFIX=%(installdir)s CUDA=$EBROOTCUDACORE" -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found buildopts = "config lib exes %s" % local_envopts installopts = local_envopts From 52d6f26e947515abce08d850717472d7266a13d2 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 1 Oct 2020 08:07:38 +0200 Subject: [PATCH 337/698] fix broken worker easyconfigs --- easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb | 2 ++ easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb | 2 ++ easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb | 2 ++ easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb | 2 ++ easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb | 2 ++ easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb | 2 ++ 6 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb index ea77925899b..10568fa1b7c 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb @@ -61,6 +61,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb index bd1b0c267a0..2c693ff8f62 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2016b.eb @@ -61,6 +61,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb index 8010198e614..b01f8c80898 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb @@ -61,6 +61,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb index 097eb6e0b22..4b19a44f403 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb @@ -61,6 +61,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb index c6304dd5758..63772fb1e21 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb @@ -63,6 +63,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb index eb8890d877e..2095d04f12c 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb @@ -63,6 +63,8 @@ exts_list = [ }), ] +preconfigopts = "export CC=mpiicc && " + modextrapaths = { 'PERL5LIB': ['share/perl5', 'lib64/perl5'], } From f4cd8ed3dc3374d4d911dc45ea960ac3a1694d3b Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 1 Oct 2020 09:20:07 +0200 Subject: [PATCH 338/698] http -> https --- easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb | 2 +- easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb index b01f8c80898..0527687dcfc 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017a.eb @@ -36,7 +36,7 @@ exts_list = [ }), ('Text::CSV', '1.95', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], 'checksums': ['7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61'], }), ('DBI', '1.637', { diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb index 4b19a44f403..0dfe03883a2 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.7-intel-2017b.eb @@ -36,7 +36,7 @@ exts_list = [ }), ('Text::CSV', '1.95', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], 'checksums': ['7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61'], }), ('DBI', '1.637', { diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb index 63772fb1e21..785bdd1f83c 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018a.eb @@ -38,7 +38,7 @@ exts_list = [ }), ('Text::CSV', '1.95', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], 'checksums': ['7e0a11d9c1129a55b68a26aa4b37c894279df255aa63ec8341d514ab848dbf61'], }), ('DBI', '1.640', { diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb index 2095d04f12c..eed2b611955 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.8-intel-2018b.eb @@ -38,7 +38,7 @@ exts_list = [ }), ('Text::CSV', '1.97', { 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['http://search.cpan.org/CPAN/authors/id/I/IS/ISHIGAKI'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], 'checksums': ['cc350462efa8d39d5c8a1da5f205bc31620cd52d9865a769c8e3ed1b41640fd5'], }), ('DBI', '1.642', { From da541defea0404be1c4d2ce4c24232cfdd3c6dbe Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Thu, 1 Oct 2020 12:23:29 +0200 Subject: [PATCH 339/698] OPERA-MS: style --- .../o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb index 683c4479edd..2b9faa5160f 100644 --- a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb @@ -33,14 +33,14 @@ files_to_copy = [ postinstallcmds = [ "echo '#!/bin/sh\n exec perl %(installdir)s/OPERA-MS.pl $@' > %(installdir)s/bin/OPERA-MS", 'chmod +x %(installdir)s/bin/OPERA-MS', - 'ln -s $(which perl) %(installdir)s/tools_opera_ms/perl', - 'cd test_files && %(installdir)s/bin/OPERA-MS ' + ' '.join([ - '--contig-file contigs.fasta', - '--short-read1 R1.fastq.gz', - '--short-read2 R2.fastq.gz', - '--long-read long_read.fastq', + 'ln -s $EBROOTPERL/bin/perl %(installdir)s/tools_opera_ms/perl', + '%(installdir)s/bin/OPERA-MS ' + ' '.join([ + '--contig-file test_files/contigs.fasta', + '--short-read1 test_files/R1.fastq.gz', + '--short-read2 test_files/R2.fastq.gz', + '--long-read test_files/long_read.fastq', '--no-ref-clustering', - '--out-dir $(mktemp -d)', + '--out-dir $TMPDIR', ]), ] @@ -50,6 +50,7 @@ sanity_check_paths = { } sanity_check_commands = [ + 'OPERA-MS --help', 'OPERA-MS check-dependency', ] From 8b5672d4b062859a77bd04cb2a161386520be392 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Thu, 1 Oct 2020 12:27:30 +0200 Subject: [PATCH 340/698] leidenalg: style --- .../l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb index 9dd63291a24..8c2bfd11d63 100644 --- a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.8.2-foss-2020a-Python-3.8.2.eb @@ -12,13 +12,13 @@ toolchain = {'name': 'foss', 'version': '2020a'} builddependencies = [ ('pkg-config', '0.29.2'), + ('PyYAML', '5.3'), ] dependencies = [ ('Python', '3.8.2'), ('igraph', '0.8.2'), ('python-igraph', '0.8.0'), - ('PyYAML', '5.3'), # Test-only ] use_pip = False @@ -34,12 +34,11 @@ exts_list = [ 'buildopts': '--use-pkg-config', 'installopts': '--use-pkg-config', 'testopts': '--use-pkg-config', + 'runtest': 'python setup.py test', 'checksums': ['02cc8e87d2000ea1da60e9efc9287764fe81e445ab9850ec728b006c37620289'], }), ] -runtest = 'python setup.py test' - sanity_check_commands = ["python -c 'import leidenalg; import igraph as ig; " "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " "leidenalg.ModularityVertexPartition)'"] From 983c2e0bb301736c50a62957939d75a4ac0c0aa3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 1 Oct 2020 12:53:40 +0200 Subject: [PATCH 341/698] adding easyconfigs: SBCL-2.0.9-GCCcore-9.3.0.eb --- .../s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..40a02abec4d --- /dev/null +++ b/easybuild/easyconfigs/s/SBCL/SBCL-2.0.9-GCCcore-9.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' +name = 'SBCL' +version = '2.0.9' + +homepage = 'http://sbcl.sourceforge.net/' +description = """ +Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is +open source / free software, with a permissive license. In addition to the +compiler and runtime system for ANSI Common Lisp, it provides an interactive +environment including a debugger, a statistical profiler, a code coverage tool, +and many other extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.bz2'] +checksums = ['c4f700350c113fe003ee93a9922146209d6fa50b63c6accc4abf90fb38cb9b9f'] + +builddependencies = [ + ('binutils', '2.34'), + ('CCL', '1.12'), +] + +parallel = False +skipsteps = ['configure'] +local_prefixarg = '--prefix=%(installdir)s' + +# Build SBCL with Clozure CL +# Using the binary distribution of SBCL to build SBCL is not trivial because +# it needs GLIBC v2.28 +build_cmd = "sh make.sh" +buildopts = "%s --xc-host=ccl" % local_prefixarg + +install_cmd = "sh install.sh" +installopts = local_prefixarg + +sanity_check_paths = { + 'files': ['bin/sbcl'], + 'dirs': ['lib/sbcl'], +} + +sanity_check_commands = ["sbcl --help"] + +modextrapaths = {'SBCL_HOME': 'lib/sbcl'} + +moduleclass = 'lang' From 158b562b6d3ac7c9d07a1bddd7cf7182113f8522 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 1 Oct 2020 14:08:05 +0200 Subject: [PATCH 342/698] adding easyconfigs: DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb and patches: DIRAC-19.0_remove-broken-tests-intel.patch --- ...AC-19.0-intel-2020a-Python-2.7.18-int64.eb | 69 +++++++++++++++++++ ...DIRAC-19.0_remove-broken-tests-intel.patch | 32 +++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb new file mode 100644 index 00000000000..d75cf2805b5 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb @@ -0,0 +1,69 @@ +easyblock = 'ConfigureMake' + +name = 'DIRAC' +version = '19.0' +versionsuffix = '-Python-%(pyver)s-int64' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://zenodo.org/record/3572669/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +patches = ['%(name)s-%(version)s_remove-broken-tests-intel.patch'] +checksums = [ + 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz + '33e884d197724fdb98cd5e395ca46d065a620eb70f19c5a120fcb0ce07ac4290', # DIRAC-19.0_remove-broken-tests-intel.patch +] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('Python', '2.7.18'), + ('Boost', '1.72.0'), + ('HDF5', '1.10.6'), + ('imkl', '2020.1.217'), +] +separate_build_dir = True + +skipsteps = ['configure'] + +parallel = 1 + +local_pre_flags = 'export CFLAGS="$CFLAGS -m64" && ' +local_pre_flags += 'export CXXFLAGS="$CXXFLAGS -m64" && ' +local_pre_flags += 'export FCFLAGS="$FCFLAGS -i8" && ' +local_pre_flags += 'export FFLAGS="$FFLAGS -i8 " && ' +local_pre_flags += 'export DEBUG=True && ' + +# BUILD +prebuildopts = local_pre_flags +prebuildopts += 'export MATH_ROOT="$MKLROOT" && ' +prebuildopts += './setup --int64 --prefix=%(installdir)s ' +prebuildopts += '--pcmsolver=OFF --cc="$CC" --cxx="$CXX" --fc="$FC" ' +prebuildopts += '--mkl=parallel ' +prebuildopts += '&& cd build && ' + +# TEST +pretestopts = local_pre_flags +pretestopts += 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +pretestopts += "cd build && " + +runtest = 'test' + +# INSTALL +preinstallopts = local_pre_flags +preinstallopts += "cd build && " + +# SANITY CHECKS +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch new file mode 100644 index 00000000000..03e2ec27a6b --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch @@ -0,0 +1,32 @@ +Removed tests which fails on intel compilers. + +"bss_energy" has slight abs difference (2.24e-07) in calculation. + +"operators_mo_mtx_elements" doesn't run when mpi is enabled (even if test doesn't use mpi) +see: https://ccportal.ims.ac.jp/en/node/2411 + +Author: Pavel Grochal (INUITS) +diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/cmake/custom/test.cmake 2020-09-24 12:54:02.524830820 +0200 +@@ -102,7 +102,7 @@ + dirac_test(basis_input "basis;short" "") + dirac_test(basis_input_scripted "basis;long" "3600") + dirac_test(bsse "basis;short" "") +-dirac_test(bss_energy "short" "") ++# dirac_test(bss_energy "short" "") + dirac_test(pam_test "short;pam" "") + dirac_test(cc_essential "short;cc" "") + dirac_test(cc_linear "short;cc" "") +@@ -158,9 +158,8 @@ + dirac_test(lucita_q_corrections "short;qcorr;ci" "") + dirac_test(x2c-SCF_to_4c-SCF "short;x2c;4c;scf" "") + dirac_test(import_mos "short;import;scf;mcscf" "") +-dirac_test(operators_mo_mtx_elements "short;operators" "") ++# dirac_test(operators_mo_mtx_elements "short;operators" "") + dirac_test(spinorbit-from-spinfree "short;scf;resolve" "") + dirac_test(spinrot "short;response" "") + # disabing eomcc expectation value test until the code is verified + #dirac_test(eomcc_expval "short;cc" "") +- + From f7b69b99c844b0c43a84f1a166fee112fa7cb5ea Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 1 Oct 2020 14:33:21 +0200 Subject: [PATCH 343/698] removed unused variable --- .../d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb index d75cf2805b5..b0cde2d295e 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb @@ -27,7 +27,6 @@ dependencies = [ ('HDF5', '1.10.6'), ('imkl', '2020.1.217'), ] -separate_build_dir = True skipsteps = ['configure'] From 1121b6880b7fa804810b936cd67951d300c125bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 1 Oct 2020 15:16:35 +0200 Subject: [PATCH 344/698] Add ncurses runtime dependency to Clang --- easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb | 1 + .../easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb | 1 + .../easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb index 69b785b442d..1389645ee55 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-8.3.0.eb @@ -49,6 +49,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.32'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb index f85720c3a96..8ac1c941d22 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -52,6 +52,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.32'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ('CUDA', local_cudaver), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb index a44f941c7ed..015c81f782a 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -52,6 +52,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.32'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ('CUDA', local_cudaver), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb index 7fd56412b38..963df6df8c9 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb @@ -49,6 +49,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.32'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ] From 024158ef96e772258304109e9efed6f93c222587 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 1 Oct 2020 15:19:58 +0200 Subject: [PATCH 345/698] Add ncurses runtime dependency to Clang --- .../c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb | 1 + .../c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb index 1d8e25e0cb8..4d5f014edba 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0-CUDA-10.1.105.eb @@ -52,6 +52,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.31.1'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ('CUDA', local_cudaver, '', True), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb index 2afdaba65aa..711414b2246 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.0-GCCcore-8.2.0.eb @@ -49,6 +49,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.31.1'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb index 456d8764512..674b649a548 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-8.0.1-GCC-8.2.0-2.31.1-CUDA-10.1.105.eb @@ -52,6 +52,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.31.1'), + ('ncurses', '6.1'), ('GMP', '6.1.2'), ('CUDA', local_cudaver), ] From 36875fcadda146077c54a54991a560be38d7b80d Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 1 Oct 2020 16:44:01 +0200 Subject: [PATCH 346/698] aarch64-fixing. --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 46 +++---- .../dada2-1.16.0-remove-sse-on-aarch64.patch | 90 ++++++++++++ .../mzR-2.22.0_use-external-boost.patch | 129 ++++++++++++++++++ 3 files changed, 235 insertions(+), 30 deletions(-) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/dada2-1.16.0-remove-sse-on-aarch64.patch create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 5eeb96b870a..cd9f435d172 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -12,8 +12,11 @@ toolchain = {'name': 'foss', 'version': '2020a'} builddependencies = [('pkg-config', '0.29.2')] +buildopts = "-fpermissive " + dependencies = [ ('R', '4.0.0'), + ('Boost', '1.72.0'), # for mzR ('HDF5', '1.10.6'), # for rhdf5 ('MariaDB-connector-c', '3.1.7'), # for RMySQL ('ncdf4', '1.17', versionsuffix), # for mzR @@ -453,10 +456,12 @@ exts_list = [ 'checksums': ['6d3a4ef1ae93ac057d8f4f9378f9ed078616310fb0f3af5aabf8bd1eadf43e09'], }), ('dada2', '1.16.0', { - 'checksums': ['20f1215fc67cf00d5019993fb3d6397c1ef418736996e15eecf36cec3cfecdc5'], - }), - ('LEA', '3.0.0', { - 'checksums': ['802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa'], + 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], + 'checksums': [ + '20f1215fc67cf00d5019993fb3d6397c1ef418736996e15eecf36cec3cfecdc5', # dada2_1.16.0.tar.gz + # dada2-1.16.0-remove-sse-on-aarch64.patch + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + ], }), ('tximport', '1.16.0', { 'checksums': ['b5f35cea2b9746ba92bc66f23c9566c2e565681e6527071e66d401072b5a2446'], @@ -549,7 +554,11 @@ exts_list = [ 'checksums': ['c5962909033d5fb9d13b34ca5ad5ba5d6343c485bc64e38ef97756d5e6a7a078'], }), ('mzR', '2.22.0', { - 'checksums': ['9509d6d831584af8866aa3d1dd1b22f4333e85fafa0c48e4b18ad1f2a34712e5'], + 'patches': ['mzR-2.22.0_use-external-boost.patch'], + 'checksums': [ + '9509d6d831584af8866aa3d1dd1b22f4333e85fafa0c48e4b18ad1f2a34712e5', # mzR_2.22.0.tar.gz + '5b524c5a0c9ffce91012a9f3b1918e5e2ed68d739316949b7790e6620ff7c8f1', # mzR-2.22.0_use-external-boost.patch + ], }), ('MSnbase', '2.14.0', { 'checksums': ['f35b9d023047dfd5ae32bf43fa166e7e3d245c4d5708fac08f84270713f3d7d2'], @@ -812,37 +821,14 @@ exts_list = [ ('stageR', '1.10.0', { 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), - ('isva', '1.9', { - 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], - }), - ('org.Mm.eg.db', '3.11.4', { - 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], - }), - ('org.Rn.eg.db', '3.11.4', { - 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], - }), - ('ROC', '1.64.0', { - 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], - }), - ('wateRmelon', '1.32.0', { - 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], - }), - ('GLAD', '2.52.0', { - 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], - }), - ('missMethyl', '1.22.0', { - 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], - }), - ('MethylSeekR', '1.28.0', { - 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], - }), ] modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], + 'dirs': ['.'], +# 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], } moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/dada2-1.16.0-remove-sse-on-aarch64.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/dada2-1.16.0-remove-sse-on-aarch64.patch new file mode 100644 index 00000000000..baab7b369a0 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/dada2-1.16.0-remove-sse-on-aarch64.patch @@ -0,0 +1,90 @@ +From c9c9bb95d5ee2f4bfc7a266ac4fe869f931ee3c1 Mon Sep 17 00:00:00 2001 +From: Terje Kvernes +Date: Mon, 28 Sep 2020 20:29:28 +0200 +Subject: [PATCH] Filter out SSE usage for non-x86_64. + + - Symbols are still maintained as they are used + in a mnumber of places. + - SSE should be set to 0 for non-x86_x64 so the + code paths expecting SSE should never be called. +--- + src/Rmain.cpp | 7 ++++++- + src/kmers.cpp | 19 +++++++++++++++++++ + 2 files changed, 25 insertions(+), 1 deletion(-) + +diff --git a/src/Rmain.cpp b/src/Rmain.cpp +index c9386fc..3459c65 100755 +--- a/src/Rmain.cpp ++++ b/src/Rmain.cpp +@@ -3,7 +3,12 @@ + ///#ifdef _WIN32 // Windows + #if defined(_WIN32) && !defined(__MINGW32__) // Windows and not MINGW + #define cpuid(info, x) __cpuidex(info, x, 0) +-#else // GCC Intrinsics ++#elif defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__) ++void cpuid(int32_t out[4], int32_t x) { ++ // Just disable it as anything better is unimplemented. ++ out[0] = 0; ++} ++#else // GCC Intrinsics on x86_64 + #include + void cpuid(int info[4], int InfoType){ + __cpuid_count(InfoType, 0, info[0], info[1], info[2], info[3]); +diff --git a/src/kmers.cpp b/src/kmers.cpp +index 651887b..5340055 100644 +--- a/src/kmers.cpp ++++ b/src/kmers.cpp +@@ -1,6 +1,8 @@ + #include + #include "dada.h" ++#if ! (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__)) + #include "emmintrin.h" ++#endif + // #if _WIN32 + // #include + // #endif +@@ -26,6 +28,15 @@ double kmer_dist(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) { + return (1. - dot); + } + ++// These should never be called, but the symbols will have to exist ++#if (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__)) ++double kmer_dist_SSEi(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) { ++ return 0.0; ++} ++double kmer_dist_SSEi_8(uint8_t *kv1, int len1, uint8_t *kv2, int len2, int k) { ++ return 0.0; ++} ++#else + // Computes kmer distance with SSE2 intrinsics. + double kmer_dist_SSEi(uint16_t *kv1, int len1, uint16_t *kv2, int len2, int k) { + size_t n_kmer = 1 << (2*k); // 4^k kmers +@@ -87,6 +98,8 @@ double kmer_dist_SSEi_8(uint8_t *kv1, int len1, uint8_t *kv2, int len2, int k) { + dot = ((double) dotsum)/((len1 < len2 ? len1 : len2) - k + 1.); + return (1. - dot); + } ++#endif ++ + + // Computes "kmer distance" with SSE2 intrinsics, based on ordered kmers (e.g. gapless align) + // If different lengths, returns -1 (invalid) +@@ -106,6 +119,11 @@ double kord_dist(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) { + return (1. - dot); + } + ++#if (defined(__ppc64__) || defined(__PPC64__) || defined(__s390x__) || defined(__aarch64__)) ++double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) { ++ return 0.0; ++} ++#else + // Computes "kmer distance" with SSE2 intrinsics, based on ordered kmers (e.g. gapless align) + // If different lengths, returns -1 (invalid) + double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int k) { +@@ -138,6 +156,7 @@ double kord_dist_SSEi(uint16_t *kord1, int len1, uint16_t *kord2, int len2, int + dot = ((double) dotsum)/((len1 < len2 ? len1 : len2) - k + 1.); + return (1. - dot); + } ++#endif + + void assign_kmer8(uint8_t *kvec8, const char *seq, int k) { // Assumes a clean seq (just 1s,2s,3s,4s) + int i, j, nti; diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch new file mode 100644 index 00000000000..51f0d3aae28 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch @@ -0,0 +1,129 @@ +diff -ru mzR.orig/src/Makevars mzR/src/Makevars +--- mzR.orig/src/Makevars 2020-04-27 22:27:42.000000000 +0200 ++++ mzR/src/Makevars 2020-10-01 14:26:45.334914542 +0200 +@@ -1,30 +1,4 @@ + PWIZOBJECTS=\ +-./boost/libs/system/src/error_code.o \ +-./boost/libs/regex/src/posix_api.o \ +-./boost/libs/regex/src/fileiter.o \ +-./boost/libs/regex/src/regex_raw_buffer.o \ +-./boost/libs/regex/src/cregex.o \ +-./boost/libs/regex/src/regex_debug.o \ +-./boost/libs/regex/src/instances.o \ +-./boost/libs/regex/src/icu.o \ +-./boost/libs/regex/src/usinstances.o \ +-./boost/libs/regex/src/regex.o \ +-./boost/libs/regex/src/wide_posix_api.o \ +-./boost/libs/regex/src/regex_traits_defaults.o \ +-./boost/libs/regex/src/winstances.o \ +-./boost/libs/regex/src/wc_regex_traits.o \ +-./boost/libs/regex/src/c_regex_traits.o \ +-./boost/libs/regex/src/cpp_regex_traits.o \ +-./boost/libs/regex/src/static_mutex.o \ +-./boost/libs/regex/src/w32_regex_traits.o \ +-./boost/libs/iostreams/src/zlib.o \ +-./boost/libs/iostreams/src/file_descriptor.o \ +-./boost/libs/filesystem/src/operations.o \ +-./boost/libs/filesystem/src/path.o \ +-./boost/libs/filesystem/src/utf8_codecvt_facet.o \ +-./boost/libs/chrono/src/chrono.o \ +-./boost/libs/chrono/src/process_cpu_clocks.o \ +-./boost/libs/chrono/src/thread_clock.o \ + ./pwiz/data/msdata/Version.o \ + ./pwiz/data/identdata/Version.o \ + ./pwiz/data/common/MemoryIndex.o \ +@@ -104,20 +78,15 @@ + + + ifeq ($(OS),Windows_NT) +-ARCH_OBJS=./boost/libs/filesystem/src/path_traits.o \ +-./boost/libs/filesystem/src/windows_file_codecvt.o \ +-./boost/libs/filesystem/src/codecvt_error_category.o \ +-./boost/libs/thread/src/win32/tss_pe.o \ +-./boost/libs/thread/src/win32/tss_dll.o \ +-./boost/libs/thread/src/win32/thread.o \ ++ARCH_OBJS=\ + ./pwiz/data/msdata/ramp/wglob.o \ + ./boost_aux/boost/nowide/iostream.o + ARCH_CPPFLAGS=-fpermissive -DWINDOWS_NATIVE -DWIN32 -DBOOST_HAS_WINTHREADS -DBOOST_THREAD_BUILD_LIB + ARCH_LIBS=-lws2_32 -lz + RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave) + else +-ARCH_OBJS=./boost/libs/thread/src/pthread/once.o \ +-./boost/libs/thread/src/pthread/thread.o ++ARCH_OBJS= ++ARCH_LIBS=-lboost_chrono -lboost_filesystem -lboost_iostreams -lboost_thread + RHDF5_LIBS=$(shell echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| "${R_HOME}/bin/R" --vanilla --slave) + endif + +@@ -133,7 +102,7 @@ + ## http://www.gamedev.net/topic/555511-is-there-a-way-to-only-disable-boost-debug-checks/ + ## + +-PWIZ_CPPFLAGS=-I./boost_aux/ -I./boost/ -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG ++PWIZ_CPPFLAGS=-I./boost_aux/ -I$(EBROOTBOOST)/include -I. -D_LARGEFILE_SOURCE -DHAVE_PWIZ_MZML_LIB -D_NODEBUG + PWIZ_LDFLAGS=-lpthread + + ## Use the R_HOME indirection to support installations of multiple R version +diff -ru mzR.orig/src/pwiz/data/identdata/IdentData.cpp mzR/src/pwiz/data/identdata/IdentData.cpp +--- mzR.orig/src/pwiz/data/identdata/IdentData.cpp 2020-04-27 22:27:42.000000000 +0200 ++++ mzR/src/pwiz/data/identdata/IdentData.cpp 2020-10-01 14:11:08.554729901 +0200 +@@ -1042,7 +1042,7 @@ + BOOST_FOREACH(CVID cleavageAgent, cleavageAgents) + { + if (!findPeptideEvidenceWithRegex(pe, peptide, peptideSequenceInContext, cleavageAgent, "", +- sip.enzymes.independent, nTerminusIsSpecific, cTerminusIsSpecific, ++ static_cast(sip.enzymes.independent), nTerminusIsSpecific, cTerminusIsSpecific, + bestSpecificity, bestResult)) + break; + } +@@ -1050,7 +1050,7 @@ + BOOST_FOREACH(const string& regex, cleavageAgentRegexes) + { + if (!findPeptideEvidenceWithRegex(pe, peptide, peptideSequenceInContext, CVID_Unknown, regex, +- sip.enzymes.independent, nTerminusIsSpecific, cTerminusIsSpecific, ++ static_cast(sip.enzymes.independent), nTerminusIsSpecific, cTerminusIsSpecific, + bestSpecificity, bestResult)) + break; + } +@@ -1104,7 +1104,7 @@ + BOOST_FOREACH(CVID cleavageAgent, cleavageAgents) + { + if (!findPeptideEvidenceWithRegex(pe, peptide, peptideSequenceInContext, cleavageAgent, "", +- sip.enzymes.independent, nTerminusIsSpecific, cTerminusIsSpecific, ++ static_cast(sip.enzymes.independent), nTerminusIsSpecific, cTerminusIsSpecific, + bestSpecificity, bestResult)) + break; + } +@@ -1112,7 +1112,7 @@ + BOOST_FOREACH(const string& regex, cleavageAgentRegexes) + { + if (!findPeptideEvidenceWithRegex(pe, peptide, peptideSequenceInContext, CVID_Unknown, regex, +- sip.enzymes.independent, nTerminusIsSpecific, cTerminusIsSpecific, ++ static_cast(sip.enzymes.independent), nTerminusIsSpecific, cTerminusIsSpecific, + bestSpecificity, bestResult)) + break; + } +diff -ru mzR.orig/src/pwiz/data/identdata/IdentData.hpp mzR/src/pwiz/data/identdata/IdentData.hpp +--- mzR.orig/src/pwiz/data/identdata/IdentData.hpp 2020-04-27 22:27:42.000000000 +0200 ++++ mzR/src/pwiz/data/identdata/IdentData.hpp 2020-10-01 14:01:40.068125601 +0200 +@@ -30,6 +30,7 @@ + #include "pwiz/data/proteome/Digestion.hpp" + #include "pwiz/data/common/ParamTypes.hpp" + #include "boost/logic/tribool.hpp" ++#include "boost/logic/tribool_io.hpp" + #include + #include + #include +diff -ru mzR.orig/src/pwiz/data/identdata/Serializer_pepXML.cpp mzR/src/pwiz/data/identdata/Serializer_pepXML.cpp +--- mzR.orig/src/pwiz/data/identdata/Serializer_pepXML.cpp 2020-04-27 22:27:42.000000000 +0200 ++++ mzR/src/pwiz/data/identdata/Serializer_pepXML.cpp 2020-10-01 14:13:48.875467067 +0200 +@@ -409,7 +409,7 @@ + void write_sample_enzyme(XMLWriter& xmlWriter, const IdentData& mzid) + { + const SpectrumIdentificationProtocol& sip = *mzid.analysisProtocolCollection.spectrumIdentificationProtocol[0]; +- bool independent = sip.enzymes.independent; ++ bool independent = static_cast(sip.enzymes.independent); + + // create a cumulative enzyme name for multiple enzymes like "Trypsin + AspN + Chymotrypsin" + string enzymeName = bal::join(sip.enzymes.enzymes | boost::adaptors::transformed(EnzymePtr_name()), " + "); From a28fee13611c108c5af5b52862ddac86ff50ff1c Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Thu, 1 Oct 2020 16:48:25 +0200 Subject: [PATCH 347/698] Remove pointless buildopt --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index cd9f435d172..78be8bf713e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -12,8 +12,6 @@ toolchain = {'name': 'foss', 'version': '2020a'} builddependencies = [('pkg-config', '0.29.2')] -buildopts = "-fpermissive " - dependencies = [ ('R', '4.0.0'), ('Boost', '1.72.0'), # for mzR From 7ab24ff7f57a2b0148487e4a8cfb8573a9fd6d9c Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Thu, 1 Oct 2020 17:03:47 +0200 Subject: [PATCH 348/698] adding easyconfigs: Biopython-1.78-intel-2020a-Python-3.8.2.eb, BLAST+-2.10.1-iimpi-2020a.eb, chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb, ClustalW2-2.1-intel-2020a.eb, MAFFT-7.471-iimpi-2020a-with-extensions.eb and patches: BLAST+-2.10.1_fix-64-icc.patch --- .../b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb | 61 +++++++++++++++++++ .../b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch | 12 ++++ ...Biopython-1.78-intel-2020a-Python-3.8.2.eb | 46 ++++++++++++++ .../c/ClustalW2/ClustalW2-2.1-intel-2020a.eb | 33 ++++++++++ ...hewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb | 52 ++++++++++++++++ ...MAFFT-7.471-iimpi-2020a-with-extensions.eb | 52 ++++++++++++++++ 6 files changed, 256 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb create mode 100644 easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb new file mode 100644 index 00000000000..58d7397bb06 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1-iimpi-2020a.eb @@ -0,0 +1,61 @@ +## +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.10.1' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'cstd': 'c++14', 'usempi': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +patches = [ + 'BLAST+-%(version)s_fix-64-icc.patch', +] +checksums = [ + '110729decf082f69b90b058c0cabaea38f771983a564308ae19cb30a68ce7b86', # ncbi-blast-2.10.1+-src.tar.gz + 'f25a537bc6fa4bc4bf0408b7b16966852aef72b9f7d60e1038afa1e41e0c9d88', # BLAST+-2.10.1_fix-64-icc.patch +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('PCRE', '8.44'), + ('Boost', '1.72.0'), + ('GMP', '6.2.0'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.4'), + ('LMDB', '0.9.24'), +] + +# avoid linking error 'cannot find -liomp5' on small helper utility that is built with gcc +preconfigopts = 'unset LIBS && ' +prebuildopts = preconfigopts + +configopts = "--with-64 --with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB " + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch new file mode 100644 index 00000000000..f9c129a9bfe --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.10.1_fix-64-icc.patch @@ -0,0 +1,12 @@ +Fix "Do not know how to compile 64-bit with compiler" error by also using -m64 when compiling with Intel compilers +author: Jakub Zárybnický (Inuits) +--- ncbi-blast-2.10.1+-src/c++/src/build-system/configure.orig 2020-10-01 13:36:23.067853000 +0200 ++++ ncbi-blast-2.10.1+-src/c++/src/build-system/configure 2020-10-01 13:47:35.131190707 +0200 +@@ -9340,6 +9340,6 @@ + mips*:GCC ) + ARCH_CFLAGS="-mips64" + ;; +- *:GCC | *Clang ) ++ *:GCC | *ICC | *Clang ) + # May not work prior to GCC 3.1. + ARCH_CFLAGS="-m64" diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..53128d5ab96 --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.78' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# required because we're building Python packages using Intel compilers on top of Python built with GCC +check_ldshared = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb new file mode 100644 index 00000000000..5caf0f43d3b --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb @@ -0,0 +1,33 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +homepage = 'http://www.ebi.ac.uk/Tools/msa/clustalw2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.ebi.ac.uk/pub/software/%(namelower)s/%(version)s'] +sources = ['%s-%%(version)s.tar.gz' % name[:-1].lower()] +checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] + +sanity_check_paths = { + 'files': ['bin/clustalw2'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..9265f54bc7a --- /dev/null +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'chewBBACA' +version = '2.5.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/B-UMMI/chewBBACA' +description = """chewBBACA stands for "BSR-Based Allele Calling Algorithm". +chewBBACA is a comprehensive pipeline including a set of functions for the +creation and validation of whole genome and core genome MultiLocus Sequence +Typing (wg/cgMLST) schemas, providing an allele calling algorithm based on Blast +Score Ratio that can be run in multiprocessor settings and a set of functions to +visualize and validate allele variation in the loci.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Biopython', '1.78', versionsuffix), + ('plotly.py', '4.8.1'), + ('BLAST+', '2.10.1'), + ('prodigal', '2.6.3'), + ('ClustalW2', '2.1'), + ('MAFFT', '7.471', '-with-extensions'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', '5.0.0', { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), + ('SPARQLWrapper', '1.8.5', { + 'modulename': 'SPARQLWrapper', + 'checksums': ['d6a66b5b8cda141660e07aeb00472db077a98d22cb588c973209c7336850fb3c'], + }), + (name, version, { + 'modulename': 'CHEWBBACA', + 'runtest': "python setup.py test", + 'checksums': ['f8960b8485672f6d39d59e53b3521db406120abc2d7db42ce4c9eac06b024a5f'], + }), +] + +sanity_check_commands = [] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb new file mode 100644 index 00000000000..144e21d2653 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.471-iimpi-2020a-with-extensions.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.471' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'usempi': True} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['2c4993e9ebdaf4dcc6ea2b0daf30f58cbbe98fdba3e2cfcb46145bb2c62e94ef'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), + ('%s MPI' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ + 'mxscarnamod', # installed by MAFFT Extensions + 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI + ]], + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} +# MAFFT MPI requires other environment variables that depend on job resources +# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html + +moduleclass = 'bio' From 638ea7ab622dc79d43f24bbec77fd00eef88e4db Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Thu, 1 Oct 2020 17:58:43 +0200 Subject: [PATCH 349/698] chewBBACA: use older MAFFT. add sanity checks --- ...Biopython-1.78-intel-2020a-Python-3.8.2.eb | 3 -- .../c/ClustalW2/ClustalW2-2.1-intel-2020a.eb | 2 +- ...hewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb | 11 +++- ...MAFFT-7.453-iimpi-2020a-with-extensions.eb | 52 +++++++++++++++++++ 4 files changed, 62 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb index 53128d5ab96..1a1861c1200 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.78-intel-2020a-Python-3.8.2.eb @@ -26,9 +26,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -# required because we're building Python packages using Intel compilers on top of Python built with GCC -check_ldshared = True - # Run only tests that don't require internet connection runtest = 'python setup.py test --offline' diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb index 5caf0f43d3b..e8b06867fd9 100644 --- a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-intel-2020a.eb @@ -15,7 +15,7 @@ easyblock = 'ConfigureMake' name = 'ClustalW2' version = '2.1' -homepage = 'http://www.ebi.ac.uk/Tools/msa/clustalw2/' +homepage = 'https://www.ebi.ac.uk/Tools/msa/clustalw2/' description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" toolchain = {'name': 'intel', 'version': '2020a'} diff --git a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb index 9265f54bc7a..93dbac10366 100644 --- a/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/c/chewBBACA/chewBBACA-2.5.5-intel-2020a-Python-3.8.2.eb @@ -22,7 +22,7 @@ dependencies = [ ('BLAST+', '2.10.1'), ('prodigal', '2.6.3'), ('ClustalW2', '2.1'), - ('MAFFT', '7.471', '-with-extensions'), + ('MAFFT', '7.453', '-with-extensions'), ] use_pip = True @@ -47,6 +47,13 @@ exts_list = [ }), ] -sanity_check_commands = [] +sanity_check_paths = { + 'files': ['bin/chewBBACA.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/CHEWBBACA'], +} + +sanity_check_commands = [ + 'chewBBACA.py --help', +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb new file mode 100644 index 00000000000..d2fee363feb --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.453-iimpi-2020a-with-extensions.eb @@ -0,0 +1,52 @@ +easyblock = 'Bundle' + +name = 'MAFFT' +version = '7.453' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program for unix-like operating systems. +It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment +of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.""" + +toolchain = {'name': 'iimpi', 'version': '2020a'} +toolchainopts = {'usempi': True} + +default_easyblock = 'ConfigureMake' +default_component_specs = { + 'source_urls': ['https://mafft.cbrc.jp/alignment/software/'], + 'sources': ['mafft-%(version)s%(versionsuffix)s-src.tgz'], + 'checksums': ['8b2f0d6249c575f80cd51278ab45dd149b8ac9b159adac20fd1ddc7a6722af11'], + 'skipsteps': ['configure'], + 'installopts': 'PREFIX=%(installdir)s', +} + +components = [ + (name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/core', + }), + ('%s Extensions' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/extensions', + }), + ('%s MPI' % name, version, { + 'start_dir': 'mafft-%(version)s%(versionsuffix)s/MPI', + }), +] + +sanity_check_paths = { + 'files': ['bin/mafft'] + ['libexec/mafft/%s' % x for x in [ + 'mxscarnamod', # installed by MAFFT Extensions + 'mpiscript', 'nodepair_mpi', # installed by MAFFT MPI + ]], + 'dirs': ['libexec/mafft'], +} + +sanity_check_commands = ['mafft --version'] + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +modextravars = {'MAFFT_N_THREADS_PER_PROCESS': '1'} +# MAFFT MPI requires other environment variables that depend on job resources +# More information at at https://mafft.cbrc.jp/alignment/software/mpi.html + +moduleclass = 'bio' From 4338a18f90a55c2f634950606cff504bd6f6cdae Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:06:47 +0200 Subject: [PATCH 350/698] Make flowClust use external GSL. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 78be8bf713e..22f8f4a8810 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -15,6 +15,7 @@ builddependencies = [('pkg-config', '0.29.2')] dependencies = [ ('R', '4.0.0'), ('Boost', '1.72.0'), # for mzR + ('GSL', '2.6'), # for flowClust ('HDF5', '1.10.6'), # for rhdf5 ('MariaDB-connector-c', '3.1.7'), # for RMySQL ('ncdf4', '1.17', versionsuffix), # for mzR @@ -742,6 +743,7 @@ exts_list = [ 'checksums': ['39b69ff7248f3832ad018f206e02642ef0cd1bf37040e00f48571a7fdaeefbf9'], }), ('flowClust', '3.26.0', { + 'installopts': "--configure-args='--with-gsl=${EBROOTGSL} --enable-bundled-gsl=false'", 'checksums': ['abe01b47e7692f335b5f0418cef6dd0dbf99df871bda49fa015dc9407cc2b31a'], }), ('openCyto', '2.0.0', { From 8ffcb860cb2fae2798574e25ed63d46f59491fd7 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:13:26 +0200 Subject: [PATCH 351/698] Reinstate tests.. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 22f8f4a8810..1eb0c475b5a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -827,8 +827,7 @@ modextrapaths = {'R_LIBS': ''} sanity_check_paths = { 'files': [], - 'dirs': ['.'], -# 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], } moduleclass = 'bio' From d84268b528fe4bad033422f8b2bee4f8878a55c6 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:16:48 +0200 Subject: [PATCH 352/698] Reinstate extensions from latest develop. --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 1eb0c475b5a..4d18bf5dd92 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -821,6 +821,30 @@ exts_list = [ ('stageR', '1.10.0', { 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), + ('isva', '1.9', { + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.11.4', { + 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], + }), + ('org.Rn.eg.db', '3.11.4', { + 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], + }), + ('ROC', '1.64.0', { + 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], + }), + ('wateRmelon', '1.32.0', { + 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], + }), + ('GLAD', '2.52.0', { + 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], + }), + ('missMethyl', '1.22.0', { + 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], + }), + ('MethylSeekR', '1.28.0', { + 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], + }), ] modextrapaths = {'R_LIBS': ''} From 5dd07718452f5d37d5dba1b82e29a41fc4c56f19 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:19:12 +0200 Subject: [PATCH 353/698] Reinstate LEA. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 4d18bf5dd92..d4c4e22c631 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -462,6 +462,9 @@ exts_list = [ 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', ], }), + ('LEA', '3.0.0', { + 'checksums': ['802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa'], + }), ('tximport', '1.16.0', { 'checksums': ['b5f35cea2b9746ba92bc66f23c9566c2e565681e6527071e66d401072b5a2446'], }), From 44a7daaadcf41ac47e285229771c9adbe8aeed4d Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:21:09 +0200 Subject: [PATCH 354/698] Whitespace fixes. --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 48 +++++++++---------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index d4c4e22c631..2e2c1149283 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -463,7 +463,7 @@ exts_list = [ ], }), ('LEA', '3.0.0', { - 'checksums': ['802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa'], + 'checksums': ['802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa'], }), ('tximport', '1.16.0', { 'checksums': ['b5f35cea2b9746ba92bc66f23c9566c2e565681e6527071e66d401072b5a2446'], @@ -825,29 +825,29 @@ exts_list = [ 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), ('isva', '1.9', { - 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], - }), - ('org.Mm.eg.db', '3.11.4', { - 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], - }), - ('org.Rn.eg.db', '3.11.4', { - 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], - }), - ('ROC', '1.64.0', { - 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], - }), - ('wateRmelon', '1.32.0', { - 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], - }), - ('GLAD', '2.52.0', { - 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], - }), - ('missMethyl', '1.22.0', { - 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], - }), - ('MethylSeekR', '1.28.0', { - 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], - }), + 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], + }), + ('org.Mm.eg.db', '3.11.4', { + 'checksums': ['12c6abb3060a85112e5061840f7845895ef29be8440eebcbfa4f4c1d73195aeb'], + }), + ('org.Rn.eg.db', '3.11.4', { + 'checksums': ['b662c9130692aa6e5a42b4e3a8e0626ff24dbfa991090f64e2fbb45a5833e42e'], + }), + ('ROC', '1.64.0', { + 'checksums': ['09f5e7fa18df843e89494860611a2e47c7653daf0a0a5964c6ae507f4e1ebd3e'], + }), + ('wateRmelon', '1.32.0', { + 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], + }), + ('GLAD', '2.52.0', { + 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], + }), + ('missMethyl', '1.22.0', { + 'checksums': ['afb73e54037abb93db3f8a594aa3fde97c55afe825d387d6096a080d7621b540'], + }), + ('MethylSeekR', '1.28.0', { + 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], + }), ] modextrapaths = {'R_LIBS': ''} From b2236055a1711d561cf5dc8868fe70f66846d182 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 03:50:33 +0200 Subject: [PATCH 355/698] More whitespace fixes. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 2e2c1149283..15323f16e25 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -14,8 +14,8 @@ builddependencies = [('pkg-config', '0.29.2')] dependencies = [ ('R', '4.0.0'), - ('Boost', '1.72.0'), # for mzR - ('GSL', '2.6'), # for flowClust + ('Boost', '1.72.0'), # for mzR + ('GSL', '2.6'), # for flowClust ('HDF5', '1.10.6'), # for rhdf5 ('MariaDB-connector-c', '3.1.7'), # for RMySQL ('ncdf4', '1.17', versionsuffix), # for mzR From 48d37881d81ec815bc3ed19d841b04c7accf3d81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 2 Oct 2020 10:14:30 +0200 Subject: [PATCH 356/698] Add ncurses runtime dependency to Clang --- easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb | 1 + easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb index 15b763db99d..2eab05a64eb 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.0-GCCcore-9.3.0.eb @@ -49,6 +49,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.34'), + ('ncurses', '6.2'), ('GMP', '6.2.0'), ] diff --git a/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb index de1d96eb850..b01fa7a6988 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-10.0.1-GCCcore-9.3.0.eb @@ -49,6 +49,7 @@ checksums = [ dependencies = [ # since Clang is a compiler, binutils is a runtime dependency too ('binutils', '2.34'), + ('ncurses', '6.2'), ('GMP', '6.2.0'), ] From 38a3b56758b04cc57caa1a60fdfcc9e424cab2fc Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 10:42:03 +0200 Subject: [PATCH 357/698] Adding JADE as a dependency as per testing. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 15323f16e25..a11474ceba8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -824,6 +824,9 @@ exts_list = [ ('stageR', '1.10.0', { 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), + ('JADE', '2.0-3', { + 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], + }), ('isva', '1.9', { 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], }), From 5eb44405cf8c708c0d2a95142a7a0131c912d339 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 23 Sep 2020 16:29:10 +0200 Subject: [PATCH 358/698] Add patch to libunwind fixing a failure on POWER --- .../libunwind-1.2.1-GCCcore-7.3.0.eb | 9 ++++--- .../libunwind-1.3.1-GCCcore-8.2.0.eb | 9 ++++--- .../libunwind-1.3.1-GCCcore-8.3.0.eb | 8 +++++-- .../libunwind-1.3.1-GCCcore-9.3.0.eb | 6 ++++- .../libunwind-1.3.1_fix_ppc64_fpreg_t.patch | 24 +++++++++++++++++++ 5 files changed, 47 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.3.1_fix_ppc64_fpreg_t.patch diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb index c01773d5893..4befaf84b02 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['3f3ecb90e28cbe53fba7a4a27ccce7aad188d3210bb1964a923a731a27a75acb'] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + '3f3ecb90e28cbe53fba7a4a27ccce7aad188d3210bb1964a923a731a27a75acb', + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] builddependencies = [('binutils', '2.30')] @@ -25,8 +29,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], - 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb index a556600f95b..3681c28c297 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8'] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + '43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8', + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] builddependencies = [('binutils', '2.31.1')] @@ -25,8 +29,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], - 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.3.0.eb index 1cb5c3eb5d4..1012104a3b5 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8'] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + '43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8', + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] builddependencies = [('binutils', '2.32')] @@ -25,7 +29,7 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb index feb47934f25..7160f197bb6 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-9.3.0.eb @@ -14,7 +14,11 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8'] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + '43997a3939b6ccdf2f669b50fdb8a4d3205374728c2923ddc2354c65260214f8', + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] builddependencies = [('binutils', '2.34')] diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1_fix_ppc64_fpreg_t.patch b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1_fix_ppc64_fpreg_t.patch new file mode 100644 index 00000000000..9a5bc488859 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1_fix_ppc64_fpreg_t.patch @@ -0,0 +1,24 @@ +From cbb75bbb49590ab60f5987ab0c9d49ca4ba2ed6b Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 2 Oct 2020 11:00:39 +0200 +Subject: [PATCH] Define the FP register size on PPC to be double + +According to GLIBC headers those are in fact double (8 Byte) not +long double (16 Byte) +--- + include/libunwind-ppc64.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/libunwind-ppc64.h b/include/libunwind-ppc64.h +index 9944628da..fed478bed 100644 +--- a/include/libunwind-ppc64.h ++++ b/include/libunwind-ppc64.h +@@ -72,7 +72,7 @@ typedef uint64_t unw_word_t; + typedef int64_t unw_sword_t; + #endif + +-typedef long double unw_tdep_fpreg_t; ++typedef double unw_tdep_fpreg_t; + + /* + * Vector register (in PowerPC64 used for AltiVec registers) From 4dcf155e2b72f39058f0401acf11f9bce017b762 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 2 Oct 2020 12:55:58 +0200 Subject: [PATCH 359/698] Fix https --- .../easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb | 2 +- .../easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb index 4befaf84b02..75217ea989e 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-7.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libunwind' version = '1.2.1' -homepage = 'http://www.nongnu.org/libunwind/' +homepage = 'https://www.nongnu.org/libunwind/' description = """The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb index 3681c28c297..1a5d4bfc278 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.3.1-GCCcore-8.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libunwind' version = '1.3.1' -homepage = 'http://www.nongnu.org/libunwind/' +homepage = 'https://www.nongnu.org/libunwind/' description = """The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain From a42885819e5c0af3ba46fa31c14e6200b404e034 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Oct 2020 14:27:39 +0000 Subject: [PATCH 360/698] adding easyconfigs: ScaLAPACK-2.1.0-gompic-2020a.eb, FFTW-3.3.8-gompic-2020a-mpi.eb, fosscuda-2020a.eb, HPL-2.3-fosscuda-2020a.eb --- .../f/FFTW/FFTW-3.3.8-gompic-2020a.eb | 17 +++++++++++ .../easyconfigs/f/fosscuda/fosscuda-2020a.eb | 29 +++++++++++++++++++ .../h/HPL/HPL-2.3-fosscuda-2020a.eb | 21 ++++++++++++++ .../ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb | 17 +++++++++++ 4 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020a.eb create mode 100644 easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-fosscuda-2020a.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020a.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020a.eb new file mode 100644 index 00000000000..e598bcd6fb4 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.8-gompic-2020a.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.8' + +homepage = 'http://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) + in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompic', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6113262f6e92c5bd474f2875fa1b01054c4ad5040f6b0da7c03c98821d9ae303'] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb new file mode 100644 index 00000000000..921ff09c9df --- /dev/null +++ b/easybuild/easyconfigs/f/fosscuda/fosscuda-2020a.eb @@ -0,0 +1,29 @@ +easyblock = 'Toolchain' + +name = 'fosscuda' +version = '2020a' + +homepage = '(none)' +description = """GCC based compiler toolchain __with CUDA support__, and including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '9.3.0' + +# toolchain used to build fosscuda dependencies +local_comp_mpi_tc = ('gompic', version) + +# compiler toolchain dependencies +# We need GCC, CUDA and OpenMPI as explicit dependencies instead of +# gompic toolchain because of toolchain preperation functions. +dependencies = [ + ('GCC', local_gccver), # part of gompic + ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # part of gompic + ('OpenMPI', '4.0.3', '', ('gcccuda', version)), # part of gompic + ('OpenBLAS', '0.3.9', '', ('GCC', local_gccver)), + ('FFTW', '3.3.8', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.1.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-fosscuda-2020a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-fosscuda-2020a.eb new file mode 100644 index 00000000000..4ac95fa12be --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-fosscuda-2020a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'fosscuda', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb new file mode 100644 index 00000000000..2ce571f666f --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.1.0-gompic-2020a.eb @@ -0,0 +1,17 @@ +name = 'ScaLAPACK' +version = '2.1.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompic', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +checksums = ['61d9216cf81d246944720cfce96255878a3f85dec13b9351f1fa0fd6768220a6'] + +dependencies = [('OpenBLAS', '0.3.9')] + +moduleclass = 'numlib' From 19974f8da5bc44623df03904cf1234637ebb92cf Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 2 Oct 2020 17:09:25 +0200 Subject: [PATCH 361/698] Add sanity_pip_check=True to hypothesis v3.66.18 for intel/2018a --- .../h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb index 2177aa2a9bb..8399a457df6 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb @@ -34,4 +34,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'tools' From e7bcfdbabad3adf1eaad76d2254290ff8e229cd7 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 2 Oct 2020 16:15:14 +0000 Subject: [PATCH 362/698] {toolchain} intelcuda/2020a --- .../h/HPL/HPL-2.3-intelcuda-2020a.eb | 21 ++++++++++ .../easyconfigs/i/iimpic/iimpic-2020a.eb | 20 ++++++++++ .../i/imkl/imkl-2020.1.217-iimpic-2020a.eb | 39 ++++++++++++++++++ .../impi-2019.7.217-iccifortcuda-2020a.eb | 40 +++++++++++++++++++ .../i/intelcuda/intelcuda-2020a.eb | 20 ++++++++++ 5 files changed, 140 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intelcuda-2020a.eb create mode 100644 easybuild/easyconfigs/i/iimpic/iimpic-2020a.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb create mode 100644 easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intelcuda-2020a.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intelcuda-2020a.eb new file mode 100644 index 00000000000..cd4ae0ee2bc --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intelcuda-2020a.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intelcuda', 'version': '2020a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpic/iimpic-2020a.eb b/easybuild/easyconfigs/i/iimpic/iimpic-2020a.eb new file mode 100644 index 00000000000..2e42b2593f3 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpic/iimpic-2020a.eb @@ -0,0 +1,20 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ +easyblock = "Toolchain" + +name = 'iimpic' +version = '2020a' + +homepage = '(none)' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA.""" + +toolchain = SYSTEM + +local_compver = '2020.1.217' + +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.0.2', '', ('iccifort', local_compver)), + ('impi', '2019.7.217', '', ('iccifortcuda', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb new file mode 100644 index 00000000000..fd364d8c74f --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2020.1.217-iimpic-2020a.eb @@ -0,0 +1,39 @@ +# This is an easyconfig file for EasyBuild, see https://easybuilders.github.io/easybuild/ + +name = 'imkl' +version = '2020.1.217' + +homepage = 'https://software.intel.com/mkl' +description = """Intel Math Kernel Library is a library of highly optimized, + extensively threaded math routines for science, engineering, and financial + applications that require maximum performance. Core math functions include + BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more.""" + +toolchain = {'name': 'iimpic', 'version': '2020a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16533/'] +sources = ['l_mkl_%(version)s.tgz'] +checksums = ['082a4be30bf4f6998e4d6e3da815a77560a5e66a68e254d161ab96f07086066d'] + +dontcreateinstalldir = True + +components = ['intel-mkl'] + +license_file = HOME + '/licenses/intel/license.lic' + +interfaces = True + +postinstallcmds = [ + # extract the examples + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_cluster_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_c.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_core_f.tgz -C %(installdir)s/mkl/examples/', + 'tar xvzf %(installdir)s/mkl/examples/examples_f95.tgz -C %(installdir)s/mkl/examples/', +] + +modextravars = { + 'MKL_EXAMPLES': '%(installdir)s/mkl/examples/', +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb new file mode 100644 index 00000000000..557e0a8eab1 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2019.7.217-iccifortcuda-2020a.eb @@ -0,0 +1,40 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild + +name = 'impi' +version = '2019.7.217' + +homepage = 'https://software.intel.com/en-us/intel-mpi-library/' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'iccifortcuda', 'version': '2020a'} + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/tec/16546/'] +sources = ['l_mpi_%(version)s.tgz'] +checksums = ['90383b0023f84ac003a55d8bb29dbcf0c639f43a25a2d8d8698a16e770ac9c07'] + +dependencies = [ + # needed by libfabric provider MLX introduced in Intel MPI v2019.6, + # https://software.intel.com/en-us/articles/improve-performance-and-stability-with-intel-mpi-library-on-infiniband + ('UCX', '1.8.0'), +] + +dontcreateinstalldir = True + +components = ['intel-mpi', 'intel-psxe', 'intel-imb'] + +# set up all the mpi commands to default to intel compilers +# set_mpi_wrappers_all = True + +modextravars = { + # to enable SLURM integration with srun (site-specific) + # 'I_MPI_PMI_LIBRARY': 'libpmi2.so', + + # set this if mpirun gives you a floating point exception (SIGFPE), see + # https://software.intel.com/en-us/forums/intel-clusters-and-hpc-technology/topic/852307 + # 'I_MPI_HYDRA_TOPOLIB': 'ipl', +} + +# may be needed if you enable I_MPI_PMI_LIBRARY above +# osdependencies = [('slurm-libpmi')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb new file mode 100644 index 00000000000..49ffa18e384 --- /dev/null +++ b/easybuild/easyconfigs/i/intelcuda/intelcuda-2020a.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'intelcuda' +version = '2020a' + +homepage = '(none)' +description = """Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, + Intel MPI & Intel MKL, with CUDA toolkit""" + +toolchain = SYSTEM + +local_compver = '2020.1.217' +dependencies = [ + ('iccifort', local_compver), + ('CUDA', '11.0.2', '', ('iccifort', local_compver)), + ('impi', '2019.7.217', '', ('iccifortcuda', version)), + ('imkl', local_compver, '', ('iimpic', version)), +] + +moduleclass = 'toolchain' From 30ca4bd12e0df01bd443dc53b6a87717b5c0d179 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 2 Oct 2020 18:36:47 +0100 Subject: [PATCH 363/698] adding easyconfigs: BLAST-2.10.1-Linux_x86_64.eb --- .../b/BLAST/BLAST-2.10.1-Linux_x86_64.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLAST/BLAST-2.10.1-Linux_x86_64.eb diff --git a/easybuild/easyconfigs/b/BLAST/BLAST-2.10.1-Linux_x86_64.eb b/easybuild/easyconfigs/b/BLAST/BLAST-2.10.1-Linux_x86_64.eb new file mode 100644 index 00000000000..05b044c1873 --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST/BLAST-2.10.1-Linux_x86_64.eb @@ -0,0 +1,33 @@ +# +# Author: Fenglai Liu +# fenglai@accre.vanderbilt.edu +# Vanderbilt University +# Updated by: +# Adam Huffman +# Big Data Institute, +# University of Oxford +# +easyblock = 'Tarball' + +name = 'BLAST' +version = '2.10.1' +versionsuffix = "-Linux_x86_64" + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological +sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = SYSTEM + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST'] +sources = ['ncbi-%(namelower)s-%(version)s+-x64-linux.tar.gz'] +checksums = ['8a96f7fac4a5541b6dfcaff4d67d3979ce450aa330b02c3ca2179ca95af096e7'] + +sanity_check_paths = { + 'files': ["bin/blastn", "bin/blastx", "bin/tblastn"], + 'dirs': [] +} + +sanity_check_commands = ['blastn -help'] + +moduleclass = 'bio' From 60f4b7304b19e41eedefe0064093a10d8f6d2f10 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 2 Oct 2020 19:47:53 +0200 Subject: [PATCH 364/698] Adding aws as a dependency for GLAD. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index a11474ceba8..9e80599211d 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -842,6 +842,9 @@ exts_list = [ ('wateRmelon', '1.32.0', { 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], }), + ('aws', '2.5', { + 'checksums': ['d526b99d17c1dfd5e399f4af1bc09c8a267add80d3b0a454790728420f0e8fd7'], + }), ('GLAD', '2.52.0', { 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], }), From 31404b18287334cf6fce6ba38007adec4bc7bfa7 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 3 Oct 2020 09:29:16 +0200 Subject: [PATCH 365/698] adding easyconfigs: mpifileutils-0.10.1-gompi-2020a.eb and patches: mpifileutils-0.10.1_fix_acl_xattr_problem.patch --- .../mpifileutils-0.10.1-gompi-2020a.eb | 42 +++++++++++++++++++ ...leutils-0.10.1_fix_acl_xattr_problem.patch | 40 ++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb create mode 100644 easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb new file mode 100644 index 00000000000..8ff992d3cfd --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'mpifileutils' +version = "0.10.1" + +homepage = 'https://hpc.github.io/mpifileutils/' + +description = """ + MPI-Based File Utilities For Distributed Systems +""" + +toolchain = {'name': 'gompi', 'version': '2020a'} + +source_urls = ['https://github.com/hpc/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['mpifileutils-%(version)s_fix_acl_xattr_problem.patch'] +checksums = [ + '4c8409ef4140f6f557d0e93f0c1267baf5d893c203b29fb7a33d9bc3c5a5d25c', # v0.10.1.tar.gz + # mpifileutils-0.10.1_fix_acl_xattr_problem.patch + 'e540ceaeb99758f4776252069d56b703411824ba83f48b474fc18785868151a2', +] + +checksums = [] +builddependencies = [ + ('CMake', '3.16.4'), +] + +dependencies = [ + ('attr', '2.4.48'), + ('bzip2', '1.0.8'), + ('dtcmp', '1.1.0'), + ('libarchive', '3.4.2'), + ('libcircle', '0.3'), + ('lwgrp', '1.0.2'), +] + +sanity_check_paths = { + 'files': ['bin/dsync', 'include/mfu.h', 'lib/libmfu.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch new file mode 100644 index 00000000000..72ad6e42556 --- /dev/null +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1_fix_acl_xattr_problem.patch @@ -0,0 +1,40 @@ +Copy of mpifileutils PR #401 + +commit 19b5e6b5d417a5b42c24f8a914fb72e297baecfb +Author: Ake Sandgren +Date: Sat Oct 3 09:17:47 2020 +0200 + + Fix problems with copying xattrs that contain ACLs causing write-protected dirs + Fixes issue https://github.com/hpc/mpifileutils/issues/400 + + Signed-off-by: Åke Sandgren + +diff --git a/src/common/mfu_flist_copy.c b/src/common/mfu_flist_copy.c +index 3d9109c..187be5d 100644 +--- a/src/common/mfu_flist_copy.c ++++ b/src/common/mfu_flist_copy.c +@@ -324,14 +324,16 @@ static int mfu_copy_xattrs( + + /* set attribute on destination object */ + if(got_val) { +- errno = 0; +- int setrc = lsetxattr(dest_path, name, val, (size_t) val_size, 0); +- if(setrc != 0) { +- /* failed to set attribute */ +- MFU_LOG(MFU_LOG_ERR, "Failed to set value for name=%s on `%s' llistxattr() (errno=%d %s)", +- name, dest_path, errno, strerror(errno) +- ); +- rc = -1; ++ if (strncmp(name, "system.posix_acl", 16)) { ++ errno = 0; ++ int setrc = lsetxattr(dest_path, name, val, (size_t) val_size, 0); ++ if(setrc != 0) { ++ /* failed to set attribute */ ++ MFU_LOG(MFU_LOG_ERR, "Failed to set value for name=%s on `%s' llistxattr() (errno=%d %s)", ++ name, dest_path, errno, strerror(errno) ++ ); ++ rc = -1; ++ } + } + } + From 258f5cd1c634449eb46907093c5bc42240c118d2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sat, 3 Oct 2020 11:04:22 +0200 Subject: [PATCH 366/698] Fix extraneous checksums entry --- .../m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb index 8ff992d3cfd..9f133d3bb42 100644 --- a/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb +++ b/easybuild/easyconfigs/m/mpifileutils/mpifileutils-0.10.1-gompi-2020a.eb @@ -20,7 +20,6 @@ checksums = [ 'e540ceaeb99758f4776252069d56b703411824ba83f48b474fc18785868151a2', ] -checksums = [] builddependencies = [ ('CMake', '3.16.4'), ] From f9131ec264cfb62d7835ce68f2df1c7332b627aa Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sat, 3 Oct 2020 13:19:56 +0200 Subject: [PATCH 367/698] Removing extensions already added by https://github.com/easybuilders/easybuild-easyconfigs/commit/55fab02a1f3d6866228436c072e1b19004750486#diff-f2a7ccd2712a57d5dff6f0bd478d7d18. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 9e80599211d..15323f16e25 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -824,9 +824,6 @@ exts_list = [ ('stageR', '1.10.0', { 'checksums': ['34c31e771fa76cb474966121baaef52eefc5a4f66b9c8e86889b7318d159353f'], }), - ('JADE', '2.0-3', { - 'checksums': ['56d68a993fa16fc6dec758c843960eee840814c4ca2271e97681a9d2b9e242ba'], - }), ('isva', '1.9', { 'checksums': ['9fd016e0b34034d271d45f8a0d0db62780bf0187112e45f610aa9237014e1d17'], }), @@ -842,9 +839,6 @@ exts_list = [ ('wateRmelon', '1.32.0', { 'checksums': ['96f737823c3646dcd24fedad2cff63393e6e4d56f165d7ea44bbbe37f0326ab0'], }), - ('aws', '2.5', { - 'checksums': ['d526b99d17c1dfd5e399f4af1bc09c8a267add80d3b0a454790728420f0e8fd7'], - }), ('GLAD', '2.52.0', { 'checksums': ['9cf6e391c1f2da12b723c5122e5183e83e4869d106e25c071700a391c187e4cd'], }), From 00f4e4986fe4ae5fe729a40e107b934739c85795 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 4 Oct 2020 09:46:21 +0200 Subject: [PATCH 368/698] LEA 'support' for aarch64 and POWER. Needs testing. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 15323f16e25..c7869c7399f 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -463,7 +463,12 @@ exts_list = [ ], }), ('LEA', '3.0.0', { - 'checksums': ['802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa'], + 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], + 'checksums': [ + '802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa', # LEA_3.0.0.tar.gz + # LEA-3.0.0_support_aarch64_and_ppc64le.patch + 'e0baa8de52a60dfa2675a0c7d771a4ebad7dc4232fa2c895792eaa8e6b4d0772', + ], }), ('tximport', '1.16.0', { 'checksums': ['b5f35cea2b9746ba92bc66f23c9566c2e565681e6527071e66d401072b5a2446'], From a12ab9f3f444b7b9219de41ed36538f3c68a22af Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 4 Oct 2020 10:12:03 +0100 Subject: [PATCH 369/698] R 4.0.0 - Fix infinite loop build bug on ppc64le --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 6 +- .../r/R/R-4.0.0_ppc64le-build-fix.patch | 55 +++++++++++++++++++ 2 files changed, 60 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/r/R/R-4.0.0_ppc64le-build-fix.patch diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 59c5ae09d7e..855b0b84cda 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -9,7 +9,11 @@ toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] -checksums = ['06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940'] +patches = ['%(name)s-%(version)s_ppc64le-build-fix.patch'] +checksums = [ + '06beb0291b569978484eb0dcb5d2339665ec745737bdfb4e873e7a5a75492940', # R-4.0.0.tar.gz + 'ae14b063be40ba2f2e73d95ae1ee0b8630ac7bbc8ec2d64830016c8d62f672ad', # R-4.0.0_ppc64le-build-fix.patch +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/r/R/R-4.0.0_ppc64le-build-fix.patch b/easybuild/easyconfigs/r/R/R-4.0.0_ppc64le-build-fix.patch new file mode 100644 index 00000000000..411d54f1108 --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.0.0_ppc64le-build-fix.patch @@ -0,0 +1,55 @@ +R build gets stuck in an infinite loop on ppc64le (https://stat.ethz.ch/pipermail/r-devel/2020-April/079382.html) +Upstream fix: https://github.com/wch/r-source/commit/2159f0296056693da2d25a4fb9d2635f769836c3 +Patch prepared for EasyBuild by Simon Branford, University of Birmingham +diff --git a/src/main/machar.c b/src/main/machar.c +index 8db54f1350f..cede6e6d582 100644 +--- a/src/main/machar.c ++++ b/src/main/machar.c +@@ -98,21 +98,22 @@ MACH_NAME(int *ibeta, int *it, int *irnd, int *ngrd, int *machep, int *negep, + { + volatile DTYPE a, b, beta, betain, betah, one, + t, temp, tempa, temp1, two, y, z, zero; +- int i, itemp, iz, j, k, mx, nxres; ++ int i, iz, j, k, mx, nxres; + + one = 1; + two = one+one; + zero = one-one; + + /* determine ibeta, beta ala malcolm. */ +- +- a = one; ++ a = one; // a = = 9.0072e+15 for 'double' is used later + do { + a = a + a; + temp = a + one; + temp1 = temp - a; + } + while(temp1 - one == zero); ++#ifdef _no_longer___did_overflow_ // on IBM PowerPPC ('Power 8') ++ int itemp; + b = one; + do { + b = b + b; +@@ -121,6 +122,9 @@ MACH_NAME(int *ibeta, int *it, int *irnd, int *ngrd, int *machep, int *negep, + } + while (itemp == 0); + *ibeta = itemp; ++#else ++ *ibeta = (int) FLT_RADIX; ++#endif + beta = *ibeta; + + /* determine it, irnd */ +diff --git a/src/main/platform.c b/src/main/platform.c +index 2cdaeed05a5..ef93c0b0e5f 100644 +--- a/src/main/platform.c ++++ b/src/main/platform.c +@@ -43,6 +43,7 @@ + #include + #include + #include /* toupper */ ++#include // -> FLT_RADIX + #include + #include + #include /* for realpath */ From 6036743db78804e09f3f41841e7fcb15c301b858 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 4 Oct 2020 14:22:08 +0200 Subject: [PATCH 370/698] LEA 'support' for aarch64 and POWER, now with the actual patch. --- .../LEA-3.0.0_support_aarch64_and_ppc64le.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch new file mode 100644 index 00000000000..ad52e5d4430 --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch @@ -0,0 +1,15 @@ +diff --git a/src/bituint/bituint.h b/src/bituint/bituint.h +index bdce07a..a793dd4 100644 +--- a/src/bituint/bituint.h ++++ b/src/bituint/bituint.h +@@ -66,8 +66,8 @@ static const bituint mask[SIZEUINT] = { + 0x40000000, + 0x80000000 + }; +-#elif defined(__x86_64__) +-// AMD64 ++#elif defined(__x86_64__) || defined(__aarch64__) || defined(__ppc64__) ++// AMD64, 64-bit ARM or 64-bit POWER + typedef uint_fast64_t bituint; + #define SIZEUINT 64 + From 2c2a5d4656aa3164f3052925e75f91cd1f29d338 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 4 Oct 2020 14:26:37 +0200 Subject: [PATCH 371/698] Futher LEA fixes from @zao. --- ...EA-3.0.0_support_aarch64_and_ppc64le.patch | 51 +++++++++++++++++-- 1 file changed, 48 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch index ad52e5d4430..9394f5ce815 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch @@ -1,5 +1,5 @@ diff --git a/src/bituint/bituint.h b/src/bituint/bituint.h -index bdce07a..a793dd4 100644 +index bdce07a..c34381c 100644 --- a/src/bituint/bituint.h +++ b/src/bituint/bituint.h @@ -66,8 +66,8 @@ static const bituint mask[SIZEUINT] = { @@ -8,8 +8,53 @@ index bdce07a..a793dd4 100644 }; -#elif defined(__x86_64__) -// AMD64 -+#elif defined(__x86_64__) || defined(__aarch64__) || defined(__ppc64__) -+// AMD64, 64-bit ARM or 64-bit POWER ++#elif defined(__x86_64__) || defined(__aarch64__) || defined(__powerpc64__) ++// AMD64, ARM64, POWERPC64 typedef uint_fast64_t bituint; #define SIZEUINT 64 +diff --git a/src/stats/ln_gamma_function.c b/src/stats/ln_gamma_function.c +index 0065874..50f7725 100644 +--- a/src/stats/ln_gamma_function.c ++++ b/src/stats/ln_gamma_function.c +@@ -136,17 +136,20 @@ static const long double log_sqrt_2pi = 9.18938533204672741780329736e-1L; + // Bernoulli numbers B(2),B(4),B(6),...,B(20). Only B(2),...,B(6) currently // + // used. // + +-static const long double B[] = { 1.0L / (long double)(6 * 2 * 1), +- -1.0L / (long double)(30 * 4 * 3), +- 1.0L / (long double)(42 * 6 * 5), +- -1.0L / (long double)(30 * 8 * 7), +- 5.0L / (long double)(66 * 10 * 9), +- -691.0L / (long double)(2730 * 12 * 11), +- 7.0L / (long double)(6 * 14 * 13), +- -3617.0L / (long double)(510 * 16 * 15), +- 43867.0L / (long double)(796 * 18 * 17), +- -174611.0L / (long double)(330 * 20 * 19) +- }; ++static long double B(int i) { ++ switch (i) { ++ case 0: return 1.0L / (long double)(6 * 2 * 1); ++ case 1: return -1.0L / (long double)(30 * 4 * 3); ++ case 2: return 1.0L / (long double)(42 * 6 * 5); ++ case 3: return -1.0L / (long double)(30 * 8 * 7); ++ case 4: return 5.0L / (long double)(66 * 10 * 9); ++ case 5: return -691.0L / (long double)(2730 * 12 * 11); ++ case 6: return 7.0L / (long double)(6 * 14 * 13); ++ case 7: return -3617.0L / (long double)(510 * 16 * 15); ++ case 8: return 43867.0L / (long double)(796 * 18 * 17); ++ case 9: return -174611.0L / (long double)(330 * 20 * 19); ++ } ++} + + static long double xLnGamma_Asymptotic_Expansion( long double x ) { + const int m = 3; +@@ -157,7 +160,7 @@ static long double xLnGamma_Asymptotic_Expansion( long double x ) { + long double lngamma = log_sqrt_2pi - xj + (xj - 0.5L) * logl(xj); + int i; + +- for (i = 0; i < m; i++) { term[i] = B[i] / xj; xj *= xx; } ++ for (i = 0; i < m; i++) { term[i] = B(i) / xj; xj *= xx; } + for (i = m - 1; i >= 0; i--) sum += term[i]; + return lngamma + sum; + } From ef278685675d37521cc2a01f0d880c4c36f30d4e Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 4 Oct 2020 14:29:37 +0200 Subject: [PATCH 372/698] Update checksums for LEA patch. --- .../R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index c7869c7399f..fba9cb2da72 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -467,7 +467,7 @@ exts_list = [ 'checksums': [ '802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa', # LEA_3.0.0.tar.gz # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'e0baa8de52a60dfa2675a0c7d771a4ebad7dc4232fa2c895792eaa8e6b4d0772', + '36244fb693e6c40e4d5a84775cc078118e81a7c0dec15905e38ea7feed1ce14f', ], }), ('tximport', '1.16.0', { From 66bfeb0a3138da8a27a56223a1a7bfab86630e65 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 4 Oct 2020 16:17:27 +0100 Subject: [PATCH 373/698] R-bundle-Bioconductor - deduplicate extenstions --- ...bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 5eeb96b870a..1b6f1a7531a 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -162,9 +162,6 @@ exts_list = [ ('impute', '1.62.0', { 'checksums': ['10541b1c2476ab5a78e1f4d2961710db1b98a1076ff33ead6f9c8fcb02353798'], }), - ('fs', '1.4.1', { - 'checksums': ['ae9103dff26ca56a34901408bd650a2949f491b2a0886c686a51a179d38b7a4e'], - }), ('shinyFiles', '0.8.0', { 'checksums': ['1ca1455c99f6559fa8a790d5f16a79485ea76ed2dc4eaf1b650665e1cee89e3f'], }), @@ -177,12 +174,6 @@ exts_list = [ ('hgu133plus2.db', '3.2.3', { 'checksums': ['a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549'], }), - ('sys', '3.3', { - 'checksums': ['a6217c2a7240ed68614006f392c6d062247dab8b9b0d498f95e947110df19b93'], - }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], - }), ('illuminaio', '0.30.0', { 'checksums': ['ec180c39921f8707c09e2226a2feaef80576f581fb872a012f42a9b2433ea844'], }), @@ -497,9 +488,6 @@ exts_list = [ ('SC3', '1.16.0', { 'checksums': ['29918e7a78858ef6602c0f461bf33e32af5d384448029ba1368be41118c2a797'], }), - ('clue', '0.3-57', { - 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], - }), ('ComplexHeatmap', '2.4.2', { 'checksums': ['14e4f92155aaf8d5c92aeab47b890641942b52599928f9ba5ac826073bef5d06'], }), @@ -743,9 +731,6 @@ exts_list = [ ('isoband', '0.2.1', { 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], }), - ('ggplot2', '3.3.0', { - 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], - }), ('ggcyto', '1.16.0', { 'checksums': ['e012f204a01c6b3427a5b29050e37c8034f44a9a5a30ba50b75dcae3d57b06c6'], }), From 858f50f14f5eb7d7719b03594241955be2b5d7d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Oct 2020 13:01:17 +0200 Subject: [PATCH 374/698] add dbarts extension to R 4.0.0 easyconfig --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 59c5ae09d7e..e3453327fb8 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2547,6 +2547,9 @@ exts_list = [ ('mhsmm', '0.4.16', { 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], }), + ('dbarts', '0.9-18', { + 'checksums': ['fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4'], + }), ] moduleclass = 'lang' From bc87cea1247c72e047ed9b0fac0e5898c3cd46d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Oct 2020 13:22:18 +0200 Subject: [PATCH 375/698] adding easyconfigs: treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb --- ...eatSens-3.0-20201002-foss-2020a-R-4.0.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..f293fc01b93 --- /dev/null +++ b/easybuild/easyconfigs/t/treatSens/treatSens-3.0-20201002-foss-2020a-R-4.0.0.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'treatSens' +local_commit = '328551e' +version = '3.0-20201002' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vdorie/treatSens' +description = """Utilities to investigate sensitivity to unmeasured confounding in parametric models + with either binary or continuous treatment.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/vdorie/%(name)s/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['994ff5b4ae61b4629cb4f015062bb7742277ad8511df222b4e2e604b2035c803'] + +dependencies = [ + ('R', '4.0.0'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 9f625bc865fd9703bcbf2c05cb7223fd9070016b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 16:55:49 +0200 Subject: [PATCH 376/698] adding easyconfigs: scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb --- ...it-uplift-0.2.0-foss-2020a-Python-3.8.2.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..2e0aacd466b --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-uplift/scikit-uplift-0.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'scikit-uplift' +version = '0.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/maks-sh/scikit-uplift' +description = """ +scikit-uplift is a Python module for classic approaches for uplift modeling built on top of scikit-learn. +Uplift prediction aims to estimate the causal impact of a treatment at the individual level. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), +] + +use_pip = True + +# pypi source has missing Readme.rst file, using github source instead +exts_list = [ + (name, version, { + 'modulename': 'sklift', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/maks-sh/scikit-uplift/archive'], + 'checksums': ['88870b8456754eeb99f1e0582e802df178a56ec648ad74d147aedb601846a571'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From f3f576d7e60dea2a85fef6023a09c2cd71435fa5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 16:59:11 +0200 Subject: [PATCH 377/698] adding easyconfigs: pylift-0.1.5-foss-2020a-Python-3.8.2.eb, XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb, pretty-yaml-20.4.0-GCCcore-9.3.0.eb, scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb --- .../pretty-yaml-20.4.0-GCCcore-9.3.0.eb | 32 +++++++++++++++++++ .../pylift-0.1.5-foss-2020a-Python-3.8.2.eb | 32 +++++++++++++++++++ ...-optimize-0.8.1-foss-2020a-Python-3.8.2.eb | 31 ++++++++++++++++++ .../XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb | 28 ++++++++++++++++ 4 files changed, 123 insertions(+) create mode 100644 easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..601a92acc8a --- /dev/null +++ b/easybuild/easyconfigs/p/pretty-yaml/pretty-yaml-20.4.0-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pretty-yaml' +local_mod = 'pyaml' +version = '20.4.0' + +homepage = 'https://github.com/mk-fg/pretty-yaml' +description = """PyYAML-based python module to produce pretty and readable YAML-serialized data. +This module is for serialization only, see ruamel.yaml module for literate YAML +parsing (keeping track of comments, spacing, line/column numbers of values, etc).""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/%s/' % local_mod] +sources = ['%s-%%(version)s.tar.gz' % local_mod] +checksums = ['29a5c2a68660a799103d6949167bd6c7953d031449d08802386372de1db6ad71'] + +builddependencies = [('binutils', '2.34')] + +multi_deps = {'Python': ['3.8.2', '2.7.18']} + +dependencies = [ + ('PyYAML', '5.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': local_mod} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..3672d1353a2 --- /dev/null +++ b/easybuild/easyconfigs/p/pylift/pylift-0.1.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'pylift' +version = '0.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/df-foundation/pylift' +description = """ pylift is an uplift library that provides, primarily: + (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class).""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf855996abfd65125cde40b378393766c379694a4b814cdecb1cadd743392730'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('pretty-yaml', '20.4.0'), + ('scikit-learn', '0.23.1', versionsuffix), + ('scikit-optimize', '0.8.1', versionsuffix), + ('Seaborn', '0.10.1', versionsuffix), + ('XGBoost', '1.2.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..fd67c43b65c --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-optimize/scikit-optimize-0.8.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'scikit-optimize' +version = '0.8.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://scikit-optimize.github.io' +description = """Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive + and noisy black-box functions.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ed5c47818959c91490120b89240527cf5ef36dc3e350dc79e5dbc22edc4ee186'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('pretty-yaml', '20.4.0'), +] + +options = {'modulename': 'skopt'} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c29f01917f5 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.2.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.2.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e5f4abcd5df6767293f31b7c58d67ea38b2689641a95b2cd8ca8935295097a36'] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From cb4f2394051c0d3fc8b62519329f46dc9f0829f7 Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 5 Oct 2020 16:08:50 +0100 Subject: [PATCH 378/698] Qt5-5.13.1 patch for Ubuntu 20.04 --- .../q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb | 2 + .../q/Qt5/Qt5-5.13.1_fix-webrtc.patch | 48 +++++++++++++++++++ 2 files changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-webrtc.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb index 38b57db6e75..00d2386f8aa 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1-GCCcore-8.3.0.eb @@ -19,12 +19,14 @@ patches = [ 'Qt5-%(version)s_fix-avx2.patch', 'Qt5-%(version)s_fix-qmake-libdir.patch', 'Qt5-%(version)s_fix-mantissatable.patch', + 'Qt5-%(version)s_fix-webrtc.patch', ] checksums = [ 'adf00266dc38352a166a9739f1a24a1e36f1be9c04bf72e16e142a256436974e', # qt-everywhere-src-5.13.1.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.13.1_fix-avx2.patch '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63', # Qt5-5.13.1_fix-qmake-libdir.patch 'cb23b917dd145b6775d7ffb3d8c143749d183d32972111f0c31133e41803f56b', # Qt5-5.13.1_fix-mantissatable.patch + '0e449fce243587b9001d8060d6417c285d4ad8fe969b1a2528a3058a29bc6af6', # Qt5-5.13.1_fix-webrtc.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-webrtc.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-webrtc.patch new file mode 100644 index 00000000000..193a44071b0 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.13.1_fix-webrtc.patch @@ -0,0 +1,48 @@ +Patch modified for Qt5 version and easybuild by A Edmondson, 5 October 2020 +Original info follows: +* https://code.qt.io/cgit/qt/qtwebengine-chromium.git/commit/?id=6e2562dd1efff + +From 6e2562dd1efff2b96848e8ec166e8c233029d6cc Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Emilio=20Cobos=20=C3=81lvarez?= +Date: Wed, 29 May 2019 15:30:32 +0200 +Subject: Fix build with recent linux kernel. +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Recent kernel commit[1] moved a bit the define for this constant. This revealed +a missing include in WebRTC. + +[1]: https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/commit/?id=0768e17073dc5 + +Bug: webrtc:10677 +Change-Id: I6ed69d307599d077760ae6ad74be10bfbdd1cac6 +Commit-Queue: Karl Wiberg +Reviewed-by: Karl Wiberg +Cr-Commit-Position: refs/heads/master@{#28108} +See-Also: https://chromium.googlesource.com/external/webrtc/+/6806550d5d51a820104a12205d1f37ce0acebf19 +Reviewed-by: Jüri Valdmann +(cherry picked from commit 74e69da92d0a895122ca65922b9a2b8b3926c882) +Reviewed-by: Michal Klocek +--- + qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physical_socket_server.cc | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physical_socket_server.cc b/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physical_socket_server.cc +index ca78499179a..e8c1474762f 100644 +--- a/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physical_socket_server.cc ++++ b/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physical_socket_server.cc +@@ -52,6 +52,10 @@ + #include "rtc_base/timeutils.h" + #include "rtc_base/win32socketinit.h" + ++#if defined(WEBRTC_LINUX) ++#include ++#endif ++ + #if defined(WEBRTC_WIN) + #define LAST_SYSTEM_ERROR (::GetLastError()) + #elif defined(__native_client__) && __native_client__ +-- +cgit v1.2.1 + From 275b8faf4835c305fe3602bc318668e852fb364b Mon Sep 17 00:00:00 2001 From: edmondac-admin Date: Mon, 5 Oct 2020 16:18:42 +0100 Subject: [PATCH 379/698] Qt5-5.12.3 patch for Ubuntu 20.04 --- .../q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb | 4 ++ .../q/Qt5/Qt5-5.12.3_fix-socketcan.patch | 37 ++++++++++++++ .../q/Qt5/Qt5-5.12.3_fix-webrtc.patch | 48 +++++++++++++++++++ 3 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-socketcan.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-webrtc.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb index 910718cb715..24a44c079ec 100644 --- a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3-GCCcore-8.2.0.eb @@ -18,11 +18,15 @@ sources = ['qt-everywhere-src-%(version)s.tar.xz'] patches = [ 'Qt5-%(version)s_fix-avx2.patch', 'Qt5-%(version)s_fix-qmake-libdir.patch', + 'Qt5-%(version)s_fix-webrtc.patch', + 'Qt5-%(version)s_fix-socketcan.patch', ] checksums = [ '6462ac74c00ff466487d8ef8d0922971aa5b1d5b33c0753308ec9d57711f5a42', # qt-everywhere-src-5.12.3.tar.xz '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc', # Qt5-5.12.3_fix-avx2.patch '50974f2ed761a8a70fbdf2e80b9107af68cc29ee951885e26fa0c19bdb6a9c7b', # Qt5-5.12.3_fix-qmake-libdir.patch + '5006df9a4d1f687e1e32af88f5fddcf729018ae50a3a1b0340f7087cdcf8d8b8', # Qt5-5.12.3_fix-webrtc.patch + 'ace318c8ef1b27da5e60eeb219cb51e98dc214102d29f27a6d8438f6e616a3a6', # Qt5-5.12.3_fix-socketcan.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-socketcan.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-socketcan.patch new file mode 100644 index 00000000000..f670f844475 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-socketcan.patch @@ -0,0 +1,37 @@ +Patch modified for Qt5 version and easybuild by A Edmondson, 5 October 2020 +Original info follows: +* https://codereview.qt-project.org/gitweb?p=qt/qtserialbus.git;a=patch;h=43d746c2c0c87c8694e835f3b052317c8fa02482 + +From 43d746c2c0c87c8694e835f3b052317c8fa02482 Mon Sep 17 00:00:00 2001 +From: Andre Hartmann +Date: Mon, 8 Jul 2019 21:35:12 +0200 +Subject: [PATCH] =?utf8?q?SocketCAN:=20Fix=20compiler=20error=20"=E2=80=98?= + =?utf8?q?SIOCGSTAMP=E2=80=99=20was=20not=20declared"?= +MIME-Version: 1.0 +Content-Type: text/plain; charset=utf8 +Content-Transfer-Encoding: 8bit + +Fixes: QTBUG-76957 +Change-Id: I8c4c86aa23137d67f5d20eedfe1c46a241c0632b +Reviewed-by: Alex Blasche +Reviewed-by: Denis Shienkov +--- + qtserialbus/src/plugins/canbus/socketcan/socketcanbackend.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/qtserialbus/src/plugins/canbus/socketcan/socketcanbackend.cpp b/qtserialbus/src/plugins/canbus/socketcan/socketcanbackend.cpp +index 74b0d1d9..a2da146f 100644 +--- a/qtserialbus/src/plugins/canbus/socketcan/socketcanbackend.cpp ++++ b/qtserialbus/src/plugins/canbus/socketcan/socketcanbackend.cpp +@@ -45,6 +45,7 @@ + + #include + #include ++#include + #include + #include + #include +-- +2.16.3 + + diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-webrtc.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-webrtc.patch new file mode 100644 index 00000000000..4b835a385e3 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.12.3_fix-webrtc.patch @@ -0,0 +1,48 @@ +Patch modified for Qt5 version and easybuild by A Edmondson, 5 October 2020 +Original info follows: +* https://code.qt.io/cgit/qt/qtwebengine-chromium.git/commit/?id=6e2562dd1efff + +From 6e2562dd1efff2b96848e8ec166e8c233029d6cc Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Emilio=20Cobos=20=C3=81lvarez?= +Date: Wed, 29 May 2019 15:30:32 +0200 +Subject: Fix build with recent linux kernel. +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Recent kernel commit[1] moved a bit the define for this constant. This revealed +a missing include in WebRTC. + +[1]: https://git.kernel.org/pub/scm/linux/kernel/git/torvalds/linux.git/commit/?id=0768e17073dc5 + +Bug: webrtc:10677 +Change-Id: I6ed69d307599d077760ae6ad74be10bfbdd1cac6 +Commit-Queue: Karl Wiberg +Reviewed-by: Karl Wiberg +Cr-Commit-Position: refs/heads/master@{#28108} +See-Also: https://chromium.googlesource.com/external/webrtc/+/6806550d5d51a820104a12205d1f37ce0acebf19 +Reviewed-by: Jüri Valdmann +(cherry picked from commit 74e69da92d0a895122ca65922b9a2b8b3926c882) +Reviewed-by: Michal Klocek +--- + qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physicalsocketserver.cc | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physicalsocketserver.cc b/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physicalsocketserver.cc +index ca78499179a..e8c1474762f 100644 +--- a/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physicalsocketserver.cc ++++ b/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/physicalsocketserver.cc +@@ -52,6 +52,10 @@ + #include "rtc_base/timeutils.h" + #include "rtc_base/win32socketinit.h" + ++#if defined(WEBRTC_LINUX) ++#include ++#endif ++ + #if defined(WEBRTC_WIN) + #define LAST_SYSTEM_ERROR (::GetLastError()) + #elif defined(__native_client__) && __native_client__ +-- +cgit v1.2.1 + From 802d17003a680c8048e41bec01dd3ee824b04607 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 17:25:20 +0200 Subject: [PATCH 380/698] adding easyconfigs: SUMO-1.7.0-foss-2020a-Python-3.8.2.eb, GL2PS-1.4.2-GCCcore-9.3.0.eb, FoX-4.1.2-GCC-9.3.0.eb --- .../easyconfigs/f/FoX/FoX-4.1.2-GCC-9.3.0.eb | 26 +++++++++ .../g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb | 34 ++++++++++++ .../SUMO-1.7.0-foss-2020a-Python-3.8.2.eb | 55 +++++++++++++++++++ 3 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-9.3.0.eb b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-9.3.0.eb new file mode 100644 index 00000000000..59d64f8646d --- /dev/null +++ b/easybuild/easyconfigs/f/FoX/FoX-4.1.2-GCC-9.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'FoX' +version = '4.1.2' + +homepage = 'http://homepages.see.leeds.ac.uk/~earawa/FoX/' +description = """FoX is an XML library written in Fortran 95. +It allows software developers to read, write and modify XML documents from Fortran applications without the +complications of dealing with multi-language development.""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} + +source_urls = ['http://homepages.see.leeds.ac.uk/~earawa/FoX/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3b749138229e7808d0009a97e2ac47815ad5278df6879a9cc64351a7921ba06f'] + +sanity_check_paths = { + 'files': ['lib/libFoX_%s.a' % x for x in ['common', 'dom', 'fsys', 'sax', 'utils', 'wcml', 'wkml', 'wxml']], + 'dirs': ['finclude', 'lib', 'bin'] +} + +modextrapaths = { + 'CPATH': ['finclude'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..062d067f575 --- /dev/null +++ b/easybuild/easyconfigs/g/GL2PS/GL2PS-1.4.2-GCCcore-9.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'GL2PS' +version = '1.4.2' + +homepage = 'https://www.geuz.org/gl2ps/' +description = """GL2PS: an OpenGL to PostScript printing library""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://geuz.org/gl2ps/src/'] +sources = [SOURCELOWER_TGZ] +checksums = ['8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('binutils', '2.34'), +] + +dependencies = [ + ('X11', '20200222'), + ('Mesa', '20.0.2'), + ('libGLU', '9.0.1'), + ('freeglut', '3.2.1'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['include/gl2ps.h', 'lib/libgl2ps.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..6fa6b39445b --- /dev/null +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'SUMO' +version = '1.7.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://sumo.dlr.de/' +description = """ +"Simulation of Urban MObility" (SUMO) is an open source, highly portable, microscopic and continuous traffic simulation +package designed to handle large networks. It allows for intermodal simulation including pedestrians and comes with a +large set of tools for scenario creation. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/eclipse/sumo/archive/'] +sources = ['v%s.tar.gz' % version.replace('.', '_')] +checksums = ['db0868318f2a602475a15ba8b83d30b686e6283b3ff753b9d112217529f2893b'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('SWIG', '4.0.1'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('Xerces-C++', '3.2.3'), + ('GL2PS', '1.4.2'), + ('GDAL', '3.0.4', versionsuffix), + ('PROJ', '7.0.0'), + ('FoX', '4.1.2'), +] + +separate_build_dir = True + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'SUMO_HOME': 'share/sumo', +} + +local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', 'emissionsMap', 'jtrrouter', + 'marouter', 'netconvert', 'netgenerate', 'od2trips', 'polyconvert', 'sumo'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins] + + ['lib/python%%(pyshortver)s/site-packages/libsumo/_libsumo.%s' % SHLIB_EXT], + 'dirs': ['bin', 'lib', 'share', 'tools'], +} + +sanity_check_commands = [ + 'sumo --help', + "python -c 'import libsumo'", +] + +moduleclass = 'data' From f417eabab55857fc66c0380b7b9d8fadcb12e613 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Oct 2020 17:27:27 +0200 Subject: [PATCH 381/698] fix PyVCF easyconfig: only supports Python 2 --- .../BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb | 2 +- ...8.3.0.eb => PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb} | 10 +++++++--- 2 files changed, 8 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/p/PyVCF/{PyVCF-0.6.8-GCC-8.3.0.eb => PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb} (81%) diff --git a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb index 2aadd350563..5f4089015e2 100644 --- a/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb +++ b/easybuild/easyconfigs/b/BAMSurgeon/BAMSurgeon-1.2-GCC-8.3.0-Python-2.7.16.eb @@ -21,7 +21,7 @@ dependencies = [ ('Velvet', '1.2.10', '-mt-kmer_191'), ('Exonerate', '2.4.0'), ('Pysam', '0.15.3'), - ('PyVCF', '0.6.8'), + ('PyVCF', '0.6.8', versionsuffix), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb similarity index 81% rename from easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb rename to easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb index c7761dfa305..246347a9e78 100644 --- a/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/p/PyVCF/PyVCF-0.6.8-GCC-8.3.0-Python-2.7.16.eb @@ -2,6 +2,7 @@ easyblock = 'PythonPackage' name = 'PyVCF' version = '0.6.8' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/jamescasbon/PyVCF' description = "A Variant Call Format reader for Python." @@ -12,13 +13,16 @@ source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'] -multi_deps = {'Python': ['3.7.4', '2.7.16']} - -dependencies = [('Pysam', '0.15.3')] +dependencies = [ + ('Python', '2.7.16'), + ('Pysam', '0.15.3'), +] download_dep_fail = True use_pip = True +fix_python_shebang_for = ['bin/*.py', 'bin/vcf_melt'] + options = {'modulename': 'vcf'} sanity_check_paths = { From 544c2fec790643ed69d0dcbae8a2de2552e7499c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 17:30:31 +0200 Subject: [PATCH 382/698] adding easyconfigs: causallift-1.0.6-foss-2020a-Python-3.8.2.eb, kedro-0.16.5-foss-2020a-Python-3.8.2.eb --- ...ausallift-1.0.6-foss-2020a-Python-3.8.2.eb | 39 ++++++++++ .../kedro-0.16.5-foss-2020a-Python-3.8.2.eb | 73 +++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..95b30ebce99 --- /dev/null +++ b/easybuild/easyconfigs/c/causallift/causallift-1.0.6-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'causallift' +version = '1.0.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/Minyus/causallift' +description = """ +CausalLift: Python package for Uplift Modeling in real-world business; +applicable for both A/B testing and observational data +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('kedro', '0.16.5', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('easydict', '1.9', { + 'checksums': ['3f3f0dab07c299f0f4df032db1f388d985bb57fa4c5be30acd25c5f9a516883b'], + }), + (name, version, { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/Minyus/causallift/archive/'], + 'checksums': ['b5a62317438d469a2bb41b75d6a9214178196a9717afe82ceabc3b6843fae9a6'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..efbd276d197 --- /dev/null +++ b/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'kedro' +version = '0.16.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/quantumblacklabs/kedro' +description = """ +Kedro is an open-source Python framework that applies software engineering +best-practice to data and machine-learning pipelines. +""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('IPython', '7.13.0', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('anyconfig', '0.9.7', { + 'checksums': ['4d6016ae6eecc5e502bc7e99ae0639c5710c5c67bde5f21b06b9eaafd9ce0e7e'], + }), + ('cachetools', '4.1.1', { + 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('arrow', '0.16.0', { + 'checksums': ['92aac856ea5175c804f7ccb96aca4d714d936f1c867ba59d747a8096ec30e90a'], + }), + ('jinja2-time', '0.2.0', { + 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], + }), + ('poyo', '0.5.0', { + 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], + }), + ('whichcraft', '0.6.1', { + 'checksums': ['acdbb91b63d6a15efbd6430d1d7b2d36e44a71697e93e19b7ded477afd9fce87'], + }), + ('cookiecutter', '1.6.0', { + 'checksums': ['1316a52e1c1f08db0c9efbf7d876dbc01463a74b155a0d83e722be88beda9a3e'], + }), + ('fsspec', '0.6.3', { + 'checksums': ['7a6d48af15b2416c5007706039e6d46d083c89229e7cdf6474b5ef5e7e687b00'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('pip-tools', '5.0.0', { + 'modulename': 'piptools', + 'checksums': ['2045d0414e9db71c036443efa229ff1b76dfe47a3cb022d6154a1c9e207f0867'], + }), + ('python-json-logger', '0.1.9', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['e3636824d35ba6a15fc39f573588cba63cf46322a5dc86fb2f280229077e9fbe'], + }), + ('toposort', '1.5', { + 'checksums': ['dba5ae845296e3bf37b042c640870ffebcdeb8cd4df45adaa01d8c5476c557dd'], + }), + (name, version, { + 'checksums': ['84f992aaa6451e3b1c9fef2671fdebcc6715b027db7e22471adf8572214da6d1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From fe1174e3bc974682935a3ec3fe65c132e5e0aedb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 18:12:18 +0200 Subject: [PATCH 383/698] update IPython to 7.15.0 --- .../easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb index efbd276d197..d18135ed81f 100644 --- a/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/k/kedro/kedro-0.16.5-foss-2020a-Python-3.8.2.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('Python', '3.8.2'), - ('IPython', '7.13.0', versionsuffix), + ('IPython', '7.15.0', versionsuffix), ] use_pip = True From b4da373cfbe677c53b4527a9389621945b4c8101 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Oct 2020 18:41:48 +0200 Subject: [PATCH 384/698] fix sanity check paths --- .../easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb index 6fa6b39445b..acdae5cac59 100644 --- a/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SUMO/SUMO-1.7.0-foss-2020a-Python-3.8.2.eb @@ -44,7 +44,7 @@ local_bins = ['activitygen', 'dfrouter', 'duarouter', 'emissionsDrivingCycle', ' sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins] + ['lib/python%%(pyshortver)s/site-packages/libsumo/_libsumo.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib', 'share', 'tools'], + 'dirs': ['bin', 'lib', 'share'], } sanity_check_commands = [ From aa718099de2271839ef8d0f6d5a43983ed8bc9d0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 5 Oct 2020 19:08:23 +0200 Subject: [PATCH 385/698] Upgrade to hypothesis/4.39.3 for intel/2018a and include setuptools to avoid installation problems --- ....eb => hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb} | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/hypothesis/{hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb => hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb} (76%) diff --git a/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb similarity index 76% rename from easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb rename to easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb index 8399a457df6..8812771cb50 100644 --- a/easybuild/easyconfigs/h/hypothesis/hypothesis-3.66.18-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/h/hypothesis/hypothesis-4.39.3-intel-2018a-Python-3.6.4.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' name = 'hypothesis' -version = '3.66.18' +version = '4.39.3' versionsuffix = '-Python-%(pyver)s' homepage = "https://github.com/HypothesisWorks/hypothesis" @@ -19,6 +19,11 @@ dependencies = [ use_pip = True exts_list = [ + ('setuptools', '38.4.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'source_urls': ['https://pypi.python.org/packages/source/s/setuptools/'], + 'checksums': ['6501fc32f505ec5b3ed36ec65ba48f1b975f52cf2ea101c7b73a08583fd12f75'], + }), ('attrs', '19.3.0', { 'modulename': 'attr', 'source_urls': ['https://pypi.python.org/packages/source/a/attrs'], @@ -30,7 +35,7 @@ exts_list = [ }), (name, version, { 'source_urls': ['https://pypi.python.org/packages/source/h/hypothesis/'], - 'checksums': ['6bcf0e565cd394080d692f4595215335a90a868325aa4869dfe7450be9a8a583'], + 'checksums': ['48978b121244e28c445007db1c3f5b2bbd5bbb8e8e8e9625b6c79860c520b7cb'], }), ] From e32a1fb8c2e2bc64947fd93d56e0cf26e71cad41 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 5 Oct 2020 21:44:31 +0200 Subject: [PATCH 386/698] adding easyconfigs: pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb, spoa-4.0.0-GCC-8.3.0.eb and patches: pyspoa-0.0.4_use-spoa-dep.patch --- .../pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb | 42 +++++++++++++++++++ .../p/pyspoa/pyspoa-0.0.4_use-spoa-dep.patch | 27 ++++++++++++ .../s/spoa/spoa-4.0.0-GCC-8.3.0.eb | 29 +++++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4_use-spoa-dep.patch create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.0.0-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..d8c636a9543 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.0.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/nanoporetech/pyspoa/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'pyspoa-%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': '3e4d1b8.tar.gz', + 'filename': 'cereal-20200423.tar.gz', + }, +] +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] +checksums = [ + 'c4c7b1625a80ed2b92f0e438eb0096a66d091d8025c45fbbd74603bd47c07efa', # pyspoa-0.0.4.tar.gz + '284cd14c1e60b36c966bcc8ce650d0b798b8a836d6c379e021e0da0dbe6ddf38', # cereal-20200423.tar.gz + 'a66532ee80d9b6194fe3da4f9cdc93a073514281a1e55664f71df82508fcbdca', # pyspoa-0.0.4_use-spoa-dep.patch +] + +dependencies = [ + ('Python', '3.7.4'), + ('pybind11', '2.4.3', versionsuffix), + ('spoa', '4.0.0'), +] + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +use_pip = True + +options = {'modulename': 'spoa'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4_use-spoa-dep.patch b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4_use-spoa-dep.patch new file mode 100644 index 00000000000..1e027c2f85a --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4_use-spoa-dep.patch @@ -0,0 +1,27 @@ +use spoa dependency provided through EasyBuild + +author: Kenneth Hoste (HPC-UGent) +--- pyspoa-0.0.4/setup.py.orig 2020-10-04 18:50:51.000000000 +0200 ++++ pyspoa-0.0.4/setup.py 2020-10-05 19:26:33.563888080 +0200 +@@ -1,3 +1,4 @@ ++import os + import sys + import setuptools + from setuptools import setup, Extension +@@ -89,14 +90,14 @@ + 'spoa', + ['pyspoa.cpp'], + include_dirs=[ +- 'src/include/spoa', ++ os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'), + 'src/vendor/cereal/include', + get_pybind_include(), + get_pybind_include(user=True), + ], + language='c++', + extra_objects=[ +- 'src/build/lib/libspoa.a' ++ os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'), + ], + + ), diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.0.0-GCC-8.3.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.0.0-GCC-8.3.0.eb new file mode 100644 index 00000000000..6bf5755f147 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.0.0-GCC-8.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.0.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/releases/download/%(version)s/'] +sources = ['spoa-v%(version)s.tar.gz'] +checksums = ['bf28bd174f8f9fa7f752f86e3b65fc82acdf983ce07911d91d267095c67402ae'] + +builddependencies = [('CMake', '3.15.3')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a', 'lib/pkgconfig/spoa-1.pc'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From fd52cd3b183aa870a0377509441303b9c9867b80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 6 Oct 2020 09:28:40 +0200 Subject: [PATCH 387/698] adding easyconfigs: medaka-1.1.1-foss-2019b-Python-3.7.4.eb, edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb, Pysam-0.16.0.1-GCC-8.3.0.eb and patches: medaka-1.1.1_use-SAMtools-dep.patch --- ...dlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb | 24 +++++++ .../medaka-1.1.1-foss-2019b-Python-3.7.4.eb | 72 +++++++++++++++++++ .../medaka-1.1.1_use-SAMtools-dep.patch | 44 ++++++++++++ .../p/Pysam/Pysam-0.16.0.1-GCC-8.3.0.eb | 40 +++++++++++ 4 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.1.1_use-SAMtools-dep.patch create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-8.3.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..84cba4bf94a --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.8.post1-GCC-8.3.0-Python-3.7.4.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'edlib' +version = '1.3.8.post1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['81bc688e8fc69d657a6b5067e104a0924b0217b7ab54547155278935d09346e0'] + +dependencies = [ + ('Python', '3.7.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..f08e854de87 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), # includes cffi, numpy + # TensorFlow 2.2.0 required by medaka, see requirements.txt + ('TensorFlow', '2.2.0', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.10'), + ('minimap2', '2.17'), + ('HTSlib', '1.10.2'), # for tabix, bgzip + ('Racon', '1.4.13'), + ('spoa', '4.0.0'), + ('networkx', '2.4', versionsuffix), + ('edlib', '1.3.8.post1', versionsuffix), + ('pyspoa', '0.0.4', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('mappy', '2.17', { + 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.1.6', { + 'checksums': ['586b819bd48d38f446b33dac4a34f33c1004beeef0baf16ae1253d5fa360b951'], + }), + ('parasail', '1.2', { + 'checksums': ['6ceef978e7d06293c38c9824f76557f3d7e137cb05487be31bf89286f7a8201e'], + }), + ('pyfaidx', '0.5.9.1', { + 'checksums': ['eda8af04ba4da4fd63fdc35a62e0e41dfc06aa1a511728dfbdd7707e3b382855'], + }), + ('xopen', '0.9.0', { + 'checksums': ['1e3918c8a5cd2bd128ba05b3b883ee322349219c99c305e10114638478e3162a'], + }), + ('whatshap', '1.0', { + 'checksums': ['fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2'], + }), + (name, version, { + 'patches': ['medaka-1.1.1_use-SAMtools-dep.patch'], + 'checksums': [ + '0b4b2b20ae49f32154e25d9c45fcec4c7b97e9b511e7c6023a00106c6b462557', # medaka-1.1.1.tar.gz + 'b5b7c69f4c132f632f0a8f775f65a37f19a977aeba7de3880575a6b32586d27e', # medaka-1.1.1_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.1_use-SAMtools-dep.patch b/easybuild/easyconfigs/m/medaka/medaka-1.1.1_use-SAMtools-dep.patch new file mode 100644 index 00000000000..6e0f1217e6d --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.1_use-SAMtools-dep.patch @@ -0,0 +1,44 @@ +use SAMtools provided as dependency rather than building libhts.a from scratch + +author: Kenneth Hoste (HPC-UGent) +--- medaka-1.1.1/build.py.orig 2020-10-05 17:35:07.157142280 +0200 ++++ medaka-1.1.1/build.py 2020-10-05 17:42:02.501328998 +0200 +@@ -3,12 +3,8 @@ + + from cffi import FFI + +-#TODO: configure this better +-samver="1.10" +-htslib_dir=os.path.join('submodules', 'samtools-{}'.format(samver), 'htslib-{}'.format(samver)) +- + libraries=['m', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'] +-library_dirs=[htslib_dir] ++library_dirs=[] + src_dir='src' + + ffibuilder = FFI() +@@ -26,10 +22,10 @@ + """, + libraries=libraries, + library_dirs=library_dirs, +- include_dirs=[src_dir, htslib_dir], ++ include_dirs=[src_dir], + sources=[os.path.join(src_dir, x) for x in ('medaka_bamiter.c', 'medaka_common.c', 'medaka_counts.c', 'fastrle.c', 'medaka_trimbam.c', 'medaka_pytrimbam.c')], + extra_compile_args=['-std=c99', '-msse3', '-O3'], +- extra_objects=['libhts.a'] ++ extra_objects=[os.path.join(os.getenv('EBROOTSAMTOOLS'), 'lib', 'libhts.a')] + ) + + cdef = [] +--- medaka-1.1.1/setup.py.orig 2020-10-05 17:54:15.908699976 +0200 ++++ medaka-1.1.1/setup.py 2020-10-05 17:54:20.498745639 +0200 +@@ -165,9 +165,6 @@ + }, + scripts=['scripts/medaka_consensus', 'scripts/medaka_variant', 'scripts/mini_align', 'scripts/hdf2tf.py'], + zip_safe=False, +- cmdclass={ +- 'build_ext': HTSBuild +- }, + ) + + if os.environ.get('MEDAKA_BINARIES') is not None: diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-8.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-8.3.0.eb new file mode 100644 index 00000000000..d2645aa3040 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.16.0.1-GCC-8.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# 0.9.1.4: +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Erich Birngruber +# Gregor Mendel Institute +# Modified by: Pavel Grochal +# INUITS + +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.16.0.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '8.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a61e98e299fa93ba121aab521081282b61bc978bb9052d33b26b38f8fe15573e'] + +multi_deps = {'Python': ['3.7.4', '2.7.16']} + +dependencies = [ + ('ncurses', '6.1'), + ('cURL', '7.66.0'), + ('XZ', '5.2.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 5bc627c12029069595ffe6b239c672eee5e603d3 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Tue, 6 Oct 2020 11:42:50 +0100 Subject: [PATCH 388/698] adding easyconfigs: GROMACS-2019.6-fosscuda-2019b.eb and patches: GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch --- .../GROMACS/GROMACS-2019.6-fosscuda-2019b.eb | 52 +++++++++++++++++++ ...and_google_test_death_style_in_tests.patch | 26 ++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019.6-fosscuda-2019b.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.6-fosscuda-2019b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.6-fosscuda-2019b.eb new file mode 100644 index 00000000000..69f0788dac6 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019.6-fosscuda-2019b.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * J. Sassmannshausen (Crick HPC team) +# * Dugan Witherick +# License:: MIT/GPL +# + +name = 'GROMACS' +version = '2019.6' + +homepage = 'http://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, + i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. +""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch', + 'GROMACS-2019_increase_test_timeout_for_GPU.patch', +] +checksums = [ + 'bebe396dc0db11a9d4cc205abc13b50d88225617642508168a2195324f06a358', # gromacs-2019.6.tar.gz + # GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch + '5f4da72b0f1eb53f6fb52a253331cbf0ecf962c27a26c2a444b119fe545614da', + # GROMACS-2019_increase_test_timeout_for_GPU.patch + '0d16f53d428155197a0ed0b0974ce03422f199d7c463c4a9156a3b99e3c86234', +] + +builddependencies = [ + ('CMake', '3.15.3'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch new file mode 100644 index 00000000000..a3b8259d557 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2019_fix_omp_num_threads_inc_threadmpi_and_google_test_death_style_in_tests.patch @@ -0,0 +1,26 @@ +Fix test execution to explicitly set OMP_NUM_THREADS when needed. +Also make sure google death test uses threadsafe mode. +Updated to unset OMP_NUM_THREADS when GMX_THREAD_MPI used. + +Åke Sandgren, 2019-01-02 +Dugan Witherick, 2020-10-06 +diff -Nru gromacs-2019.6.orig/src/testutils/TestMacros.cmake gromacs-2019.6/src/testutils/TestMacros.cmake +--- gromacs-2019.6.orig/src/testutils/TestMacros.cmake 2020-10-05 16:56:52.373971000 +0100 ++++ gromacs-2019.6/src/testutils/TestMacros.cmake 2020-10-06 09:36:18.348994000 +0100 +@@ -153,8 +153,15 @@ + list(APPEND _cmd -ntmpi ${ARG_MPI_RANKS}) + endif() + endif() ++ if (ARG_OPENMP_THREADS) ++ if (NOT GMX_THREAD_MPI) ++ set(_cmd "env" "OMP_NUM_THREADS=${ARG_OPENMP_THREADS}" ${_cmd}) ++ else() ++ set(_cmd "env" "--unset=OMP_NUM_THREADS" ${_cmd}) ++ endif() ++ endif() + add_test(NAME ${NAME} +- COMMAND ${_cmd} --gtest_output=xml:${_xml_path}) ++ COMMAND ${_cmd} --gtest_death_test_style=threadsafe --gtest_output=xml:${_xml_path}) + set_tests_properties(${NAME} PROPERTIES LABELS "${_labels}") + set_tests_properties(${NAME} PROPERTIES TIMEOUT ${_timeout}) + add_dependencies(tests ${EXENAME}) From d1329ff430592919738cdd6e8722ed60ab2dd787 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 10:23:31 +0200 Subject: [PATCH 389/698] Inplace update of Horovod to 0.20.3 --- ...od-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/h/Horovod/{Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb => Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb} (90%) diff --git a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb similarity index 90% rename from easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb rename to easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb index 93a050893a4..2470b55fa5c 100644 --- a/easybuild/easyconfigs/h/Horovod/Horovod-0.20.0-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/Horovod/Horovod-0.20.3-fosscuda-2019b-TensorFlow-2.3.1-Python-3.7.4.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Horovod' -version = '0.20.0' +version = '0.20.3' local_tf_version = '2.3.1' versionsuffix = '-TensorFlow-%s-Python-%%(pyver)s' % local_tf_version @@ -32,7 +32,7 @@ exts_list = [ 'checksums': ['820c9245cebdec7257211cbe88745101d5d6a042bca11336d78ebd4897ddbc82'], }), ('horovod', version, { - 'checksums': ['88522b65d83cb9690193b200e2e8fd1e08864b27d72b7ff1bbc5e7b8ae4f32ed'], + 'checksums': ['6ebc90d627af486d44335ed48489e1e8dc190607574758867c52e4e17d75a247'], }), ] From 7c82f6740abc25d409aa51e8b1c3252dea52d155 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 11:20:54 +0200 Subject: [PATCH 390/698] [OpenBLAS] Add patches fixing miscomputation and performance issues --- .../o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb | 8 ++++++++ .../o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb | 8 ++++++++ .../o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 8 ++++++++ 3 files changed, 24 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb index 5bf04fcaec4..84769201122 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb @@ -18,11 +18,19 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', + 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ '49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab', # v0.3.3.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', + '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb index dbdc57e59f8..476ac3c4e8a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb @@ -19,6 +19,9 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', + 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ '4b4b4453251e9edb5f57465bf2b3cf67b19d811d50c8588cdf2ea1f201bb834f', # v0.3.4.tar.gz @@ -26,6 +29,11 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.4_disable_AVX512_dgemm_kernel.patch '56d5034869ebd7b63c7af23eadd0935280d4d57ac3b0d35956c64015a3103da9', + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', + '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index b9155e2755b..4260d7ac24b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -19,6 +19,9 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', + 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ '0950c14bd77c90a6427e26210d6dab422271bc86f9fc69126725833ecdaa0e85', # v0.3.5.tar.gz @@ -26,6 +29,11 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.5_disable_AVX512_dgemm_kernel.patch '56d5034869ebd7b63c7af23eadd0935280d4d57ac3b0d35956c64015a3103da9', + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', + '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below From 6b05dcfee50076f9b595547a128dfaa9099723f9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 11:22:16 +0200 Subject: [PATCH 391/698] [OpenBLAS] Add patches fixing miscomputation and performance issues --- .../o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb | 8 ++++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb | 8 ++++++++ 2 files changed, 16 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb index 0e1ebe09411..04fb6eb628b 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb @@ -19,6 +19,9 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', + 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ 'e64c8fe083832ffbc1459ab6c72f71d53afd3b36e8497c922a15a06b72e9002f', # v0.3.6.tar.gz @@ -26,6 +29,11 @@ checksums = [ '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz # OpenBLAS-0.3.6_disable_AVX512_dgemm_kernel.patch 'eb262478e58e6f53c987627d47207d16b2a4d282b430a054766e46881df16b8b', + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', + '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb index bcaefb5cbc4..f1e21707f74 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb @@ -15,11 +15,19 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', + 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ 'bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379', # v0.3.7.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', + '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below From 745270e7596068496ea93f537c4f72c9efd66d45 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 11:23:31 +0200 Subject: [PATCH 392/698] [OpenBLAS] Add patches fixing miscomputation and performance issues --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb | 6 ++++++ .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb | 6 ++++++ 2 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb index 712606a3a19..7d650adad08 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.8-GCC-9.2.0.eb @@ -15,12 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', ] checksums = [ '8f86ade36f0dbed9ac90eb62575137388359d97d8f93093b38abe166ad7ef3a8', # v0.3.8.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb index 96804433717..75f3b80647f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.9-GCC-9.3.0.eb @@ -15,12 +15,18 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', + 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', 'OpenBLAS-0.3.9_fix-lapack_h.patch', ] checksums = [ '17d4677264dfbc4433e97076220adc79b050e4f8a083ea3f853a53af253bc380', # v0.3.9.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch + 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', + # OpenBLAS-0.3.7_reinit-threads-after-fork.patch + 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', '9210a94ae418b4ce6d9f7fab4e00dd3155451f5ef3769536a4d954a2149ca733', # OpenBLAS-0.3.9_fix-lapack_h.patch ] From 3c3a5ecc03702a5821e359cfe745f52f0835bd40 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 7 Oct 2020 11:39:46 +0200 Subject: [PATCH 393/698] Upgrade of silx config to include extension hdf5plugin --- .../silx-0.13.2-foss-2019b-Python-3.7.4.eb | 22 ++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb index 103831418d8..efee4607300 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'silx' version = '0.13.2' @@ -10,10 +10,6 @@ development of data assessment, reduction and analysis applications at synchrotr toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['0bc5a5a30499b9d620c795a20948151a4057aba16ff08dfe637f7a923b4697d4'] - dependencies = [ ('Python', '3.7.4'), @@ -32,4 +28,20 @@ use_pip = True download_dep_fail = True sanity_pip_check = True +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('hdf5plugin', '2.3.1', { + 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], + }), + ('silx', version, { + 'checksums': ['0bc5a5a30499b9d620c795a20948151a4057aba16ff08dfe637f7a923b4697d4'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + + moduleclass = 'vis' From ccb39522d60a5f9a391cb514f20fa18408a02cc6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 11:56:52 +0200 Subject: [PATCH 394/698] Backport patch to 0.3.3 --- .../OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb | 8 +++--- .../OpenBLAS-0.3.3_fix-dscal-inline-asm.patch | 28 +++++++++++++++++++ .../OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb | 4 +-- .../OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb | 8 +++--- 4 files changed, 38 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3_fix-dscal-inline-asm.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb index 84769201122..d172775ab92 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3-GCC-8.2.0-2.31.1.eb @@ -1,7 +1,7 @@ name = 'OpenBLAS' version = '0.3.3' -homepage = 'http://xianyi.github.com/OpenBLAS/' +homepage = 'https://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} @@ -11,7 +11,7 @@ toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble - 'http://www.netlib.org/lapack/timing/', + 'https://www.netlib.org/lapack/timing/', 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] @@ -20,7 +20,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + 'OpenBLAS-0.3.3_fix-dscal-inline-asm.patch', ] checksums = [ '49d88f4494ae780e3d7fa51769c00d982d7cdb73e696054ac3baa81d42f13bab', # v0.3.3.tar.gz @@ -30,7 +30,7 @@ checksums = [ 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', - '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch + 'c88b8445f58f36654e2b26186ca7c9307d4cebd6cbfa837cf81e0165e8513fbc', # OpenBLAS-0.3.3_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3_fix-dscal-inline-asm.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3_fix-dscal-inline-asm.patch new file mode 100644 index 00000000000..54d708da95d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.3_fix-dscal-inline-asm.patch @@ -0,0 +1,28 @@ +Backport of the below patch done by Alexander Grund (TU Dresden) + +From: Bart Oldeman +Date: Wed, 12 Feb 2020 14:11:44 +0000 +Subject: [PATCH] Fix inline asm in dscal: mark x, x1 as clobbered. Fixes #2408 + +The leaq instructions in dscal_kernel_inc_8 modify x and x1 so they +must be declared as input/output constraints, otherwise the compiler +may assume the corresponding registers are not modified. +diff --git a/kernel/x86_64/dscal.c b/kernel/x86_64/dscal.c +index ef9a0a6b..4562bbbd 100644 +--- a/kernel/x86_64/dscal.c ++++ b/kernel/x86_64/dscal.c +@@ -136,10 +136,10 @@ static void dscal_kernel_inc_8(BLASLONG n, FLOAT *alpha, FLOAT *x, BLASLONG inc_ + "jnz 1b \n\t" + + : +- : +- "r" (n), // 0 +- "r" (x), // 1 +- "r" (x1), // 2 ++ "+r" (n), // 0 ++ "+r" (x), // 1 ++ "+r" (x1) // 2 ++ : + "r" (alpha), // 3 + "r" (inc_x), // 4 + "r" (inc_x3) // 5 diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb index 476ac3c4e8a..2a710cb4521 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.4-GCC-8.2.0-2.31.1.eb @@ -21,7 +21,7 @@ patches = [ '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + 'OpenBLAS-0.3.3_fix-dscal-inline-asm.patch', ] checksums = [ '4b4b4453251e9edb5f57465bf2b3cf67b19d811d50c8588cdf2ea1f201bb834f', # v0.3.4.tar.gz @@ -33,7 +33,7 @@ checksums = [ 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', - '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch + 'c88b8445f58f36654e2b26186ca7c9307d4cebd6cbfa837cf81e0165e8513fbc', # OpenBLAS-0.3.3_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb index 4260d7ac24b..73fd9e6a594 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.5-GCC-8.2.0-2.31.1.eb @@ -1,7 +1,7 @@ name = 'OpenBLAS' version = '0.3.5' -homepage = 'http://xianyi.github.com/OpenBLAS/' +homepage = 'https://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} @@ -11,7 +11,7 @@ toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble - 'http://www.netlib.org/lapack/timing/', + 'https://www.netlib.org/lapack/timing/', 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] @@ -21,7 +21,7 @@ patches = [ '%(name)s-%(version)s_disable_AVX512_dgemm_kernel.patch', 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', - 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', + 'OpenBLAS-0.3.3_fix-dscal-inline-asm.patch', ] checksums = [ '0950c14bd77c90a6427e26210d6dab422271bc86f9fc69126725833ecdaa0e85', # v0.3.5.tar.gz @@ -33,7 +33,7 @@ checksums = [ 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch 'a9d7a7bb07b92db13d3fbebe5410b328e7cd28e48aace53e49530287626c8ec8', - '2e494213e6785187ab1286cda8538452f9fa897ae5110159e3bb441239f84424', # OpenBLAS-0.3.8_fix-dscal-inline-asm.patch + 'c88b8445f58f36654e2b26186ca7c9307d4cebd6cbfa837cf81e0165e8513fbc', # OpenBLAS-0.3.3_fix-dscal-inline-asm.patch ] # extensive testing can be enabled by uncommenting the line below From e9a4ba381f1f36e3b66c9317b79a2e8f8bfae6dc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 11:59:07 +0200 Subject: [PATCH 395/698] Fix https --- .../easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb | 4 ++-- easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb index 04fb6eb628b..a4c75eecd50 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.6-GCC-8.3.0-2.32.eb @@ -1,7 +1,7 @@ name = 'OpenBLAS' version = '0.3.6' -homepage = 'http://xianyi.github.com/OpenBLAS/' +homepage = 'https://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} @@ -11,7 +11,7 @@ toolchainopts = {'vectorize': False} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble - 'http://www.netlib.org/lapack/timing/', + 'https://www.netlib.org/lapack/timing/', 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb index f1e21707f74..8e57e0da19f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb @@ -1,14 +1,14 @@ name = 'OpenBLAS' version = '0.3.7' -homepage = 'http://xianyi.github.com/OpenBLAS/' +homepage = 'https://xianyi.github.com/OpenBLAS/' description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = [ # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble - 'http://www.netlib.org/lapack/timing/', + 'https://www.netlib.org/lapack/timing/', 'https://github.com/xianyi/OpenBLAS/archive/', ] sources = ['v%(version)s.tar.gz'] From b9ea566da6d1a70ece75eeaf36b8debfc0f64a6d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 12:03:39 +0200 Subject: [PATCH 396/698] Add patches --- ...BLAS-0.3.7_fix-missing-sync-on-power.patch | 22 ++++++++ ...BLAS-0.3.7_reinit-threads-after-fork.patch | 50 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch new file mode 100644 index 00000000000..191ed747bb4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch @@ -0,0 +1,22 @@ +From c9d32674eaa2602184c2719dde15ac3fbebf41b7 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Sun, 9 Aug 2020 19:17:04 +0200 +Subject: [PATCH] Add memory barrier to the blas_lock implementation for Linux + +as recommended by cparrott73 in #2760 +--- + common_power.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/common_power.h b/common_power.h +index aa19794b5..e0685f760 100644 +--- a/common_power.h ++++ b/common_power.h +@@ -105,6 +105,7 @@ static void INLINE blas_lock(volatile unsigned long *address){ + " bne- 1f\n" + " stwcx. %2,0, %1\n" + " bne- 0b\n" ++ " isync\n" + "1: " + : "=&r"(ret) + : "r"(address), "r" (val) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch new file mode 100644 index 00000000000..a4075d8535d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch @@ -0,0 +1,50 @@ +From 3094fc6c83c7a623f9a7e7846eb711a8a99ddfff Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Thu, 1 Oct 2020 15:41:42 +0200 +Subject: [PATCH] Lazyly reinit threads after a fork in OMP mode + +This initializes the per-thread memory buffers which get +cleared/released on a fork via pthread_at_fork. Not doing so leads to +each thread calling blas_memory_alloc on almost every execution which +slows down the code significantly as the threads race for the memory +allocation using locks to serialize that. +--- + driver/others/blas_server_omp.c | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c +index d126955e4..da0a5674a 100644 +--- a/driver/others/blas_server_omp.c ++++ b/driver/others/blas_server_omp.c +@@ -48,6 +48,21 @@ + + #else + ++#ifndef likely ++#ifdef __GNUC__ ++#define likely(x) __builtin_expect(!!(x), 1) ++#else ++#define likely(x) (x) ++#endif ++#endif ++#ifndef unlikely ++#ifdef __GNUC__ ++#define unlikely(x) __builtin_expect(!!(x), 0) ++#else ++#define unlikely(x) (x) ++#endif ++#endif ++ + #ifndef OMP_SCHED + #define OMP_SCHED static + #endif +@@ -350,6 +365,9 @@ static void exec_threads(blas_queue_t *queue, int buf_index){ + + int exec_blas(BLASLONG num, blas_queue_t *queue){ + ++ // Handle lazy re-init of the thread-pool after a POSIX fork ++ if (unlikely(blas_server_avail == 0)) blas_thread_init(); ++ + BLASLONG i, buf_index; + + if ((num <= 0) || (queue == NULL)) return 0; From 928d024041eeaa81fa4d2a9e7c1ea709aab321ed Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 12:06:57 +0200 Subject: [PATCH 397/698] Add patches --- ...BLAS-0.3.7_fix-missing-sync-on-power.patch | 22 ++++++++ ...BLAS-0.3.7_reinit-threads-after-fork.patch | 50 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch new file mode 100644 index 00000000000..191ed747bb4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch @@ -0,0 +1,22 @@ +From c9d32674eaa2602184c2719dde15ac3fbebf41b7 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Sun, 9 Aug 2020 19:17:04 +0200 +Subject: [PATCH] Add memory barrier to the blas_lock implementation for Linux + +as recommended by cparrott73 in #2760 +--- + common_power.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/common_power.h b/common_power.h +index aa19794b5..e0685f760 100644 +--- a/common_power.h ++++ b/common_power.h +@@ -105,6 +105,7 @@ static void INLINE blas_lock(volatile unsigned long *address){ + " bne- 1f\n" + " stwcx. %2,0, %1\n" + " bne- 0b\n" ++ " isync\n" + "1: " + : "=&r"(ret) + : "r"(address), "r" (val) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch new file mode 100644 index 00000000000..a4075d8535d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch @@ -0,0 +1,50 @@ +From 3094fc6c83c7a623f9a7e7846eb711a8a99ddfff Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Thu, 1 Oct 2020 15:41:42 +0200 +Subject: [PATCH] Lazyly reinit threads after a fork in OMP mode + +This initializes the per-thread memory buffers which get +cleared/released on a fork via pthread_at_fork. Not doing so leads to +each thread calling blas_memory_alloc on almost every execution which +slows down the code significantly as the threads race for the memory +allocation using locks to serialize that. +--- + driver/others/blas_server_omp.c | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c +index d126955e4..da0a5674a 100644 +--- a/driver/others/blas_server_omp.c ++++ b/driver/others/blas_server_omp.c +@@ -48,6 +48,21 @@ + + #else + ++#ifndef likely ++#ifdef __GNUC__ ++#define likely(x) __builtin_expect(!!(x), 1) ++#else ++#define likely(x) (x) ++#endif ++#endif ++#ifndef unlikely ++#ifdef __GNUC__ ++#define unlikely(x) __builtin_expect(!!(x), 0) ++#else ++#define unlikely(x) (x) ++#endif ++#endif ++ + #ifndef OMP_SCHED + #define OMP_SCHED static + #endif +@@ -350,6 +365,9 @@ static void exec_threads(blas_queue_t *queue, int buf_index){ + + int exec_blas(BLASLONG num, blas_queue_t *queue){ + ++ // Handle lazy re-init of the thread-pool after a POSIX fork ++ if (unlikely(blas_server_avail == 0)) blas_thread_init(); ++ + BLASLONG i, buf_index; + + if ((num <= 0) || (queue == NULL)) return 0; From a77161199fbffe3aad9c475b8ea91377049726fc Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 7 Oct 2020 12:10:18 +0200 Subject: [PATCH 398/698] Add patches --- ...BLAS-0.3.7_fix-missing-sync-on-power.patch | 22 ++++++++ ...BLAS-0.3.7_reinit-threads-after-fork.patch | 50 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch new file mode 100644 index 00000000000..191ed747bb4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-missing-sync-on-power.patch @@ -0,0 +1,22 @@ +From c9d32674eaa2602184c2719dde15ac3fbebf41b7 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Sun, 9 Aug 2020 19:17:04 +0200 +Subject: [PATCH] Add memory barrier to the blas_lock implementation for Linux + +as recommended by cparrott73 in #2760 +--- + common_power.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/common_power.h b/common_power.h +index aa19794b5..e0685f760 100644 +--- a/common_power.h ++++ b/common_power.h +@@ -105,6 +105,7 @@ static void INLINE blas_lock(volatile unsigned long *address){ + " bne- 1f\n" + " stwcx. %2,0, %1\n" + " bne- 0b\n" ++ " isync\n" + "1: " + : "=&r"(ret) + : "r"(address), "r" (val) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch new file mode 100644 index 00000000000..a4075d8535d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_reinit-threads-after-fork.patch @@ -0,0 +1,50 @@ +From 3094fc6c83c7a623f9a7e7846eb711a8a99ddfff Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Thu, 1 Oct 2020 15:41:42 +0200 +Subject: [PATCH] Lazyly reinit threads after a fork in OMP mode + +This initializes the per-thread memory buffers which get +cleared/released on a fork via pthread_at_fork. Not doing so leads to +each thread calling blas_memory_alloc on almost every execution which +slows down the code significantly as the threads race for the memory +allocation using locks to serialize that. +--- + driver/others/blas_server_omp.c | 18 ++++++++++++++++++ + 1 file changed, 18 insertions(+) + +diff --git a/driver/others/blas_server_omp.c b/driver/others/blas_server_omp.c +index d126955e4..da0a5674a 100644 +--- a/driver/others/blas_server_omp.c ++++ b/driver/others/blas_server_omp.c +@@ -48,6 +48,21 @@ + + #else + ++#ifndef likely ++#ifdef __GNUC__ ++#define likely(x) __builtin_expect(!!(x), 1) ++#else ++#define likely(x) (x) ++#endif ++#endif ++#ifndef unlikely ++#ifdef __GNUC__ ++#define unlikely(x) __builtin_expect(!!(x), 0) ++#else ++#define unlikely(x) (x) ++#endif ++#endif ++ + #ifndef OMP_SCHED + #define OMP_SCHED static + #endif +@@ -350,6 +365,9 @@ static void exec_threads(blas_queue_t *queue, int buf_index){ + + int exec_blas(BLASLONG num, blas_queue_t *queue){ + ++ // Handle lazy re-init of the thread-pool after a POSIX fork ++ if (unlikely(blas_server_avail == 0)) blas_thread_init(); ++ + BLASLONG i, buf_index; + + if ((num <= 0) || (queue == NULL)) return 0; From 5f8ba4b7d4760d549b1dcda854f026bb6c82fead Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Oct 2020 09:32:29 +0200 Subject: [PATCH 399/698] add missing download_dep_fail and sanity_pip_check to pyspoa easyconfig --- .../p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb index d8c636a9543..d107b486c6b 100644 --- a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.0.4-GCC-8.3.0-Python-3.7.4.eb @@ -34,9 +34,13 @@ dependencies = [ ('spoa', '4.0.0'), ] +download_dep_fail = True + preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " use_pip = True options = {'modulename': 'spoa'} +sanity_pip_check = True + moduleclass = 'lib' From 1e6fee50bb83a4221583ac6643ed457a34e2f330 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Oct 2020 11:13:43 +0200 Subject: [PATCH 400/698] add exceptions to check_dep_vars in tests to allow Pysam 0.16.0.1 and TensorFlow 2.2.0 as deps for medaka 1.1.1 built with foss/2019b --- test/easyconfigs/easyconfigs.py | 50 +++++++++++++++++++-------------- 1 file changed, 29 insertions(+), 21 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 86d2cc419d1..bae127af1af 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -241,36 +241,44 @@ def check_dep_vars(self, dep, dep_vars): if re.search('; versionsuffix: .*-CUDA-[0-9.]+', key): dep_vars.pop(key) - # some software packages require an old version of a particular dependency + # some software packages require a specific (older/newer) version of a particular dependency old_dep_versions = { + # EMAN2 2.3 requires Boost(.Python) 1.64.0 + 'Boost': [('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-'])], + 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], + # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) + 'Jellyfish': [(r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2'])], # libxc 2.x or 3.x is required by ABINIT, AtomPAW, CP2K, GPAW, horton, PySCF, WIEN2k # (Qiskit depends on PySCF) - 'libxc': (r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', r'PySCF-', - r'Qiskit-', r'WIEN2k-']), - # OPERA requires SAMtools 0.x - 'SAMtools': (r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', r'CGmapTools-0\.1\.2', - r'BatMeth2-2\.1']), - # Kraken 1.x requires Jellyfish 1.x (Roary & metaWRAP depend on Kraken 1.x) - 'Jellyfish': (r'1\.', [r'Kraken-1\.', r'Roary-3\.12\.0', r'metaWRAP-1\.2']), - # EMAN2 2.3 requires Boost(.Python) 1.64.0 - 'Boost': ('1.64.0;', [r'Boost.Python-1\.64\.0-', r'EMAN2-2\.3-']), - 'Boost.Python': ('1.64.0;', [r'EMAN2-2\.3-']), + 'libxc': [(r'[23]\.', [r'ABINIT-', r'AtomPAW-', r'CP2K-', r'GPAW-', r'horton-', + r'PySCF-', r'Qiskit-', r'WIEN2k-'])], # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) # both scVelo and Python-Geometric depend on numba - 'LLVM': (r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), - # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka - 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + 'LLVM': [(r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2'])], # rampart requires nodejs > 10, artic-ncov2019 requires rampart - 'nodejs': ('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13']), + 'nodejs': [('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13'])], + # OPERA requires SAMtools 0.x + 'SAMtools': [(r'0\.', [r'ChimPipe-0\.9\.5', r'Cufflinks-2\.2\.1', r'OPERA-2\.0\.6', + r'CGmapTools-0\.1\.2', r'BatMeth2-2\.1'])], + 'TensorFlow': [ + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), + # artic-ncov2019 requires medaka + ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # medaka 1.1.1 requires TensorFlow 2.2.0 (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep) + ('2.2.0;', ['medaka-1.1.1-']), + ], + # medaka 1.1.1 requires Pysam 0.16.0.1, + # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation + 'Pysam': [('0.16.0.1;', ['medaka-1.1.1-'])], } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): - version_pattern, parents = old_dep_versions[dep] - # filter out known old dependency versions - if re.search('^version: %s' % version_pattern, key): - # only filter if the easyconfig using this dep variants is known - if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): - dep_vars.pop(key) + for version_pattern, parents in old_dep_versions[dep]: + # filter out known old dependency versions + if re.search('^version: %s' % version_pattern, key): + # only filter if the easyconfig using this dep variants is known + if all(any(re.search(p, x) for p in parents) for x in dep_vars[key]): + dep_vars.pop(key) # filter out ELSI variants with -PEXSI suffix if dep == 'ELSI' and len(dep_vars) > 1: From 1a723255eb9aea9fbd01865e6c6b9296f6809aa9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Oct 2020 11:50:33 +0200 Subject: [PATCH 401/698] fix exception made for TensorFlow 2.2.0 in check_dep_vars, also used as dep for Horovod 0.19.5 (indicated by versionsuffix) --- test/easyconfigs/easyconfigs.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bae127af1af..18504d4490e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -264,8 +264,9 @@ def check_dep_vars(self, dep, dep_vars): # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), - # medaka 1.1.1 requires TensorFlow 2.2.0 (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep) - ('2.2.0;', ['medaka-1.1.1-']), + # medaka 1.1.1 requires TensorFlow 2.2.0 (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); + # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5 + ('2.2.0;', ['medaka-1.1.1-', 'Horovod-0.19.5-']), ], # medaka 1.1.1 requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation From 39a94b7a109a7cf49e8865c4c1dd063fa974f5e9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Oct 2020 12:19:34 +0200 Subject: [PATCH 402/698] add comment on strict requirement for Pysam 0.16.0.1 in medaka 1.1.1 easyconfig --- .../easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb index f08e854de87..3119ab53a5f 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb @@ -15,6 +15,7 @@ dependencies = [ ('TensorFlow', '2.2.0', versionsuffix), ('Biopython', '1.75', versionsuffix), ('h5py', '2.10.0', versionsuffix), + # Pysam 0.16.0.1 is strictly required, see requirements.txt ('Pysam', '0.16.0.1'), ('SAMtools', '1.10'), ('minimap2', '2.17'), From aba11991c03f695a8ffbb3df57461a0c59f7632f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Oct 2020 20:32:58 +0200 Subject: [PATCH 403/698] adding easyconfigs: awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb --- ...wscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..b455fe4e15f --- /dev/null +++ b/easybuild/easyconfigs/a/awscli/awscli-2.0.55-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'awscli' +version = '2.0.55' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pypi.python.org/pypi/awscli' +description = 'Universal Command Line Environment for AWS' + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('Python', '3.8.2'), + ('PyYAML', '5.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('botocore', '1.17.12', { + 'source_urls': ['https://github.com/boto/botocore/archive/'], + # use specific commit that corresponds to 2.0.0dev59, + # which is strictly required by awscli 2.0.55 (see 'requirements' in setup.py) + 'source_tmpl': '65e2c02.tar.gz', + 'checksums': ['1899e4442ec687e67709346a3c707af0db8cb98c741369daa95b3a68ef24f8fb'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), + ('docutils', '0.15.2', { + 'checksums': ['a2aeea129088da402665e92e0b25b04b073c04b2dce4ab65caaa38b7ce2e1a99'], + }), + ('cryptography', '2.8', { + 'checksums': ['3cda1f0ed8747339bbdf71b9f38ca74c7b592f24f65cdb3ab3765e4b02871651'], + }), + ('s3transfer', '0.3.3', { + 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], + }), + ('ruamel.yaml', '0.15.100', { + 'checksums': ['8e42f3067a59e819935a2926e247170ed93c8f0b2ab64526f888e026854db2e4'], + }), + ('prompt_toolkit', '2.0.10', { + 'checksums': ['f15af68f66e664eaa559d4ac8a928111eebd5feda0c11738b5998045224829db'], + }), + ('distro', '1.5.0', { + 'checksums': ['0e58756ae38fbd8fc3020d54badb8eae17c5b9dcbed388b17bb55b8a5928df92'], + }), + (name, version, { + 'source_urls': ['https://github.com/aws/aws-cli/archive/'], + 'source_tmpl': '%(version)s.tar.gz', + 'checksums': ['9404f9c223912bc432df1fd13e66d2b87abb6fc19640c23dda32a73f67722d64'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = ["aws help"] + +sanity_check_paths = { + 'files': ['bin/aws'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'tools' From b23925919b8d091878ef88b2e7cc7c081976c017 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Oct 2020 11:16:54 +0200 Subject: [PATCH 404/698] adding easyconfigs: wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb --- ...wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..e8ba9f475a0 --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.8.30-gcccuda-2019b-Python-3.7.4.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.8.30' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.wandb.com/' +description = """ +CLI and Python API for Weights and Biases (wandb), a tool for visualizing and +tracking your machine learning experiments.""" + +toolchain = {'name': 'gcccuda', 'version': '2019b'} + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), + ('GitPython', '3.1.0', versionsuffix), + ('PyYAML', '5.1.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('nvidia-ml-py3', '7.352.0', { + 'modulename': 'pynvml', + 'checksums': ['390f02919ee9d73fe63a98c73101061a6b37fa694a793abf56673320f1f51277'], + }), + ('configparser', '3.8.1', { + 'checksums': ['bc37850f0cc42a1725a796ef7d92690651bf1af37d744cc63161dac62cabee17'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('argh', '0.26.2', { + 'checksums': ['e9535b8c84dc9571a48999094fda7f33e63c3f1b74f3e5f3ac0105a58405bb65'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('watchdog', '0.9.0', { + 'checksums': ['965f658d0732de3188211932aeb0bb457587f04f63ab4c1e33eab878e9de961d'], + }), + ('shortuuid', '0.5.0', { + 'checksums': ['d08fd398f40f8baf87e15eef8355e92fa541bca4eb8465fefab7ee22f92711b9'], + }), + ('gql', '0.2.0', { + 'checksums': ['ad0f0b8226428d727c8e1d1cac4e521d83ed024d814921bd55b8adb997dadf4b'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('graphql-core', '1.1', { + 'modulename': 'graphql', + 'checksums': ['63bb8593aeeadb0a53e14207b910027fe51158d017927fad87326dac806185ee'], + }), + ('sentry-sdk', '0.14.3', { + 'checksums': ['bb90a4e19c7233a580715fc986cc44be2c48fc10b31e71580a2037e1c94b6950'], + }), + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + (name, version, { + 'checksums': ['0ed6ee15bf9635e0244ec7bf1d803405fd3834e6a339a48e58229dc8205737e8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wanbd', 'wandb', 'wandb-docker-run', 'watchmedo', 'wb']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 2fd5a20d1f6ce9a50849bb8b8369bc8acf678b19 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 10:55:13 +0100 Subject: [PATCH 405/698] Perl: DB_File requires DB as a dep --- easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb index cf4d9641267..7bf8eea4d1b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.28.1-GCCcore-8.2.0.eb @@ -16,6 +16,7 @@ builddependencies = [('binutils', '2.31.1')] dependencies = [ ('zlib', '1.2.11'), # for Net::SSLeay ('expat', '2.2.6'), # for XML::Parser + ('DB', '18.1.32'), # for DB_File ] # OpenSSL is required for Net::SSLeay diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb index 7549b61ff0e..50ac5521256 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.0-GCCcore-8.3.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('expat', '2.2.7'), # for XML::Parser ('ncurses', '6.1'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu + ('DB', '18.1.32'), # for DB_File ] # OpenSSL is required for Net::SSLeay diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 44d508b47b5..6ca4390cbc3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -21,6 +21,7 @@ dependencies = [ ('expat', '2.2.9'), # for XML::Parser ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu + ('DB', '18.1.32'), # for DB_File ] # OpenSSL is required for Net::SSLeay From 0ea4ef59f7d527fde7f3050e9ad8105835f41a4b Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 10:56:27 +0100 Subject: [PATCH 406/698] Add new DB for GCCcore 10.2.0 and Perl: DB_File requires DB as a dep --- .../d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ .../p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 1 + 2 files changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..35c967bb558 --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +# EasyBuild easyconfig +name = 'DB' +version = '18.1.40' + +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' + +description = """Berkeley DB enables the development of custom data management + solutions, without the overhead traditionally associated with such custom + projects.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +# download via +# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, +# requires registration +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/db_%s' % x for x in ['archive', 'checkpoint', 'convert', 'deadlock', 'dump', 'hotbackup', + 'load', 'log_verify', 'printlog', 'recover', 'replicate', 'stat', + 'tuner', 'upgrade', 'verify']] + + ['include/db.h', 'lib/libdb.a', 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 5ec6cca0e69..18b17c57ec6 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -18,6 +18,7 @@ dependencies = [ ('expat', '2.2.9'), # for XML::Parser ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.0'), # for Term::ReadLine::Gnu + ('DB', '18.1.40'), # for DB_File ] # OpenSSL is required for Net::SSLeay From acfcca7629799fd1b7718ae575bc295ee80ebf21 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 11:02:06 +0100 Subject: [PATCH 407/698] checksums --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index 35c967bb558..3437dbddff7 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # https://www.oracle.com/technetwork/products/berkeleydb/downloads/, # requires registration sources = [SOURCELOWER_TAR_GZ] +checksums = ['0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8'] builddependencies = [('binutils', '2.35')] From 87d7f24ca81d7e855dcf48df5e2cf54e674ddcd1 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 14:46:10 +0100 Subject: [PATCH 408/698] patch out installation attempt of missing docs --- .../d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 2 +- .../d/DB/DB-18.1.40_fix_doc_install.patch | 16 ++++++++++++++++ 2 files changed, 17 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/d/DB/DB-18.1.40_fix_doc_install.patch diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index 3437dbddff7..d2d28cd5fff 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # https://www.oracle.com/technetwork/products/berkeleydb/downloads/, # requires registration sources = [SOURCELOWER_TAR_GZ] -checksums = ['0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8'] +patches = ['%(name)s-%(version)s_fix_doc_install.patch'] builddependencies = [('binutils', '2.35')] diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40_fix_doc_install.patch b/easybuild/easyconfigs/d/DB/DB-18.1.40_fix_doc_install.patch new file mode 100644 index 00000000000..4fa66bee4ac --- /dev/null +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40_fix_doc_install.patch @@ -0,0 +1,16 @@ +Neither bdb-sql nor gsg_db_server documentation is in db-18.1.40.tar.gz +so remove them from the installation +Patch by Simon Branford, University of Birmingham +--- dist/Makefile.in.orig 2020-10-09 14:38:54.261041000 +0100 ++++ dist/Makefile.in 2020-10-09 14:39:21.587980661 +0100 +@@ -1299,8 +1299,8 @@ + + # We install csharp docs even on UNIX so we don't have a + # broken link on the landing page. +-DOCLIST=api_reference articles bdb-sql collections csharp gsg \ +- gsg_db_rep gsg_db_server gsg_txn index.html installation \ ++DOCLIST=api_reference articles collections csharp gsg \ ++ gsg_db_rep gsg_txn index.html installation \ + java license porting programmer_reference upgrading + + install_docs: From cce665912cef63fa2c97ce852df31779aa6b6b32 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 9 Oct 2020 15:06:55 +0100 Subject: [PATCH 409/698] checksums --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index d2d28cd5fff..d57cfc30de6 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -15,6 +15,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} # requires registration sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-%(version)s_fix_doc_install.patch'] +checksums = [ + '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz + '441f48568156f72f02a8662998d293cc7edad687604b4f8af722f21c6db2a52d', # DB-18.1.40_fix_doc_install.patch +] builddependencies = [('binutils', '2.35')] From 9be20e7876190daaa8681ad3011452bdfcf2ec2a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 9 Oct 2020 19:39:45 +0200 Subject: [PATCH 410/698] add Autotools as build dep for medaka 1.1.1 --- .../m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb index 3119ab53a5f..550726dfa89 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.1-foss-2019b-Python-3.7.4.eb @@ -9,6 +9,8 @@ description = "medaka is a tool to create a consensus sequence from nanopore seq toolchain = {'name': 'foss', 'version': '2019b'} +builddependencies = [('Autotools', '20180311')] + dependencies = [ ('Python', '3.7.4'), # includes cffi, numpy # TensorFlow 2.2.0 required by medaka, see requirements.txt From 28d75bea1721e966e2851de23b25c76255172cc8 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Fri, 9 Oct 2020 23:05:06 +0200 Subject: [PATCH 411/698] Fix dbarts for non-x86_64 on R-4.0.0-foss-2020a.eb, fixes #11449 --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 27 ++++++++++--------- .../R/dbarts-0.9-18_fix-simd-on-non-x86.patch | 12 +++++++++ 2 files changed, 26 insertions(+), 13 deletions(-) create mode 100644 easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index bec125b8699..532446b885b 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -118,11 +118,11 @@ exts_list = [ 'checksums': ['b6d056f75d45e315943a4618f5f62802612cd8931ba3f9f474b595140a3cfb93'], }), ('ff', '2.2-14.2', { + 'patches': ['ff-2.2-14.2_aarch64_support.patch'], 'checksums': [ - 'f8c06ac333ffe3545cdf56531619865176e1827728f7aeeba82d135d5c5e37e4', - 'beae9b31d7962b035329e07f4dc09308ca3a527327885d1c4ba9a1dd105e0bbd' # ff_2.2-14.2_aarch64_support.patch + 'f8c06ac333ffe3545cdf56531619865176e1827728f7aeeba82d135d5c5e37e4', # ff_2.2-14.2.tar.gz + 'beae9b31d7962b035329e07f4dc09308ca3a527327885d1c4ba9a1dd105e0bbd', # ff-2.2-14.2_aarch64_support.patch ], - 'patches': ['ff-2.2-14.2_aarch64_support.patch'], }), ('bnlearn', '4.5', { 'checksums': ['a8047625533260a855d309b3c0785cbeec0f9ec13f284b6664a1f61638138578'], @@ -2125,15 +2125,13 @@ exts_list = [ 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], }), ('liquidSVM', '1.2.4', { - 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ - '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', + '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], @@ -2247,8 +2245,7 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', - 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], + 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], @@ -2316,7 +2313,7 @@ exts_list = [ ('grImport2', '0.2-0', { 'checksums': ['a102a2d877e42cd4e4e346e5510a77b2f3e57b43ae3c6d5c272fdceb506b00a7'], }), - ('preseqR', '4.0.0', { + ('preseqR', version, { 'checksums': ['0143db473fb9a811f9cf582a348226a5763e62d9857ce3ef4ec41412abb559bc'], }), ('idr', '1.2', { @@ -2419,8 +2416,7 @@ exts_list = [ 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], }), ('rstantools', '2.0.0', { - 'checksums': [('4ae78aa39c3d4897f453e621a09961d6f2cda27a1b5657d4d4b32d3d89bd80c6', - 'd200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a')], + 'checksums': ['d200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a'], }), ('bayesplot', '1.7.1', { 'checksums': ['820ca9ca3258fc68333e75fd60898c0d0f08f513b66c161ca6159a54ad54006b'], @@ -2552,7 +2548,12 @@ exts_list = [ 'checksums': ['fab573abdc0dd44e8c8bc7242a1428df20b3ec64c4c194e5f1f907393f902d01'], }), ('dbarts', '0.9-18', { - 'checksums': ['fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4'], + 'patches': ['dbarts-0.9-18_fix-simd-on-non-x86.patch'], + 'checksums': [ + 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz + # dbarts-0.9-18_fix-simd-on-non-x86.patch + 'bcc6d9322e477b1868d0ca764664475520cb615ad8cf35543f234779eddfb3e2', + ], }), ] diff --git a/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch b/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch new file mode 100644 index 00000000000..321cc7ad4d2 --- /dev/null +++ b/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch @@ -0,0 +1,12 @@ +diff -ru dbarts.orig/src/misc/simd.c dbarts/src/misc/simd.c +--- dbarts.orig/src/misc/simd.c 2019-08-19 21:14:16.000000000 +0200 ++++ dbarts/src/misc/simd.c 2020-10-09 10:53:05.299232350 +0200 +@@ -33,7 +33,7 @@ + + // if not on any x86 descendent, use pure C no matter what + #if !defined(__i386) && !defined(_X86_) && !defined(__x86_64__) && !defined(_M_AMD64) && !defined (_M_X64) +-static misc_simd_instructionSet misc_simd_getMaxSIMDInstructionSet(void) ++misc_simd_instructionSet misc_simd_getMaxSIMDInstructionSet(void) { + return MISC_INST_C; + } + #else From ae3eaf1c41c256c99087f85768619d5d97297de5 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sat, 10 Oct 2020 08:45:21 +0200 Subject: [PATCH 412/698] Reinstate checksums and fix patch comments. --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 9 ++++++--- .../r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch | 9 +++++++++ 2 files changed, 15 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 532446b885b..250ce11d955 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2132,6 +2132,7 @@ exts_list = [ # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], @@ -2245,7 +2246,8 @@ exts_list = [ 'checksums': ['4152a1c3c652979e97870e5c50c45a243d0ad8d4ff968091160e3d66509f61db'], }), ('rda', '1.0.2-2.1', { - 'checksums': ['eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e'], + 'checksums': [('6918b62f51252b57f2c05b99debef6136b370f594dc3ae6466268e4c35578ef8', + 'eea3a51a2e132a023146bfbc0c384f5373eb3ea2b61743d7658be86a5b04949e')], }), ('sampling', '2.8', { 'checksums': ['356923f35971bb55f7e97b178aede3366374aa3ad3d24a97be765660553bf21a'], @@ -2416,7 +2418,8 @@ exts_list = [ 'checksums': ['3ad01f82132bf75960ae0d8a81cae84eaf4a9ab262f183fc3d6439189e4a3aed'], }), ('rstantools', '2.0.0', { - 'checksums': ['d200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a'], + 'checksums': [('4ae78aa39c3d4897f453e621a09961d6f2cda27a1b5657d4d4b32d3d89bd80c6', + 'd200a4d8c62d8577fdba819bf770e7abb11c57c3332f4498e1d30ce824598b3a')], }), ('bayesplot', '1.7.1', { 'checksums': ['820ca9ca3258fc68333e75fd60898c0d0f08f513b66c161ca6159a54ad54006b'], @@ -2552,7 +2555,7 @@ exts_list = [ 'checksums': [ 'fd99f99d1a24c16596767246618cf240ebd8d86fa82b0e5ce65b737b9afb4ac4', # dbarts_0.9-18.tar.gz # dbarts-0.9-18_fix-simd-on-non-x86.patch - 'bcc6d9322e477b1868d0ca764664475520cb615ad8cf35543f234779eddfb3e2', + '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', ], }), ] diff --git a/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch b/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch index 321cc7ad4d2..ce3396a0560 100644 --- a/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch +++ b/easybuild/easyconfigs/r/R/dbarts-0.9-18_fix-simd-on-non-x86.patch @@ -1,3 +1,12 @@ +# The fallback branch in simd.c for non-x86 and non-x64 systems (like ARM and PowerPC) has a +# syntactically invalid definition: https://github.com/vdorie/dbarts/blob/master/src/misc/simd.c#L34-L38 +# +# The function needs to be non-static to have linkage as indicated by its declaration and is missing +# its opening curly brace. +# +# https://github.com/vdorie/dbarts/issues/35 +# +# Author: Lars Viklund (@zao) diff -ru dbarts.orig/src/misc/simd.c dbarts/src/misc/simd.c --- dbarts.orig/src/misc/simd.c 2019-08-19 21:14:16.000000000 +0200 +++ dbarts/src/misc/simd.c 2020-10-09 10:53:05.299232350 +0200 From 5999763a16b0e8fbbbbb5ac6f9f73413f03f9e74 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sat, 10 Oct 2020 12:36:11 +0200 Subject: [PATCH 413/698] tabs vs space --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 250ce11d955..eb63cd24cbf 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2132,7 +2132,7 @@ exts_list = [ # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], From 9176362ef1770727617c65a3849ae8935d5c53ec Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sat, 10 Oct 2020 13:51:33 +0200 Subject: [PATCH 414/698] Relate comments to content. --- easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index eb63cd24cbf..7b502c6855a 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -2126,13 +2126,13 @@ exts_list = [ }), ('liquidSVM', '1.2.4', { 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], - 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', # liquidSVM_1.2.4.tar.gz # liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch '46b09e441c3b59af535f20d8db0dee7f1d6a7ddd511175d252115b53cb8b86f8', ], # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC + 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', }), ('oddsratio', '2.0.0', { 'checksums': ['89bf3c68a6ded6a98f4ee8d487c29605ad00ac5f8db9b8bf1a52144e65332553'], From cc17b70cad4c4815c399a75ec3f4a758a6f8d447 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Oct 2020 16:01:12 +0200 Subject: [PATCH 415/698] use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 --- easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb | 8 ++++---- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb | 8 ++++---- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb | 8 ++++---- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb | 8 ++++---- 4 files changed, 16 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb index e78db86de34..22c53f87711 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb @@ -10,10 +10,10 @@ projects.""" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} -# download via -# http://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] checksums = ['2ea8b8bc0611d9b4c2b9fee84a4a312dddfec007067af6e02ed46a26354181bb'] builddependencies = [ diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb index ea7c5cdb279..b133b262320 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb @@ -10,10 +10,10 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '8.2.0'} -# download via -# http://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.31.1')] diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb index ce9ab9e5781..3b297f7f57b 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.3.0.eb @@ -10,10 +10,10 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '8.3.0'} -# download via -# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.32')] diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb index 39fc5d2137e..2c9691d0d9a 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-9.3.0.eb @@ -10,10 +10,10 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# download via -# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] checksums = ['fa1fe7de9ba91ad472c25d026f931802597c29f28ae951960685cde487c8d654'] builddependencies = [('binutils', '2.34')] From ca341d621bcfeee766c9b8376c1e162cf6668fae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 10 Oct 2020 16:52:07 +0200 Subject: [PATCH 416/698] use https in homepage for DB 18.1.x --- easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb | 2 +- easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb index 22c53f87711..3f962f760be 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.25-GCCcore-7.3.0.eb @@ -2,7 +2,7 @@ name = 'DB' version = '18.1.25' -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' description = """Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb index b133b262320..0993a0905ba 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.32-GCCcore-8.2.0.eb @@ -2,7 +2,7 @@ name = 'DB' version = '18.1.32' -homepage = 'http://www.oracle.com/technetwork/products/berkeleydb' +homepage = 'https://www.oracle.com/technetwork/products/berkeleydb' description = """Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom From d62b2a3ac73f38ea165f261ac0d1c674fc546717 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 10 Oct 2020 19:20:43 +0100 Subject: [PATCH 417/698] Switch to homebrew mirror for DB source --- easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb index d57cfc30de6..6b601fe0f4b 100644 --- a/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB/DB-18.1.40-GCCcore-10.2.0.eb @@ -10,10 +10,10 @@ description = """Berkeley DB enables the development of custom data management toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -# download via -# https://www.oracle.com/technetwork/products/berkeleydb/downloads/, -# requires registration -sources = [SOURCELOWER_TAR_GZ] +# use Homebrew source mirror to allow auto-downloading source tarball +# (Oracle website - https://www.oracle.com/technetwork/products/berkeleydb/downloads/ - requires reigstration) +source_urls = ['https://bintray.com/homebrew/mirror/download_file?file_path='] +sources = [{'download_filename': 'berkeley-db-%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] patches = ['%(name)s-%(version)s_fix_doc_install.patch'] checksums = [ '0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8', # db-18.1.40.tar.gz From 3109ed8c7b9fd278eede8630ef8e0808d774ac35 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 11 Oct 2020 11:42:34 +0200 Subject: [PATCH 418/698] adding easyconfigs: UnZip-6.0-GCCcore-9.3.0.eb --- .../u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..d60ec1b9bcc --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-9.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 689ea5fd3b168ea34f3ed9e026292ea7588a3379 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Sun, 11 Oct 2020 11:43:45 +0200 Subject: [PATCH 419/698] Depend on UnZip. Requires http://github.com/easybuilders/easybuild-easyconfigs/pull/11457 --- easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb index 02f9fd742c7..00bf3500083 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('ncurses', '6.2'), ('SQLite', '3.31.1'), ('XZ', '5.2.5'), + ('UnZip', '6.0'), ('GMP', '6.2.0'), # required for pycrypto ('libffi', '3.3'), # required for cryptography # OS dependency should be preferred if the os version is more recent then this version, From c16652451ad36a49a3614f888945c9abca4bb2dd Mon Sep 17 00:00:00 2001 From: jkaplan Date: Mon, 12 Oct 2020 14:19:28 +0800 Subject: [PATCH 420/698] adding easyconfigs: UDUNITS-2.2.26-foss-2020a.eb --- .../u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb new file mode 100644 index 00000000000..e5d4993f5c6 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.26-foss-2020a.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.26' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.unidata.ucar.edu/downloads/udunits'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['368f4869c9c7d50d2920fa8c58654124e9ed0d8d2a8c714a9d7fdadc08c7356d'] + +dependencies = [('expat', '2.2.9')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From a3c068e871c3a53bb1ef9d627673123e167691d7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Oct 2020 10:42:57 +0200 Subject: [PATCH 421/698] Add support for building OpenBLAS on ARM TSV110 with GCC 8.3 --- .../o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb | 2 ++ .../OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch | 16 ++++++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb index 8e57e0da19f..e9da12d3743 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7-GCC-8.3.0.eb @@ -15,6 +15,7 @@ sources = ['v%(version)s.tar.gz'] patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), + 'OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch', 'OpenBLAS-0.3.7_fix-missing-sync-on-power.patch', 'OpenBLAS-0.3.7_reinit-threads-after-fork.patch', 'OpenBLAS-0.3.8_fix-dscal-inline-asm.patch', @@ -23,6 +24,7 @@ checksums = [ 'bde136122cef3dd6efe2de1c6f65c10955bbb0cc01a520c2342f5287c28f9379', # v0.3.7.tar.gz 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + '5d5ec94002daefe10a839f621bf083c85fbda6c55c5e486f48375a2891f405c5', # OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch # OpenBLAS-0.3.7_fix-missing-sync-on-power.patch 'aefe4254caa14612eaf9a203b3f870f3b43724d28da7d7ab484810b4278f198f', # OpenBLAS-0.3.7_reinit-threads-after-fork.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch new file mode 100644 index 00000000000..93cea4ee057 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.7_fix-build-on-arm-tsv110.patch @@ -0,0 +1,16 @@ +GCC 8 Doesn't have support for -mtune=tsv110 yet (added in GCC 9.1), so use the similar cortex-a57 instead + +author: Alexander Grund (TU Dresden) +diff --git a/Makefile.arm64 b/Makefile.arm64 +index 4d10ff68..742041d6 100644 +--- a/Makefile.arm64 ++++ b/Makefile.arm64 +@@ -40,6 +40,6 @@ FCOMMON_OPT += -march=armv8.1-a -mtune=thunderx2t99 + endif + + ifeq ($(CORE), TSV110) +-CCOMMON_OPT += -march=armv8.2-a -mtune=tsv110 +-FCOMMON_OPT += -march=armv8.2-a -mtune=tsv110 ++CCOMMON_OPT += -march=armv8.2-a -mtune=cortex-a57 ++FCOMMON_OPT += -march=armv8.2-a -mtune=cortex-a57 + endif From 27674d48fc91e4e43c3bc5b670dc3da6fbf9d437 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 11:35:53 +0200 Subject: [PATCH 422/698] create source tarball for Dalton 2016 via 'git clone' --- .../d/Dalton/Dalton-2016-intel-2017b-i8.eb | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb index a10c9e730f7..0c4d722d921 100644 --- a/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb +++ b/easybuild/easyconfigs/d/Dalton/Dalton-2016-intel-2017b-i8.eb @@ -4,19 +4,25 @@ name = 'Dalton' version = '2016' versionsuffix = '-i8' -homepage = 'http://daltonprogram.org/' +homepage = 'https://daltonprogram.org/' description = """The Dalton code is a powerful tool for a wide range of molecular properties at different levels of theory. Any published work arising from use of one of the Dalton2016 programs must acknowledge that by a proper reference, - http://www.daltonprogram.org/www/citation.html.""" + https://www.daltonprogram.org/www/citation.html.""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'i8': True, 'usempi': True, 'openmp': True} -# use git clone --recurse-submodules -b release/2016 git@gitlab.com:dalton/dalton.git -# to fetch source, then make the bizpped tarball -sources = [SOURCE_TAR_BZ2] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://gitlab.com/dalton', + 'repo_name': 'dalton', + 'tag': 'release/2016', + 'recursive': True, + }, +}] patches = [ '%(name)s-%(version)s-fix-cmake-install.patch', '%(name)s-%(version)s-use-EB-install-for-dalton-script.patch', @@ -26,20 +32,14 @@ patches = [ '%(name)s-%(version)s_intel_lowopt.patch', ] checksums = [ - # Dalton-2016.tar.bz2 - 'c78bf22293a7fc75465d96079ef39bdaa1f134127766a936763e25eaeb8958a8', - # Dalton-2016-fix-cmake-install.patch - '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', + None, # no checksum for Dalton-2016.tar.gz source tarball which is created via 'git clone' + '3159b03a488d6f5ee23d468be02ea62eacd08cbdf68cd64ef4e5a0d469a6718b', # Dalton-2016-fix-cmake-install.patch # Dalton-2016-use-EB-install-for-dalton-script.patch '570bd128fe0be69ef377c373b69bf64eb8d0908bc960903509cbc68ff275ae13', - # Dalton-2016-fix-uninits.patch - '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', - # Dalton-2016-fix-bad-includepath-add.patch - '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', - # Dalton-2016_cmake-obey-EB-variables.patch - '69c6d9c110c78c064544052ae5dcb8721f49744f7a5cbf3a0f4d1170d7d22927', - # Dalton-2016_intel_lowopt.patch - '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', + '5d93c59e8afa24d8b07a216bc73d7cc250230709a988cf8e1dd107f8a69543fc', # Dalton-2016-fix-uninits.patch + '6d4dab7af92674e3e6713143f4d8886925ac1328f64c4cc5d071e6eee855c350', # Dalton-2016-fix-bad-includepath-add.patch + '69c6d9c110c78c064544052ae5dcb8721f49744f7a5cbf3a0f4d1170d7d22927', # Dalton-2016_cmake-obey-EB-variables.patch + '4942d95e77845fab8b196c88f390e630971559e51632ca280434dbc0eed26757', # Dalton-2016_intel_lowopt.patch ] builddependencies = [('CMake', '3.9.5')] From d21f85e39a64020e80fe68ad434a5a19e122a605 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 12 Oct 2020 13:27:21 +0200 Subject: [PATCH 423/698] Change to CMakeMake and add MPI version --- ...AC-19.0-intel-2020a-Python-2.7.18-int64.eb | 79 +- ...9.0-intel-2020a-Python-2.7.18-mpi-int64.eb | 74 + .../DIRAC-19.0_fix-bss_energy_test.patch | 3028 +++++++++++++++++ .../d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch | 1398 ++++++++ .../d/DIRAC/DIRAC-19.0_fix_test_path.patch | 26 + ...DIRAC-19.0_remove-broken-tests-intel.patch | 18 +- .../DIRAC-19.0_use_easybuild_opts_intel.patch | 33 + 7 files changed, 4602 insertions(+), 54 deletions(-) create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_test_path.patch create mode 100644 easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb index b0cde2d295e..a51f922eca5 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'DIRAC' version = '19.0' @@ -8,56 +8,53 @@ homepage = 'http://www.diracprogram.org' description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'i8': True} source_urls = ['https://zenodo.org/record/3572669/files/'] sources = ['DIRAC-%(version)s-Source.tar.gz'] -patches = ['%(name)s-%(version)s_remove-broken-tests-intel.patch'] +patches = [ + '%(name)s-%(version)s_remove-broken-tests-intel.patch', + '%(name)s-%(version)s_fix-bss_energy_test.patch', + '%(name)s-%(version)s_use_easybuild_opts_intel.patch', + '%(name)s-%(version)s_fix_test_path.patch', +] checksums = [ 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz - '33e884d197724fdb98cd5e395ca46d065a620eb70f19c5a120fcb0ce07ac4290', # DIRAC-19.0_remove-broken-tests-intel.patch -] - -builddependencies = [ - ('CMake', '3.16.4'), -] - -dependencies = [ - ('Python', '2.7.18'), - ('Boost', '1.72.0'), - ('HDF5', '1.10.6'), - ('imkl', '2020.1.217'), + '5ae7ade408310a0309178876e9f5ddc80ecd6b85c862c88899fcdca386dd9c70', # DIRAC-19.0_remove-broken-tests-intel.patch + '13c7b19da10a7db585fb6d57eda8474cb71cdd89d6c4844e80276d3aa05e2b4f', # DIRAC-19.0_fix-bss_energy_test.patch + '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch + '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch ] -skipsteps = ['configure'] - +builddependencies = [('CMake', '3.16.4')] + +dependencies = [('Python', '2.7.18')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DENABLE_BLAS=off ' +configopts += '-DENABLE_LAPACK=off ' +configopts += '-DMKL_FLAG=off ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=False ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=True ' +configopts += '-DEXPLICIT_LIBS="${LIBLAPACK_MT}" ' +configopts += '-DENABLE_PCMSOLVER=OFF ' +configopts += '-G"Unix Makefiles" ' + +prebuildopts = "make -j36 ; make -j36 ; make -j36 ;" parallel = 1 -local_pre_flags = 'export CFLAGS="$CFLAGS -m64" && ' -local_pre_flags += 'export CXXFLAGS="$CXXFLAGS -m64" && ' -local_pre_flags += 'export FCFLAGS="$FCFLAGS -i8" && ' -local_pre_flags += 'export FFLAGS="$FFLAGS -i8 " && ' -local_pre_flags += 'export DEBUG=True && ' - -# BUILD -prebuildopts = local_pre_flags -prebuildopts += 'export MATH_ROOT="$MKLROOT" && ' -prebuildopts += './setup --int64 --prefix=%(installdir)s ' -prebuildopts += '--pcmsolver=OFF --cc="$CC" --cxx="$CXX" --fc="$FC" ' -prebuildopts += '--mkl=parallel ' -prebuildopts += '&& cd build && ' - -# TEST -pretestopts = local_pre_flags -pretestopts += 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -pretestopts += "cd build && " - -runtest = 'test' - -# INSTALL -preinstallopts = local_pre_flags -preinstallopts += "cd build && " +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +runtest = 'test ARGS=-j16' -# SANITY CHECKS sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], 'dirs': ['share/dirac/basis'], diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb new file mode 100644 index 00000000000..450913679b8 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb @@ -0,0 +1,74 @@ +easyblock = 'CMakeMake' + +name = 'DIRAC' +version = '19.0' +versionsuffix = '-Python-%(pyver)s-mpi-int64' + +homepage = 'http://www.diracprogram.org' +description = "DIRAC: Program for Atomic and Molecular Direct Iterative Relativistic All-electron Calculations" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'i8': True} + +source_urls = ['https://zenodo.org/record/3572669/files/'] +sources = ['DIRAC-%(version)s-Source.tar.gz'] +patches = [ + '%(name)s-%(version)s_remove-broken-tests-intel.patch', + '%(name)s-%(version)s_fix-bss_energy_test.patch', + '%(name)s-%(version)s_use_easybuild_opts_intel.patch', + '%(name)s-%(version)s_fix_test_path.patch', + '%(name)s-%(version)s_fix_mpi_tests.patch', +] +checksums = [ + 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz + '5ae7ade408310a0309178876e9f5ddc80ecd6b85c862c88899fcdca386dd9c70', # DIRAC-19.0_remove-broken-tests-intel.patch + '13c7b19da10a7db585fb6d57eda8474cb71cdd89d6c4844e80276d3aa05e2b4f', # DIRAC-19.0_fix-bss_energy_test.patch + '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch + '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch + 'ccc26fc320f0967211b6390244b1fa359ba5d0294071d5d2cb9e36b4652a52b2', # DIRAC-19.0_fix_mpi_tests.patch +] + +builddependencies = [('CMake', '3.16.4')] + +dependencies = [('Python', '2.7.18')] + +separate_build_dir = True + +configopts = '-DCMAKE_BUILD_TYPE=RELEASE ' +configopts += '-DENABLE_BLAS=off ' +configopts += '-DENABLE_LAPACK=off ' +configopts += '-DMKL_FLAG=off ' +configopts += '-DBLAS_LANG=Fortran ' +configopts += '-DLAPACK_LANG=Fortran ' +configopts += '-DENABLE_MPI=True ' +configopts += '-DENABLE_OPENMP=False ' +configopts += '-DENABLE_CODE_COVERAGE=False ' +configopts += '-DENABLE_STATIC_LINKING=False ' +configopts += '-DENABLE_PROFILING=False ' +configopts += '-DENABLE_RUNTIMECHECK=False ' +configopts += '-DENABLE_64BIT_INTEGERS=True ' +configopts += '-DEXPLICIT_LIBS="${LIBSCALAPACK_MT}" ' +configopts += '-DENABLE_PCMSOLVER=OFF ' +configopts += '-G"Unix Makefiles" ' + +parallel = 1 + +pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' +# WARNING! +# running the tests with more than 1 MPI process might break some tests: +# 18 - polprp_ph -> ERROR READING HEADER MDCINT +# 20 - eomcc/eom_ea_h2o.out -> extra state +# 26 - eomea_energy_symmetry/eom_ea_dc_noinv_overlap_c_oo_v_-Omega_f2_c_oo_v_turbomole-dz.out -> extra state +# 46 - fscc_restart -> ENERGY TOTAL WRONG, maybe missing some file, like in polprp_ph? +# Test 20/26 fails on cascadelake and not on haswell and skylake +pretestopts += 'export DIRAC_MPI_COMMAND="mpirun -np 1 " && ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], + 'dirs': ['share/dirac/basis'], +} + +sanity_check_commands = ["pam-dirac --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch new file mode 100644 index 00000000000..7cb717bd553 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch @@ -0,0 +1,3028 @@ +# it seems that bss_energy test is broken, the reference calculation is form 2004 +# The fact that only the SCF energy different and the consecutive post-HF correlation +# energies are the same s a strong hnt that the HF wavefunction should be the same, +# but the energies for some reason are different. +# THe test was recalulated suing the following compilers/BLAS libaries on cascadelake +# architecture, and the results are practially the same. +# Based on this facts, the reference test result was changed to the intel result below. +# +# gfortran 9.3.0 openblas 0.3.9 cascadelake: +# @ SCF energy : -9505.779747269898508 +# @ MP2 correlation energy : -0.221846247868918 +# @ CCSD correlation energy : -0.222547639202710 +# @ 4th order triples correction : -0.000001799879971 +# @ 5th order triples (T) correction : -0.000000000059407 +# @ 5th order triples -T correction : -0.000000000472828 +# @ Total MP2 energy : -9506.001593517767105 +# @ Total CCSD energy : -9506.002294909101693 +# @ Total CCSD+T energy : -9506.002296708980793 +# @ Total CCSD(T) energy : -9506.002296709040820 +# @ Total CCSD-T energy : -9506.002296709453731 +# +# ifort 2020.1 mkl 2020.1 cascadelake: +# @ SCF energy : -9505.779747269911240 +# @ MP2 correlation energy : -0.221846247868917 +# @ CCSD correlation energy : -0.222547639202709 +# @ 4th order triples correction : -0.000001799879971 +# @ 5th order triples (T) correction : -0.000000000059407 +# @ 5th order triples -T correction : -0.000000000472828 +# @ Total MP2 energy : -9506.001593517779838 +# @ Total CCSD energy : -9506.002294909114426 +# @ Total CCSD+T energy : -9506.002296708993526 +# @ Total CCSD(T) energy : -9506.002296709053553 +# @ Total CCSD-T energy : -9506.002296709466464 +# +# OCT 5th 2020 by B. Hajgato (UGent) +diff -ru DIRAC-19.0-Source.orig/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out DIRAC-19.0-Source/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out +--- DIRAC-19.0-Source.orig/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out 2019-12-12 17:26:14.000000000 +0100 ++++ DIRAC-19.0-Source/test/bss_energy/result/HF.bss_sfb.cc_cisd_Z80H.lsym.dir.out 2020-10-05 14:16:03.472742000 +0200 +@@ -1,175 +1,342 @@ +-Master : DIRAC allocating 10000000 words of memory +-****************************************************************************** +-* * +-* O U T P U T * +-* from * +-* * +-* @@@@@ @@ @@@@@ @@@@ @@@@@ * +-* @@ @@ @@ @@ @@ @@ @@ * +-* @@ @@ @@ @@@@@ @@@@@@ @@ * +-* @@ @@ @@ @@ @@ @@ @@ @@ * +-* @@@@@ @@ @@ @@ @@ @@ @@@@@ * +-* * +-* * +-%}ZS)S?$=$)]S?$%%>SS$%S$ZZ6cHHMHHHHHHHHMHHM&MHbHH6$L/:$)S6HMMMMMMMMMMMMMMMMMMMMMMR6M]&&$6HR$&6(i::::::|i|:::::::-:-:: +-$S?$$)$?$%?))?S/]#MMMMMMMMMMMMMMMMMMMMMMMMMMHM1HRH9R&$$$|):?:/://|:/::/:/.::.: +-SS$%%?$%((S)?Z[6MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM&HF$$&/)S?<~::!!:::::::/:-:|. +-SS%%%%S$%%%$$MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHHHHHM>?/S/:/:::':/://:/::-:: +-?$SSSS?%SS$)MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/4?:S:/:::/:::/:/:::.:: +-S$(S?S$%(?$HMMMMMMMMMMMMMMMMM#&7RH99MMMMMMMMMMMMMMMMMMHHHd$/:::::/::::::-//.:. +-(?SS(%)S&HMMMMMMMMMMMMMMMMM#S|///???$9HHMMMMMMMMMDSZ&1S/??~:///::|/!:/-:-:. +-$S?%?:``?/*?##*)$:/> `((%://::/:::::/::/ +-S$($$)HdMMMMMMMMMMMMMMMP: . ` ` ` ` `- `Z<:>?::/:::::|:i +-c%%%&HMMMMMMMMMMMMMMMM6: `$%)>%%!::::: +-S?%/MMMMMMMMMMMMMMMMMMH- /ZSS>?:?~:;/:: +-$SZ?MMMMMMMMMMMMMMMMMH?. "&((/?//?|:::: +-$%$%&MMMMMMMMMMMMMMMMM:. ?%/S:: $%%< ,HMMMMMMMF :::?:///:|:: +-)[$S$S($|_i:#>::*H&?/::.::/:"://:?>>':&HMHSMMMM$:'- MMHMMMMHHT .)i/?////:::/ +-$$[$$>$}:dHH&$$--?S::-:.:::--/-:``./::>%Zi?)&/?`:.' `H?$T*" ` /%?>%:)://ii| +-$&=&/ZS}$RF<:?/-.|%r/:::/:/:'.-.-..|::S//!`"`` >??: `SSb[Z(Z?&%:::../S$$:>:::i`.`. '-.' ` ,>%%%:>/>/!|:/ +-$$&/F&1$c$?>:>?/,>?$$ZS/::/:-: ... |S?S)S?<~::::: +-&$&$&$k&>>|?<:?Z&S$$$/$S///||..- -.- /((S$:%<:///:/ +-$&>1MHHMMMM6M9MMMM$Z$}$S%/:::.'. .:/,,,dcb>/:. ((SSSS%:)!//i| +-MMMMMMMMMMMR&&RRRHR&&($(?:|i::- .:%&S&$[&H&'' ../>%;/?>??:<::> +-MMMMMMMMMMMMS/}S$&&H&[$SS//:::.:. . . .v?://: +-MMMMMMMMMMMM?}$/$$kMM&&$(%/?//:..'. .|//1d/`://?*/*/"` ' .:/(SS$%(S%)):%~ +-MMMMMMMMMMMM(}$$>&&MMHR#$S%%:?::.:|-.':;&&b/D/$p=qpv//b/~' :/~~%%??$=$)Z$S+; +-MMMMMMMMMMMM[|S$$Z1]MMMMD[$?$:>)/::: :/?:`'???bD&{b<<-' .,:/)|SS(}Z/$$?/[&]HMMMMMMMH1[/7SS(?:/..-` ::/Sc,/_, _<$?SS%$S/&c&&$&>//< +-MMMMMMMMMMMMR `$&&&HMM9MMMMMMM&&c$%%:/:/:.:.:/??/''" _MMHk/7S/]dq&1S<&&>$&Z$/?_.bHMMMMMMMMMMM&6HRM9H6]Zk +-MMMMMMMMMMMMMMM/ `TMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH6RH&R6& +-MMMMMMMMMMMMMMMM -|?HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMFHH6HMD&& +-MMMMMMMMMMMMMMMMk ..:~?9MMMMMMMMMMMMM#':MMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MHkR6&F +-MMMMMMMMMMMMMMMMM/ .-!:%$ZHMMMMMMMMMR' dMMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MRMHH9& +-MMMMMMMMMMMMMMMMMML,:.-|::/?&&MMMMMM' .MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHRMH&&6 +-MMMMMMMMMMMMMMMMMMMc%>/:::i<:SMMMMMMHdMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHM&969k +-MMMMMMMMMMMMMMMMMMMMSS/$$/(|HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHH&HH& +-MMMMMMMMMMMMMMMMMMMM6S/?/MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMR96H1DR1 +-MMMMMMMMMMMMMMMMMMMMM&$MHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH691&& +-MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&R&9Z +-MMMMMMMMMMMMMMMMMMMMMMMMMRHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&96][6 +-MMMMMMMMMMMMMMMMMMMMMMMMp?:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM96HH1][F +-MMMMMMMMMMMMMMMMMMMMMMMM> -HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&1k&$& +-****************************************************************************** +-* * +-* ======================================================= * +-* Program for Atomic and Molecular * +-* Direct Iterative Relativistic Allelectron Calculations * +-* ======================================================= * +-* * +-* VERSION 04.1 SEPTEMBER 2004 * +-* * +-****************************************************************************** +-* * +-* Written by: * +-* * +-* Hans Joergen Aa. Jensen University of Southern Denmark Denmark * +-* Trond Saue CNRS/ULP Strasbourg France * +-* Lucas Visscher Vrije Universiteit Amsterdam Netherlands * +-* * +-* with contributions from: * +-* * +-* Vebjoern Bakken University of Oslo Norway * +-* Ephraim Eliav University of Tel Aviv Israel * +-* Thomas Enevoldsen University of Southern Denmark Denmark * +-* Timo Fleig University of Duesseldorf Germany * +-* Olav Fossgaard University of Tromsoe Norway * +-* Trygve Helgaker University of Oslo Norway * +-* Jon K. Laerdahl University of Oslo Norway * +-* Christoffer V. Larsen University of Southern Denmark Denmark * +-* Patrick Norman Linkoeping University Sweden * +-* Jeppe Olsen Aarhus University Denmark * +-* Markus Pernpointner Vrije Universiteit Amsterdam Netherlands * +-* Jesper K. Pedersen University of Southern Denmark Denmark * +-* Kenneth Ruud University of Tromsoe Norway * +-* Pawel Salek Stockholm Inst. of Technology Sweden * +-* Joost van Stralen Vrije Universiteit Amsterdam Netherlands * +-* Joern Thyssen University of Southern Denmark Denmark * +-* Olivier Visser University of Groningen Netherlands * +-* Toke Winther University of Southern Denmark Denmark * +-* * +-* This is an experimental code. The authors accept no responsibility * +-* for the performance of the code or for the correctness of the results. * +-* * +-* The code (in whole or part) is not to be reproduced for further * +-* distribution without the written permission of the authors or * +-* their representatives. * +-* * +-* If results obtained with this code are published, an * +-* appropriate citation would be: * +-* * +-* "Dirac, a relativistic ab initio electronic structure program", * +-* release DIRAC04.1 (2004), * +-* written by H. J. Aa. Jensen, T. Saue, and L. Visscher * +-* with contributions from V. Bakken, E. Eliav, T. Enevoldsen, T. Fleig, * +-* O. Fossgaard, T. Helgaker, J. K. Laerdahl, C. V. Larsen, P. Norman, * +-* J. Olsen, M. Pernpointner, J. K. Pedersen, K. Ruud, P. Salek, * +-* J. N. P. van Stralen, J. Thyssen, O. Visser, and T. Winther * +-* (http://dirac.chem.sdu.dk). * +-* * +-* (for a suitable BibTEX entry, see * +-* ) * +-* * +-****************************************************************************** +- Version : Dirac 4.1 (patchlevel 0) +- Hostname : quantonakessa.u-strasbg.fr +- Operating system : Linux 2.6.8-1.521 +- Machine : i686 +- Run : Sequential +- Last compilation : 16:31:43 Dec 5 2004 (by ilias@) +- FORTRAN compiler : g77 -g -ffast-math -fautomatic -fno-f2c -fno-globals -Wno-globals -fno-second-underscore +- C compiler : gcc -ffast-math -g +- Basis set dir. : /home/ilias/Dirac_main_trunk_dbg/test/37.bss.energies/:/home/ilias/Dirac_main_trunk_dbg/basis/:/home/ilias/Dirac_main_trunk_dbg/basis_dalton/ +- +- Date and time (Linux) : Sun Dec 5 16:41:19 2004 +- +- +- ************************************************************************* +- ********************************* LiH ********************************* +- ************************************************************************* ++DIRAC serial starts by allocating 64000000 words ( 488.28 MB - 0.477 GB) of memory ++ out of the allowed maximum of 2147483648 words ( 16384.00 MB - 16.000 GB) ++ ++Note: maximum allocatable memory for serial run can be set by pam --aw/--ag ++ ++ ******************************************************************************* ++ * * ++ * O U T P U T * ++ * from * ++ * * ++ * @@@@@ @@ @@@@@ @@@@ @@@@@ * ++ * @@ @@ @@ @@ @@ @@ @@ * ++ * @@ @@ @@ @@@@@ @@@@@@ @@ * ++ * @@ @@ @@ @@ @@ @@ @@ @@ * ++ * @@@@@ @@ @@ @@ @@ @@ @@@@@ * ++ * * ++ * * ++ %}ZS)S?$=$)]S?$%%>SS$%S$ZZ6cHHMHHHHHHHHMHHM&MHbHH6$L/:$)S6HMMMMMMMMMMMMMMMMMMMMMMR6M]&&$6HR$&6(i::::::|i|:::::::-:-::( ++ $S?$$)$?$%?))?S/]#MMMMMMMMMMMMMMMMMMMMMMMMMMHM1HRH9R&$$$|):?:/://|:/::/:/.::.:$ ++ SS$%%?$%((S)?Z[6MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM&HF$$&/)S?<~::!!:::::::/:-:|.S ++ SS%%%%S$%%%$$MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHHHHHM>?/S/:/:::`:/://:/::-::S ++ ?$SSSS?%SS$)MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM/4?:S:/:::/:::/:/:::.::? ++ S$(S?S$%(?$HMMMMMMMMMMMMMMMMM#&7RH99MMMMMMMMMMMMMMMMMMHHHd$/:::::/::::::-//.:.S ++ (?SS(%)S&HMMMMMMMMMMMMMMMMM#S|///???$9HHMMMMMMMMMDSZ&1S/??~:///::|/!:/-:-:.( ++ $S?%?:``?/*?##*)$:/> `((%://::/:::::/::/$ ++ S$($$)HdMMMMMMMMMMMMMMMP: . ` ` ` ` `- `Z<:>?::/:::::|:iS ++ c%%%&HMMMMMMMMMMMMMMMM6: `$%)>%%!:::::c ++ S?%/MMMMMMMMMMMMMMMMMMH- /ZSS>?:?~:;/::S ++ $SZ?MMMMMMMMMMMMMMMMMH?. \"&((/?//?|:::$ ++ $%$%&MMMMMMMMMMMMMMMMM:. ?%/S:: $%%< ,HMMMMMMMF :::?:///:|:::$ ++ )[$S$S($|_i:#>::*H&?/::.::/:\"://:?>>`:&HMHSMMMM$:`- MMHMMMMHHT .)i/?////::/) ++ $$[$$>$}:dHH&$$--?S::-:.:::--/-:``./::>%Zi?)&/?`:.` `H?$T*\" ` /%?>%:)://ii$ ++ $&=&/ZS}$RF<:?/-.|%r/:::/:/:`.-.-..|::S//!`\"`` >??: `SSb[Z(Z?&%:::../S$$:>:::i`.`. `-.` ` ,>%%%:>/>/!|:/Z ++ $$&/F&1$c$?>:>?/,>?$$ZS/::/:-: ... |S?S)S?<~:::::$ ++ &$&$&$k&>>|?<:?Z&S$$$/$S///||..- -.- /((S$:%<:///:/= ++ $&>1MHHMMMM6M9MMMM$Z$}$S%/:::.`. .:/,,,dcb>/:. ((SSSS%:)!//i|$ ++ MMMMMMMMMMMR&&RRRHR&&($(?:|i::- .:%&S&$[&H&`` ../>%;/?>??:<::>M ++ MMMMMMMMMMMMS/}S$&&H&[$SS//:::.:. . . .v?://:M ++ MMMMMMMMMMMM?}$/$$kMM&&$(%/?//:..`. .|//1d/`://?*/*/\"` ` .:/(SS$%(S%)):%M ++ MMMMMMMMMMMM(}$$>&&MMHR#$S%%:?::.:|-.`:;&&b/D/$p=qpv//b/~` :/~~%%??$=$)Z$S+;M ++ MMMMMMMMMMMM[|S$$Z1]MMMMD[$?$:>)/::: :/?:``???bD&{b<<-` .,:/)|SS(}Z/$$?/[&]HMMMMMMMH1[/7SS(?:/..-` ::/Sc,/_, _<$?SS%$S/&c&&$&>//$&Z$/?_.bHMMMMMMMMMMM&6HRM9H6]ZkM ++ MMMMMMMMMMMMMMM/ `TMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH6RH&R6&M ++ MMMMMMMMMMMMMMMM -|?HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMFHH6HMD&&M ++ MMMMMMMMMMMMMMMMk ..:~?9MMMMMMMMMMMMM#`:MMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MHkR6&FM ++ MMMMMMMMMMMMMMMMM/ .-!:%$ZHMMMMMMMMMR` dMMMMMMMMMMMMMMMMMMMMMMMMMMMMM9MRMHH9&M ++ MMMMMMMMMMMMMMMMMML,:.-|::/?&&MMMMMM` .MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHRMH&&6M ++ MMMMMMMMMMMMMMMMMMMc%>/:::i<:SMMMMMMHdMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHM&969kM ++ MMMMMMMMMMMMMMMMMMMMSS/$$/(|HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHH&HH&M ++ MMMMMMMMMMMMMMMMMMMM6S/?/MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMR96H1DR1M ++ MMMMMMMMMMMMMMMMMMMMM&$MHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHMH691&&M ++ MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&R&9ZM ++ MMMMMMMMMMMMMMMMMMMMMMMMMRHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&96][6M ++ MMMMMMMMMMMMMMMMMMMMMMMMp?:MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM96HH1][FM ++ MMMMMMMMMMMMMMMMMMMMMMMM> -HMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMH&1k&$&M ++ ******************************************************************************* ++ * * ++ * ========================================================= * ++ * Program for Atomic and Molecular * ++ * Direct Iterative Relativistic All-electron Calculations * ++ * ========================================================= * ++ * * ++ * * ++ * Written by: * ++ * * ++ * Andre S. P. Gomes CNRS/Universite de Lille France * ++ * Trond Saue Universite Toulouse III France * ++ * Lucas Visscher Vrije Universiteit Amsterdam Netherlands * ++ * Hans Joergen Aa. Jensen University of Southern Denmark Denmark * ++ * Radovan Bast UiT The Arctic University of Norway * ++ * * ++ * with contributions from: * ++ * * ++ * Ignacio Agustin Aucar Northeast National University Argentina * ++ * Vebjoern Bakken University of Oslo Norway * ++ * Kenneth G. Dyall Schrodinger, Inc., Portland USA * ++ * Sebastien Dubillard University of Strasbourg France * ++ * Ulf Ekstroem University of Oslo Norway * ++ * Ephraim Eliav University of Tel Aviv Israel * ++ * Thomas Enevoldsen University of Southern Denmark Denmark * ++ * Elke Fasshauer University of Aarhus Denmark * ++ * Timo Fleig Universite Toulouse III France * ++ * Olav Fossgaard UiT The Arctic University of Norway * ++ * Loic Halbert Universite de Lille France * ++ * Erik D. Hedegaard Lund University Sweden * ++ * Trygve Helgaker University of Oslo Norway * ++ * Benjamin Helmich-Paris Max Planck Institute f. Coal Res. Germany * ++ * Johan Henriksson Linkoeping University Sweden * ++ * Miroslav Ilias Matej Bel University Slovakia * ++ * Christoph R. Jacob TU Braunschweig Germany * ++ * Stefan Knecht ETH Zuerich Switzerland * ++ * Stanislav Komorovsky UiT The Arctic University of Norway * ++ * Ossama Kullie University of Kassel Germany * ++ * Jon K. Laerdahl University of Oslo Norway * ++ * Christoffer V. Larsen University of Southern Denmark Denmark * ++ * Yoon Sup Lee KAIST, Daejeon South Korea * ++ * Huliyar S. Nataraj BME/Budapest Univ. Tech. & Econ. Hungary * ++ * Malaya Kumar Nayak Bhabha Atomic Research Centre India * ++ * Patrick Norman Stockholm Inst. of Technology Sweden * ++ * Malgorzata Olejniczak University of Warsaw Poland * ++ * Jeppe Olsen Aarhus University Denmark * ++ * Jogvan Magnus H. Olsen University of Southern Denmark Denmark * ++ * Young Choon Park KAIST, Daejeon South Korea * ++ * Jesper K. Pedersen University of Southern Denmark Denmark * ++ * Markus Pernpointner University of Heidelberg Germany * ++ * Roberto Di Remigio UiT The Arctic University of Norway * ++ * Kenneth Ruud UiT The Arctic University of Norway * ++ * Pawel Salek Stockholm Inst. of Technology Sweden * ++ * Bernd Schimmelpfennig Karlsruhe Institute of Technology Germany * ++ * Bruno Senjean University of Leiden Netherlands * ++ * Avijit Shee University of Michigan USA * ++ * Jetze Sikkema Vrije Universiteit Amsterdam Netherlands * ++ * Andreas J. Thorvaldsen UiT The Arctic University of Norway * ++ * Joern Thyssen University of Southern Denmark Denmark * ++ * Joost van Stralen Vrije Universiteit Amsterdam Netherlands * ++ * Marta L. Vidal Technical University of Denmark Denmark * ++ * Sebastien Villaume Linkoeping University Sweden * ++ * Olivier Visser University of Groningen Netherlands * ++ * Toke Winther University of Southern Denmark Denmark * ++ * Shigeyoshi Yamamoto Chukyo University Japan * ++ * * ++ * For more information about the DIRAC code see http://diracprogram.org * ++ * * ++ * This is an experimental code. The authors accept no responsibility * ++ * for the performance of the code or for the correctness of the results. * ++ * * ++ * The code (in whole or part) is not to be reproduced for further * ++ * distribution without the written permission of the authors or * ++ * their representatives. * ++ * * ++ * If results obtained with this code are published, an * ++ * appropriate citation would be: * ++ * * ++ * DIRAC, a relativistic ab initio electronic structure program, * ++ * Release DIRAC19 (2019), written by * ++ * A. S. P. Gomes, T. Saue, L. Visscher, H. J. Aa. Jensen, and R. Bast, * ++ * with contributions from I. A. Aucar, V. Bakken, K. G. Dyall, * ++ * S. Dubillard, U. Ekstroem, E. Eliav, T. Enevoldsen, E. Fasshauer, * ++ * T. Fleig, O. Fossgaard, L. Halbert, E. D. Hedegaard, T. Helgaker, * ++ * J. Henriksson, M. Ilias, Ch. R. Jacob, S. Knecht, S. Komorovsky, * ++ * O. Kullie, J. K. Laerdahl, C. V. Larsen, Y. S. Lee, H. S. Nataraj, * ++ * M. K. Nayak, P. Norman, M. Olejniczak, J. Olsen, J. M. H. Olsen, * ++ * Y. C. Park, J. K. Pedersen, M. Pernpointner, R. Di Remigio, K. Ruud, * ++ * P. Salek, B. Schimmelpfennig, B. Senjean, A. Shee, J. Sikkema, * ++ * A. J. Thorvaldsen, J. Thyssen, J. van Stralen, M. L. Vidal, S. Villaume, * ++ * O. Visser, T. Winther, and S. Yamamoto (see http://diracprogram.org). * ++ * * ++ ******************************************************************************* ++ ++ ++Version information ++------------------- ++ ++Branch | ++Commit hash | ++Commit author | ++Commit date | ++ ++ ++Configuration and build information ++----------------------------------- ++ ++Who compiled | vsc43020 ++Compiled on server | node3403.kirlia.os ++Operating system | Linux-3.10.0-1127.8.2.el7.ug.x86_64 ++CMake version | 3.16.4 ++CMake generator | Unix Makefiles ++CMake build type | release ++Configuration time | 2020-10-05 12:06:36.697767 ++Python version | 2.7.1 ++Fortran compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort ++Fortran compiler version | 19.1 ++Fortran compiler flags | -w -assume byterecl -g -traceback -DVAR_IFORT -i8 ++C compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/icc ++C compiler version | 19.1 ++C compiler flags | -g -wd981 -wd279 -wd383 -wd1572 -wd177 ++C++ compiler | /apps/gent/CO7/cascadelake-ib/software/iccifort/2020.1.217/compilers_and_libraries_2020.1.217/linux/bin/intel64/icpc ++C++ compiler version | 19.1.1 ++C++ compiler flags | -Wno-unknown-pragmas ++Static linking | False ++64-bit integers | True ++MPI parallelization | False ++MPI launcher | unknown ++Math libraries | unknown ++Builtin BLAS library | OFF ++Builtin LAPACK library | OFF ++Explicit libraries | unknown ++Compile definitions | HAVE_MKL_BLAS;HAVE_MKL_LAPACK;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;HAS_PCMSOLVER;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES ++ ++ ++ LAPACK integer*4/8 selftest passed ++ Selftest of ISO_C_BINDING Fortran - C/C++ interoperability PASSED ++ ++Execution time and host ++----------------------- ++ ++ ++ Date and time (Linux) : Mon Oct 5 14:12:56 2020 ++ Host name : node3403.kirlia.os ++ ++ ++Contents of the input file ++-------------------------- ++ ++**DIRAC ++.TITLE ++ LiH ++.WAVE F ! Activate integral and wave functions modules ++**GENERAL ++**INTEGRALS ++.PRINT ++1 ++.NUCMOD ! 1-Point nucleus, 2-gaussian ++2 ++**HAMILTONIAN ++.SPINFREE ++.BSS ++109 ++.CMPEIG ++.PRINT ++2 ++**WAVE FUNCTIONS ! What method (DHF,MP2,CC..) ++.SCF ++.RELCCSD ++.LUCITA ++*SCF ++.CLOSED SHELL ++10 ++.INTFLG ! Specify what 2-el.integrals to include ++1 1 0 ++.EVCCNV ! Energy convergence... ++1.0E-10 1.0D-7 ++*LUCITA ++.INIWFC ++ DHFSCF ++.CITYPE ++ SDCI ++.MULTIP ++ 3 ++**MOLTRA ++# needed for parallel run ++.SCHEME ++4 ++.ACTIVE ++energy -1000 999999 0.1 ++**RELCCSD ++.NELEC ++ 4 4 ++.INTERFACE ++DIRAC ++.TIMING ++.PRINT ++ 1 ++*CCSORT ++.USEOE ++*END OF ++ ++ ++ ++Contents of the molecule file ++----------------------------- ++ ++INTGRL ++X ++X ++C 2 A ++ 80.0 1 ++X 0.0000000000 0.0000000000 2.000000000 ++LARGE 3 1 1 1 ++f 5 0 ++ 90000 ++ 50000 ++ 9000 ++ 4000 ++ 300 ++f 3 0 ++ 35000 ++ 7000 ++ 900 ++f 1 0 ++ 900 ++ 1. 1 ++H 0.00000000000 .0000000000 .0000000000 ++LARGE 1 1 ++f 2 0 ++ 1.00 ++ 0.25 ++FINISH ++ ++ ++ ************************************************************************* ++ ********************************* LiH ********************************* ++ ************************************************************************* + + Jobs in this run: + * Wave function + + +- ************************************************************************** +- ************************** General DIRAC set-up ************************** +- ************************************************************************** +- ++ ************************************************************************** ++ ************************** General DIRAC set-up ************************** ++ ************************************************************************** ++ ++ CODATA Recommended Values of the Fundamental Physical Constants: 1998 ++ Peter J. Mohr and Barry N. Taylor ++ Journal of Physical and Chemical Reference Data, Vol. 28, No. 6, 1999 + * The speed of light : 137.0359998 ++ * Running in two-component mode + * Direct evaluation of the following two-electron integrals: + - LL-integrals +- - SL-integrals +- - SS-integrals + * Spherical transformation embedded in MO-transformation + for large components + * Transformation to scalar RKB basis embedded in + MO-transformation for small components + * Thresholds for linear dependence: +- Large components: 1.00E-06 +- Small components: 1.00E-08 ++ Large components: 1.00D-06 ++ Small components: 1.00D-08 + * General print level : 0 + + +- ************************************************************************* +- ****************** Output from HERMIT input processing ****************** +- ************************************************************************* ++ ************************************************************************* ++ ****************** Output from HERMIT input processing ****************** ++ ************************************************************************* + + Default print level: 1 + Nuclear model: Gaussian charge distribution. +@@ -181,20 +348,9 @@ + + + +- Set-up from HR2INP: +- ------------------- +- +- Print level in TWOINT: 1 +- Extra output for the following shells: 0 0 0 0 +- * Direct calculation of Fock matrices in SO-basis. +- * Default screening threshold in direct Fock matrix construction: 1.00E-12 +- * Separate density screening of Coulomb integral batches +- * Separate density screening of exchange integral batches +- +- +- ************************************************************************* +- ****************** Output from READIN input processing ****************** +- ************************************************************************* ++ *************************************************************************** ++ ****************** Output from MOLECULE input processing ****************** ++ *************************************************************************** + + + +@@ -207,29 +363,20 @@ + Coordinates are entered in Angstroms and converted to atomic units. + - Conversion factor : 1 bohr = 0.52917721 A + +- Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011788914E+08 +- +- Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248239171E+09 ++ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 ++ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 + + +- SYMADD: Requested addition of symmetry +- -------------------------------------- ++ SYMADD: Detection of molecular symmetry ++ --------------------------------------- + +- Symmetry threshold: 0.50E-05 ++ Symmetry test threshold: 5.00E-06 + +- Original Coordinates +- -------------------- +- 80 0.00000000 0.00000000 3.77945227 1 +- 1 0.00000000 0.00000000 0.00000000 1 ++ The molecule has been centered at center of mass + +- Symmetry class found: C(oo,v) ++ Symmetry point group found: C(oo,v) + +- Centered and Rotated +- -------------------- +- 80 0.00000000 0.00000000 0.01876567 1 +- 1 0.00000000 0.00000000 -3.76068660 1 +- +- The following elements were found: X Y ++ The following symmetry elements were found: X Y + + + Symmetry Operations +@@ -239,8 +386,8 @@ + + + +- SYMGRP:Point group information +- ------------------------------ ++ SYMGRP:Point group information ++ ------------------------------ + + Full group is: C(oo,v) + Represented as: C2v +@@ -254,9 +401,9 @@ + + | E C2z Oxz Oyz + -----+-------------------- +- E | E +- C2z | C2z E +- Oxz | Oxz Oyz E ++ E | E C2z Oxz Oyz ++ C2z | C2z E Oyz Oxz ++ Oxz | Oxz Oyz E C2z + Oyz | Oyz Oxz C2z E + + * Character table +@@ -272,15 +419,15 @@ + + | A1 B1 B2 A2 + -----+-------------------- +- A1 | A1 +- B1 | B1 A1 +- B2 | B2 A2 A1 ++ A1 | A1 B1 B2 A2 ++ B1 | B1 A1 A2 B2 ++ B2 | B2 A2 A1 B1 + A2 | A2 B2 B1 A1 + + +- ************************** +- *** Output from DBLGRP *** +- ************************** ++ ************************** ++ *** Output from DBLGRP *** ++ ************************** + + * One fermion irrep: E1 + * Real group. NZ = 1 +@@ -288,8 +435,8 @@ + E1 x E1 : A1 + A2 + B1 + B2 + + +- Spinor structure +- ---------------- ++ Spinor structure ++ ---------------- + + + * Fermion irrep no.: 1 +@@ -299,8 +446,8 @@ + Sb | B2 (3) B1 (4) | + + +- Quaternion symmetries +- --------------------- ++ Quaternion symmetries ++ --------------------- + + Rep T(+) + ----------------------------- +@@ -309,27 +456,39 @@ + B2 k + A2 i + ++ QM-QM nuclear repulsion energy : 21.167088332000 ++ ++ ++ ++ Isotopic Masses ++ --------------- ++ ++ X 201.970617 ++ H 1.007825 ++ ++ Total mass: 202.978442 amu ++ Natural abundance: 29.856 % ++ ++ Center-of-mass coordinates (a.u.): 0.000000000000000 0.000000000000000 0.000000000000000 ++ + + Atoms and basis sets + -------------------- + +- Number of atom types: 2 ++ Number of atom types : 2 + Total number of atoms: 2 + + label atoms charge prim cont basis + ---------------------------------------------------------------------- +- X 1 80 20 20 L - [5s3p1d|5s3p1d] +- 49 49 S - [3s6p3d1f|3s6p3d1f] +- H 1 1 2 2 L - [2s|2s] +- 6 6 S - [2p|2p] ++ X 1 80 20 20 L - [5s3p1d|5s3p1d] ++ H 1 1 2 2 L - [2s|2s] + ---------------------------------------------------------------------- +- 22 22 L - large components +- 55 55 S - small components ++ 22 22 L - large components + ---------------------------------------------------------------------- +- total: 2 81 77 77 ++ total: 2 81 22 22 + + Cartesian basis used. +- Threshold for integrals: 1.00E-15 ++ Threshold for integrals (to be written to file): 1.00D-15 + + + References for the basis sets +@@ -339,8 +498,8 @@ + Basis set typed explicitly in input file + + +- Cartesian Coordinates +- --------------------- ++ Cartesian Coordinates (bohr) ++ ---------------------------- + + Total number of coordinates: 6 + +@@ -355,28 +514,37 @@ + + + ++ Cartesian coordinates in XYZ format (Angstrom) ++ ---------------------------------------------- ++ ++ 2 ++ ++X 0.0000000000 0.0000000000 0.0099303649 ++H 0.0000000000 0.0000000000 -1.9900696351 ++ ++ + Symmetry Coordinates + -------------------- + +- Number of coordinates in each symmetry: 2 2 2 0 ++ Number of coordinates in each symmetry: 2 2 2 0 + + +- Symmetry 1 ++ Symmetry A1 ( 1) + +- 1 X z 3 +- 2 H z 6 ++ 1 X z 3 ++ 2 H z 6 + + +- Symmetry 2 ++ Symmetry B1 ( 2) + +- 3 X x 1 +- 4 H x 4 ++ 3 X x 1 ++ 4 H x 4 + + +- Symmetry 3 ++ Symmetry B2 ( 3) + +- 5 X y 2 +- 6 H y 5 ++ 5 X y 2 ++ 6 H y 5 + + + Interatomic separations (in Angstroms): +@@ -398,41 +566,36 @@ + bond distance: H X 2.000000 + + +- Nuclear repulsion energy : 21.167088332000 ++ ++ Nuclear repulsion energy : 21.167088332000 Hartree + + +- GETLAB: AO-labels +- ----------------- ++ GETLAB: AO-labels ++ ----------------- + + * Large components: 11 +- 1 L X s 2 L X px 3 L X py 4 L X pz 5 L X dxx 6 L X dxy +- 7 L X dxz 8 L X dyy 9 L X dyz 10 L X dzz 11 L H s +- * Small components: 23 +- 12 S X s 13 S X px 14 S X py 15 S X pz 16 S X dxx 17 S X dxy +- 18 S X dxz 19 S X dyy 20 S X dyz 21 S X dzz 22 S X fxxx 23 S X fxxy +- 24 S X fxxz 25 S X fxyy 26 S X fxyz 27 S X fxzz 28 S X fyyy 29 S X fyyz +- 30 S X fyzz 31 S X fzzz 32 S H px 33 S H py 34 S H pz ++ 1 L X 1 s 2 L X 1 px 3 L X 1 py 4 L X 1 pz 5 L X 1 dxx 6 L X 1 dxy ++ 7 L X 1 dxz 8 L X 1 dyy 9 L X 1 dyz 10 L X 1 dzz 11 L H 1 s ++ * Small components: 0 + + +- GETLAB: SO-labels +- ----------------- ++ ++ GETLAB: SO-labels ++ ----------------- + + * Large components: 11 + 1 L A1 X s 2 L A1 X pz 3 L A1 X dxx 4 L A1 X dyy 5 L A1 X dzz 6 L A1 H s + 7 L B1 X px 8 L B1 X dxz 9 L B2 X py 10 L B2 X dyz 11 L A2 X dxy +- * Small components: 23 +- 12 S A1 X s 13 S A1 X pz 14 S A1 X dxx 15 S A1 X dyy 16 S A1 X dzz 17 S A1 X fxxz +- 18 S A1 X fyyz 19 S A1 X fzzz 20 S A1 H pz 21 S B1 X px 22 S B1 X dxz 23 S B1 X fxxx +- 24 S B1 X fxyy 25 S B1 X fxzz 26 S B1 H px 27 S B2 X py 28 S B2 X dyz 29 S B2 X fxxy +- 30 S B2 X fyyy 31 S B2 X fyzz 32 S B2 H py 33 S A2 X dxy 34 S A2 X fxyz ++ * Small components: 0 ++ + + + Symmetry Orbitals + ----------------- + +- Number of orbitals in each symmetry: 36 18 18 5 ++ Number of orbitals in each symmetry: 13 4 4 1 + Number of large orbitals in each symmetry: 13 4 4 1 +- Number of small orbitals in each symmetry: 23 14 14 4 ++ Number of small orbitals in each symmetry: 0 0 0 0 + + * Large component functions + +@@ -459,123 +622,90 @@ + + 1 functions: X dxy + +-* Small component functions +- +- Symmetry A1 ( 1) +- +- 3 functions: X s +- 6 functions: X pz +- 3 functions: X dxx +- 3 functions: X dyy +- 3 functions: X dzz +- 1 functions: X fxxz +- 1 functions: X fyyz +- 1 functions: X fzzz +- 2 functions: H pz +- +- Symmetry B1 ( 2) +- +- 6 functions: X px +- 3 functions: X dxz +- 1 functions: X fxxx +- 1 functions: X fxyy +- 1 functions: X fxzz +- 2 functions: H px +- +- Symmetry B2 ( 3) +- +- 6 functions: X py +- 3 functions: X dyz +- 1 functions: X fxxy +- 1 functions: X fyyy +- 1 functions: X fyzz +- 2 functions: H py +- +- Symmetry A2 ( 4) + +- 3 functions: X dxy +- 1 functions: X fxyz +- +- +- *************************************************************************** +- *************************** Hamiltonian defined *************************** +- *************************************************************************** +- +- * Print level : 2 +- * Barysz-Sadlej-Snijders Hamiltonian. Type code -109 ++ *************************************************************************** ++ *************************** Hamiltonian defined *************************** ++ *************************************************************************** ++ ++ * Print level: 2 ++ * Barysz-Sadlej-Snijders Hamiltonian. Type code: 109 ++ Reference: ++ H. J. Aa. Jensen and M. Ilias, ++ "Two-component relativistic methods based on the quaternion modified Dirac equation. I: ++ from Douglas-Kroll-Hess second order method to the infinite order two-component method.", ++ J. Chem. Phys., in preparation. ++ * Running in two-component mode + with the following modifications: + - Spin-orbit interactions neglected + * Default integral flags passed to all modules +- - LL-integrals: T +- - LS-integrals: T +- - SS-integrals: T +- - GT-integrals: F ++ - LL-integrals: 1 ++ - LS-integrals: 0 ++ - SS-integrals: 0 ++ - GT-integrals: 0 ++ * Comparing eigenvalues between parent 4c and derived 2c one-electron Hamiltonians. + * Basis set: + - uncontracted large component basis set +- - uncontracted small component basis set +- +- +- Information about the restricted kinetic balance scheme: +- * Default RKB projection: +- 1: Pre-projection in scalar basis +- 2: Removal of unphysical solutions (via diagonalization of free particle Hamiltonian) +- +- +- ********************************************************************************* +- *************************** Memory required by HERMIT *************************** +- ********************************************************************************* +- +-=========================================================================== +- Maximum memory load for two-electron integral processing: +-=========================================================================== +- * LL-integrals: +- 2(X Lp) 2(X Lp) 2(X Lp) 2(X Lp) 19958 +- * SL-integrals: +- 8(X Sd) 6(X Sp) 2(X Lp) 2(X Lp) 74456 +- * SS-integrals: +- 8(X Sd) 6(X Sp) 8(X Sd) 6(X Sp) 274736 + + +- ************************************************************************** +- ************************** Wave function module ************************** +- ************************************************************************** ++ ************************************************************************** ++ ************************** Wave function module ************************** ++ ************************************************************************** ++ ++ Wave function types requested (in input order): ++ HF ++ RELCCSD ++ LUCITA + +- Jobs in this run (in execution order): ++ Wave function jobs in execution order (expanded): + * Hartree-Fock calculation + * Run RELCCSD code + * Run LUCITA CI code + =========================================================================== +- DHFINP: Set-up for Hartree-Fock calculation: ++ *SCF: Set-up for Hartree-Fock calculation: + =========================================================================== + * Number of fermion irreps: 1 +- * Closed shell DHF calculation with 10 electrons in +- 5 orbitals in Fermion irrep 1 +- * Bare nucleus screening correction used for start guess +- - INFO: bare nucleus correction disabled becauseabs(molecular charge) .gt. 2 ++ * Closed shell SCF calculation with 10 electrons in 5 orbitals. ++ - INFO: bare nucleus correction disabled because abs(molecular charge) .gt. 10 ++ * Sum of atomic potentials used for start guess + * General print level : 0 +- ***** TRIAL FUNCTION ***** ++ ++ ***** INITIAL TRIAL SCF FUNCTION ***** + * Trial vectors read from file DFCOEF +- ***** CONVERGENCE CRITERIA ***** ++ * Scaling of active-active block correction to open shell Fock operator 0.500000 ++ to improve convergence (default value). ++ The final open-shell orbital energies are recalculated with 1.0 scaling, ++ such that all occupied orbital energies correspond to Koopmans' theorem ionization energies. ++ ++ ***** SCF CONVERGENCE CRITERIA ***** + * Convergence on norm of error vector (gradient). +- Desired convergence:1.000E-10 +- Allowed convergence:1.000E-07 ++ Desired convergence:1.000D-10 ++ Allowed convergence:1.000D-07 + + ***** CONVERGENCE CONTROL ***** + * Fock matrix constructed using differential density matrix + with optimal parameter. + * DIIS (in MO basis) +- * DIIS will be activated when convergence reaches : 1.00E+20 ++ * DIIS will be activated when convergence reaches : 1.00D+20 + - Maximum size of B-matrix: 10 + * Damping of Fock matrix when DIIS is not activated. + Weight of old matrix : 0.250 + * Maximum number of SCF iterations : 50 +- * Quadratic convergent Hartree-Fock +- - Maximum number of macro iterations: 25 +- - Maximum number of micro iterations: 25 ++ * No quadratic convergent Hartree-Fock + * Contributions from 2-electron integrals to Fock matrix: + LL-integrals. ++ ---> accepted user's setting through .INTFLG ++ * NB!!! No e-p rotations in 2nd order optimization. + ***** OUTPUT CONTROL ***** + * Only electron eigenvalues written out. ++=========================================================================== ++ **RELCC: Set-up for Coupled Cluster calculations ++=========================================================================== ++=========================================================================== ++ TRPINP: Property integral transformation ++=========================================================================== ++ * Print level: 0 ++ *The following operators will be transformed: ++--------------------------------------------------------------------------- + + + +@@ -613,7 +743,6 @@ + No explicit orbitals specified for index 2 + No explicit orbitals specified for index 3 + No explicit orbitals specified for index 4 +- * Size of batches for strategy 4 (parallel only): -1 + + + ******************************************************************************** +@@ -622,407 +751,540 @@ + + + +- ************************************************************************* +- ************************ End of input processing ************************ +- ************************************************************************* ++ ************************************************************************* ++ ************************ End of input processing ************************ ++ ************************************************************************* ++ ++ ++ ++ *************************************************************************** ++ ****************** Output from MOLECULE input processing ****************** ++ *************************************************************************** ++ ++ ++ ++ Title Cards ++ ----------- ++ ++ X ++ X ++ ++ Coordinates are entered in Angstroms and converted to atomic units. ++ - Conversion factor : 1 bohr = 0.52917721 A ++ ++ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 ++ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 ++ ++ ++ SYMADD: Detection of molecular symmetry ++ --------------------------------------- ++ ++ Symmetry test threshold: 5.00E-06 ++ ++ The molecule has been centered at center of mass ++ ++ Symmetry point group found: C(oo,v) + ++ The following symmetry elements were found: X Y + + +- Generating Lowdin matrix: +- ------------------------- ++ Symmetry Operations ++ ------------------- + +- L A1 * Deleted: 1(Proj: 1, Lindep: 0) +- L B1 * Deleted: 0(Proj: 0, Lindep: 0) +- L B2 * Deleted: 0(Proj: 0, Lindep: 0) +- L A2 * Deleted: 0(Proj: 0, Lindep: 0) +- S A1 * Deleted: 4(Proj: 4, Lindep: 0) +- S B1 * Deleted: 1(Proj: 1, Lindep: 0) +- S B2 * Deleted: 1(Proj: 1, Lindep: 0) +- S A2 * Deleted: 0(Proj: 0, Lindep: 0) ++ Symmetry operations: 2 + + +- *** Output from MAKE_DKH *** +- ---------------------------- + +-* MAKE_DKH: Applied the restricted kinetic balance ! ++ SYMGRP:Point group information ++ ------------------------------ + +- MAKE_DKH: All consistency checks are included for IPRHAM= 2 ++Full group is: C(oo,v) ++Represented as: C2v + ++ * The point group was generated by: + +-MAKE_DKH: Order of Douglas-Kroll : 9 ++ Reflection in the yz-plane ++ Reflection in the xz-plane + +-MAKE_DKH: spinfree "before" +- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.3E+04 +- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 8.4E+07 +- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 8.4E+07 +- LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.2E+08 ++ * Group multiplication table + +- Free particle matrix in the ON basis "theta" in fermion corep 1/1 +- *** Norm of the i,j,k imag. parts *** :0.000000E+00 ++ | E C2z Oxz Oyz ++ -----+-------------------- ++ E | E C2z Oxz Oyz ++ C2z | C2z E Oyz Oxz ++ Oxz | Oxz Oyz E C2z ++ Oyz | Oyz Oxz C2z E + ++ * Character table + +- MAKE_DKH: Diagonalizing (Jacobi) the real part of the FP matrix in the ON "theta" basis ! ++ | E C2z Oxz Oyz ++ -----+-------------------- ++ A1 | 1 1 1 1 ++ B1 | 1 -1 1 -1 ++ B2 | 1 -1 -1 1 ++ A2 | 1 1 -1 -1 + ++ * Direct product table + ++ | A1 B1 B2 A2 ++ -----+-------------------- ++ A1 | A1 B1 B2 A2 ++ B1 | B1 A1 A2 B2 ++ B2 | B2 A2 A1 B1 ++ A2 | A2 B2 B1 A1 + +- MAKE_DKH: Free particle (in ON basis "theta") eigenvalues : +- ----------------------------------------------------------- + +- *** Fermion corep 1/ 1 +-Shell no FP eigval FP eigval+2c^2 bos.symm. diff. +- 1 -21 -0.129732E+06 -0.110953E+06 1 -.4802E-09 +- 2 -20 -0.836934E+05 -0.649145E+05 1 -.2256E-09 +- 3 -19 -0.836934E+05 -0.649145E+05 3 -.1892E-09 +- 4 -18 -0.836934E+05 -0.649145E+05 2 -.1892E-09 +- 5 -17 -0.822138E+05 -0.634350E+05 1 -.9895E-09 +- 6 -16 -0.545585E+05 -0.357796E+05 1 0.8004E-10 +- 7 -15 -0.510946E+05 -0.323157E+05 1 -.1128E-09 +- 8 -14 -0.510946E+05 -0.323157E+05 2 -.1364E-09 +- 9 -13 -0.510946E+05 -0.323157E+05 3 -.1364E-09 +- 10 -12 -0.425134E+05 -0.237345E+05 1 -.5957E-09 +- 11 -11 -0.404803E+05 -0.217014E+05 1 -.1096E-09 +- 12 -10 -0.404803E+05 -0.217014E+05 4 -.1501E-10 +- 13 -9 -0.404803E+05 -0.217014E+05 2 -.1546E-10 +- 14 -8 -0.404803E+05 -0.217014E+05 3 -.8640E-11 +- 15 -7 -0.404803E+05 -0.217014E+05 1 -.8640E-11 +- 16 -6 -0.396666E+05 -0.208877E+05 1 -.1378E-09 +- 17 -5 -0.396666E+05 -0.208877E+05 2 -.2674E-09 +- 18 -4 -0.396666E+05 -0.208877E+05 3 -.2674E-09 +- 19 -3 -0.379967E+05 -0.192179E+05 1 -.7850E-09 +- 20 -2 -0.375600E+05 -0.187811E+05 1 -.1429E-08 +- 21 -1 -0.375581E+05 -0.187792E+05 1 -.8020E-09 +- 22 1 0.346467E+00 0.187792E+05 1 -.8020E-09 +- 23 2 0.223659E+01 0.187811E+05 1 -.1429E-08 +- 24 3 0.439003E+03 0.192179E+05 1 -.7850E-09 +- 25 4 0.210882E+04 0.208877E+05 3 -.2674E-09 +- 26 5 0.210882E+04 0.208877E+05 2 -.2674E-09 +- 27 6 0.210882E+04 0.208877E+05 1 -.1378E-09 +- 28 7 0.292258E+04 0.217014E+05 2 -.8640E-11 +- 29 8 0.292258E+04 0.217014E+05 4 -.8640E-11 +- 30 9 0.292258E+04 0.217014E+05 3 -.1546E-10 +- 31 10 0.292258E+04 0.217014E+05 1 -.1501E-10 +- 32 11 0.292258E+04 0.217014E+05 1 -.1096E-09 +- 33 12 0.495565E+04 0.237345E+05 1 -.5957E-09 +- 34 13 0.135369E+05 0.323157E+05 3 -.1364E-09 +- 35 14 0.135369E+05 0.323157E+05 2 -.1364E-09 +- 36 15 0.135369E+05 0.323157E+05 1 -.1128E-09 +- 37 16 0.170007E+05 0.357796E+05 1 0.8004E-10 +- 38 17 0.446561E+05 0.634350E+05 1 -.9895E-09 +- 39 18 0.461356E+05 0.649145E+05 3 -.1892E-09 +- 40 19 0.461356E+05 0.649145E+05 2 -.1892E-09 +- 41 20 0.461356E+05 0.649145E+05 1 -.2256E-09 +- 42 21 0.921740E+05 0.110953E+06 1 -.4802E-09 ++ ************************** ++ *** Output from DBLGRP *** ++ ************************** + +- MAKE_DKH: The average difference for e-p pairing of all +-free particle eigenvalues in fermion symmetry 1/1 0.664817E-09 ++ * One fermion irrep: E1 ++ * Real group. NZ = 1 ++ * Direct product decomposition: ++ E1 x E1 : A1 + A2 + B1 + B2 + + +- MAKE_DKH: Full unit =C+.S.C matrix +- ----------------------------------------- ++ Spinor structure ++ ---------------- + +-* Fermion irp no.1/1 + +- Sum of diagonal elements /N: 0.10000E+01 +- Sum of off-diagonal elements : 0.36613E-13 ++ * Fermion irrep no.: 1 ++ La | A1 (1) A2 (2) | ++ Sa | A2 (1) A1 (2) | ++ Lb | B1 (3) B2 (4) | ++ Sb | B2 (3) B1 (4) | + + +- MAKE_DKH: Diagonal =A+.A matrix +- ---------------------------------------- ++ Quaternion symmetries ++ --------------------- + +-* Fermion irp no.1/1 ++ Rep T(+) ++ ----------------------------- ++ A1 1 ++ B1 j ++ B2 k ++ A2 i + +- Sum of diagonal elements /N : 0.84270E+00 +- Sum of off-diagonal elements : 0.12334E-14 ++ QM-QM nuclear repulsion energy : 21.167088332000 + +- MAKE_DKH: "A" kinem. electr. factors; ferm irp:1/1 + +- A^2_ovlp A^2_calc diff; + +- 0.9999907753 0.9999907753 0.52180E-14 +- 0.9999404563 0.9999404563 0.99920E-14 +- 0.9885782673 0.9885782673 0.21094E-14 +- 0.9495199724 0.9495199724 0.75495E-14 +- 0.9495199724 0.9495199724 0.75495E-14 +- 0.9495199724 0.9495199724 0.85487E-14 +- 0.9326639752 0.9326639752 0.00000E+00 +- 0.9326639752 0.9326639752 0.00000E+00 +- 0.9326639752 0.9326639752 0.00000E+00 +- 0.9326639752 0.9326639752 -.11102E-15 +- 0.9326639752 0.9326639752 0.33307E-15 +- 0.8956024566 0.8956024566 0.88818E-15 +- 0.7905530164 0.7905530164 0.23315E-14 +- 0.7905530164 0.7905530164 0.23315E-14 +- 0.7905530164 0.7905530164 0.72164E-14 +- 0.7624242951 0.7624242951 0.17986E-13 +- 0.6480166494 0.6480166494 0.00000E+00 +- 0.6446430762 0.6446430762 -.88818E-15 +- 0.6446430762 0.6446430762 -.88818E-15 +- 0.6446430762 0.6446430762 0.39968E-14 +- 0.5846254366 0.5846254366 0.72164E-14 ++ Isotopic Masses ++ --------------- + +- DIFFERENCES A^2_ovlp-A^2_calc/N :0.405496E-14 ++ X 201.970617 ++ H 1.007825 + +- MAKE_DKH: Elim. spin-orbit comp. "BEFORE" from full H1 in TBUF ++ Total mass: 202.978442 amu ++ Natural abundance: 29.856 % + ++ Center-of-mass coordinates (a.u.): 0.000000000000000 0.000000000000000 0.000000000000000 + + +- CHECK_R: A * R - B zero matrix +- ------------------------------ ++ Atoms and basis sets ++ -------------------- + +- * Fermion irp 1/1 +- CHECK_R: Norm of A.R - B:.115394974462E-16 ++ Number of atom types : 2 ++ Total number of atoms: 2 + ++ label atoms charge prim cont basis ++ ---------------------------------------------------------------------- ++ X 1 80 20 20 L - [5s3p1d|5s3p1d] ++ H 1 1 2 2 L - [2s|2s] ++ ---------------------------------------------------------------------- ++ 22 22 L - large components ++ 55 55 S - small components ++ ---------------------------------------------------------------------- ++ total: 2 81 77 77 + +- CHECK_R: Final H(pp)*R+H(ep)-R*H(ee)-R*H(pe)*R +- ---------------------------------------------- ++ Cartesian basis used. ++ Threshold for integrals (to be written to file): 1.00D-15 + +- Fermion corep 1/1 * norm: .149366743390E-09 + ++ References for the basis sets ++ ----------------------------- + +- U1CHECK: Unit U1+ * U1 matrix +- ----------------------------- ++ Atom type 1 2 ++ Basis set typed explicitly in input file + +- * fermion irp 1/1 + +- Sum of diagonal elements /N: 0.10000E+01 +- Sum of off-diagonal elements :-0.29210E-14 ++ Cartesian Coordinates (bohr) ++ ---------------------------- + ++ Total number of coordinates: 6 + +- U1CHECK: Again unit U1+ * U1 matrix +- ----------------------------------- + +- * fermion irp 1/1 ++ 1 X x 0.0000000000 ++ 2 y 0.0000000000 ++ 3 z 0.0187656701 + +- Sum of diagonal elements /N: 0.10000E+01 +- Sum of off-diagonal elements :-0.29213E-14 ++ 4 H x 0.0000000000 ++ 5 y 0.0000000000 ++ 6 z -3.7606865977 + +- U1CHECK: Elim. spin-orbit comp. "BEFORE" from H1(ee) in |k> + + ++ Cartesian coordinates in XYZ format (Angstrom) ++ ---------------------------------------------- + +- U1CHECK: 2 times constructed H2c in ON |k_e> basis +- -------------------------------------------------- ++ 2 ++ ++X 0.0000000000 0.0000000000 0.0099303649 ++H 0.0000000000 0.0000000000 -1.9900696351 + +- Difference between 2 H2c in |k_e> basis: 0.556080026E-10 + ++ Symmetry Coordinates ++ -------------------- + +- MAKE_DKH: *** 4c/2c electronic eigenvalues in |k> basis *** +- ----------------------------------------------------------- ++ Number of coordinates in each symmetry: 2 2 2 0 + +- *** Fermion corep 1 + +- 4c |k> 2c |k> diff 4c-2c ++ Symmetry A1 ( 1) + +- 1 -3236.0719838003 -3236.0719838004 0.10004E-10 +- 2 -666.1102369681 -666.1102369681 -0.70486E-11 +- 3 -484.6930272186 -484.6930272186 -0.81855E-11 +- 4 -484.6930119987 -484.6930119987 -0.88107E-11 +- 5 -484.6930119987 -484.6930119987 0.42064E-11 +- 6 -21.6367704194 -21.6367704194 -0.17444E-11 +- 7 -20.3646920050 -20.3646920050 0.32827E-11 +- 8 860.2027281682 860.2027281682 0.21600E-11 +- 9 860.2027332163 860.2027332163 -0.92086E-11 +- 10 860.2027332163 860.2027332163 -0.69349E-11 +- 11 860.2027483566 860.2027483566 -0.11482E-10 +- 12 860.2027483566 860.2027483566 -0.17394E-10 +- 13 6589.3364114013 6589.3364114013 0.20009E-10 +- 14 6589.3364145579 6589.3364145579 0.81855E-11 +- 15 6589.3364145580 6589.3364145580 0.18190E-11 +- 16 6779.9912032733 6779.9912032733 -0.27285E-11 +- 17 26566.1471385053 26566.1471385053 0.21828E-10 +- 18 29535.0133983962 29535.0133983963 -0.43656E-10 +- 19 29535.0133990459 29535.0133990459 0.54570E-10 +- 20 29535.0133990460 29535.0133990459 0.50932E-10 +- 21 59748.6160858676 59748.6160858674 0.17462E-09 ++ 1 X z 3 ++ 2 H z 6 + + +- LOWDHAO: Full(L+S) unit C+ * S * C matrix +- ----------------------------------------- ++ Symmetry B1 ( 2) + +- * fermion corep 1/1 ++ 3 X x 1 ++ 4 H x 4 + +- Sum of diagonal elements /N: 0.10000E+01 +- Sum of off-diagonal elements : 0.57558E-13 + ++ Symmetry B2 ( 3) + +- LOWDHAO: (LL) unit C+ * S * C matrix +- ------------------------------------ ++ 5 X y 2 ++ 6 H y 5 + +- *** Fermion corep 1/1 + +- Sum of diagonal elements /N: 0.10000E+01 +- Sum of off-diagonal elements : 0.21513E-13 ++ Interatomic separations (in Angstroms): ++ --------------------------------------- + +- LOWDHAO: Transforming H2c from AO "xhi" to ON Lowdin_L basis ++ X H + +- LOWDHAO: Difference between various constructed H2c in AO basis: 0.33913E+04 ++ X 0.000000 ++ H 2.000000 0.000000 + + +- Difference between various constructed H2c in Lowdin basis: 0.52900E+04 + + ++ Bond distances (angstroms): ++ --------------------------- + +- LOWDHAO: Electr. eigenv. of H(2c)/H(4c) in "theta" basis +- -------------------------------------------------------- ++ atom 1 atom 2 distance ++ ------ ------ -------- ++ bond distance: H X 2.000000 + +- *** Fermion corep 1 + +- -21 -163745.9628988874 +- -20 -109766.4091627979 +- -19 -98263.9166309379 +- -18 -97660.2507125821 +- -17 -97660.2507121498 +- -16 -62699.0373156405 +- -15 -61337.8251471301 +- -14 -56735.8818256817 +- -13 -56735.8818235711 +- -12 -46739.5121078201 +- -11 -43934.8520198212 +- -10 -43613.6808107422 +- -9 -43613.6808034596 +- -8 -42251.1320214283 +- -7 -42251.1320136060 +- -6 -42251.1319979688 +- -5 -41671.9396359513 +- -4 -41671.9396210424 +- -3 -39401.3294452374 +- -2 -37582.2335071497 +- -1 -37579.6683961926 +- 1 -3236.0719838003 -3236.0719838003 0.40927E-11 +- 2 -666.1102369744 -666.1102369681 0.63131E-08 +- 3 -621.6459032252 -484.6930272186 0.13695E+03 +- 4 -417.4757122056 -484.6930119987 -0.67217E+02 +- 5 -417.4757012483 -484.6930119987 -0.67217E+02 +- 6 -21.6367704054 -21.6367704193 -0.13957E-07 +- 7 -20.3646919717 -20.3646920050 -0.33277E-07 +- 8 803.0610555687 860.2027281682 0.57142E+02 +- 9 803.0610694840 860.2027332163 0.57142E+02 +- 10 899.5011687780 860.2027332163 -0.39298E+02 +- 11 899.5011750728 860.2027483566 -0.39298E+02 +- 12 899.5011876600 860.2027483566 -0.39298E+02 +- 13 5622.9859361077 6589.3364114013 0.96635E+03 +- 14 6779.9912032728 6589.3364145579 -0.19065E+03 +- 15 7094.0397325779 6589.3364145579 -0.50470E+03 +- 16 7094.0397349051 6779.9912032733 -0.31405E+03 +- 17 26043.2377394187 26566.1471385053 0.52291E+03 +- 18 26566.1471385052 29535.0133983962 0.29689E+04 +- 19 31514.7993417130 29535.0133990459 -0.19798E+04 +- 20 31514.7993422125 29535.0133990459 -0.19798E+04 +- 21 59748.6160858669 59748.6160858677 0.76398E-09 + +- MAKE_DKH:Two-component BSS mode - positronic shells deleted ! ++ Nuclear repulsion energy : 21.167088332000 Hartree + + +- GMOTRA: BSS relativistic atomic integrals and picture change +- transformation matrix were written to the new file BSSMAT. ++ Nuclear contribution to dipole moments ++ -------------------------------------- + ++ au Debye + +- ********************************************************************** +- ************************* Orbital dimensions ************************* +- ********************************************************************** ++ z -2.25943299 -5.74295899 + +-No. of electronic orbitals (NESH): 21 +-No. of positronic orbitals (NPSH): 0 +-Total no. of orbitals (NORB): 21 ++ 1 Debye = 2.54177000 a.u. + ++Total time used in ONEGEN (CPU) 0.00263200s and (WALL) 0.00324607s + +- WARNING : linear symmetry is not implemented for spinfree or Levy-Leblond yet +- continue calculation in lower symmetry + ++ Generating Lowdin canonical matrix: ++ ----------------------------------- + +- ********************************************************************************************** +- ************************* Two-component relativistic HF calculations ************************* +- ********************************************************************************************** ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 2.6D-02 ++ L A1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.26E-01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 ++ L B1 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 ++ L B2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.0D+00 ++ L A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.10E+01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 ++ S A1 * Deleted: 4(Proj: 4, Lindep: 0) Smin: 0.40E-01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 ++ S B1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.40E-01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.0D-02 ++ S B2 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.40E-01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 6.0D-01 ++ S A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.60E+00 + + +- ONEFCK: BSS transformed one-electron relativistic integrals were read from the file BSSMAT. ++ *** Output from MAKE_BSS *** ++ ---------------------------- + +-*** INFO *** No trial vectors found. Using bare nucleus approximation for initial trial vectors. + +-########## START ITERATION NO. 1 ########## Sun Dec 5 16:41:19 2004 + +-It. 1 -10691.35545564 1.00E+20 0.00E+00 0.00E+00 0.00199999s Bare nuc. Sun Dec 5 ++ *** Output from the EXTR_BSS_INFO routine *** ++ --------------------------------------------- + +-########## START ITERATION NO. 2########## Sun Dec 5 16:41:19 2004 ++ * Transforming the one-electron DIRAC bare nucleus operator. ++ * Order of the Douglas-Kroll-Hess/BSS transformation :...infinite ! ++ * Applied the preliminary free-particle ("k") basis transformation (two-step method). ++ * R-equation solving applied : YR-equation 2 (Trond) ++ * Elimination of spin-orbit terms from the Dirac bare nuclei in RKB/"k" basis (spinfree "BEFORE / AT THE BEGINNING") ++ * AMFI contribution is NOT included. ++ * Prepare the picture-change transformation matrixes ++ - special case - spin-free ++ * I2COFK parameter for H2c specification set to:1 + ++ MAKE_BSS: 4c Lowdin AO to MO transf. matrix is written to the BSSMAT file. + +-* GETGAB: label "GABAOXXX" not found; calling GABGEN. ++ ++ Output from MODHAM ++ ------------------ ++ ++ * Applied strict kinetic balance ! ++ ++ HANDLE_RKB: RKB transf. matrix (TMAT, basic) has been written to the BSSMAT file. ++ ++ HANDLE_RKB: BSSMAT file - EOFLABEL added. ++ ++ GET_A_FAC: Average differences for A-factors (fsym 1/1) : 0.45836351D-14 ++ ++ R matrix (in ON basis) was read from BSSMAT into VMAT. ++ ++ H2CFINAL: H1AO_DK ++ ++ AO_LL elements were written into the BSSMAT file, EOFLABEL renewed. ++ ++ GETPCTMAT: U1_ONBAS (4c ON->2c ON) read into TBUF. ++ ++ ++ Output from LINSYM ++ ------------------ ++ ++ ++ Parity MJ Functions(total) Functions(LC) Functions(SC) ++ 1 2/2 8 8 0 ++ 1 4/2 2 2 0 ++ ++ ++ CMP_EIGVAL: Eigenvalues of H4c and H2c Hamiltonians - comparison ++ ----------------------------------------------------------------- ++ ++ *** Fermion corep 1/1 ++ ++ -21 -163745.9628958011 ++ -20 -101498.5164538892 ++ -19 -101498.5164532745 ++ -18 -101498.5164532736 ++ -17 -98263.9166308309 ++ -16 -62699.0373156246 ++ -15 -58261.8837181770 ++ -14 -58261.8837150353 ++ -13 -58261.8837150346 ++ -12 -46739.5121078193 ++ -11 -42795.4291439501 ++ -10 -42795.4291401592 ++ -9 -42795.4291401592 ++ -8 -42795.4291288378 ++ -7 -42795.4291288378 ++ -6 -42461.8986879892 ++ -5 -42461.8986541794 ++ -4 -42461.8986541793 ++ -3 -39401.3294452367 ++ -2 -37582.2335096555 ++ -1 -37579.6684238590 ++ 1 -3236.0719837237 -3233.2186407425 -0.28533D+01 ++ 2 -666.1102369328 -664.5651063909 -0.15451D+01 ++ 3 -484.6930272181 -484.6930272173 -0.77148D-09 ++ 4 -484.6930119982 -21.6367703419 -0.46306D+03 ++ 5 -484.6930119982 -20.3646916349 -0.46433D+03 ++ 6 -21.6367704194 0.0000000000 -0.21637D+02 ++ 7 -20.3646920050 0.0000000000 -0.20365D+02 ++ 8 860.2027281682 0.0000000000 0.86020D+03 ++ 9 860.2027332163 0.0000000000 0.86020D+03 ++ 10 860.2027332164 0.0000000000 0.86020D+03 ++ 11 860.2027483566 0.0000000000 0.86020D+03 ++ 12 860.2027483566 0.0000000000 0.86020D+03 ++ 13 6589.3364114109 0.0000000000 0.65893D+04 ++ 14 6589.3364145675 0.0000000000 0.65893D+04 ++ 15 6589.3364145676 0.0000000000 0.65893D+04 ++ 16 6779.9912035175 0.0000000000 0.67800D+04 ++ 17 26566.1471391791 6286.2328868840 0.20280D+05 ++ 18 29535.0133986390 6589.3364114112 0.22946D+05 ++ 19 29535.0133992886 21540.9186642361 0.79941D+04 ++ 20 29535.0133992886 29535.0133986389 0.64972D-06 ++ 21 59748.6160887879 40911.9536790837 0.18837D+05 ++ ++ ++ PROP2BSS: 2comp. operator (indxpr= 1) P2C_0001->Overlap matrix was written to the BSSMAT file in LL block. ++ ...operator was NOT picture change transformed ++ ++ PROP2BSS: 2comp. operator (indxpr= 2) P2C_0002->Nuc. attraction was written to the BSSMAT file in LL block. ++ ...operator was NOT picture change transformed ++ ++ PROP2BSS: 2comp. operator (indxpr= 3) P2C_0003->Beta matrix was written to the BSSMAT file in LL block. ++ ...operator was NOT picture change transformed ++ ++ PROP2BSS: 2comp. operator (indxpr= 4) P2C_0004->Kinetic energy was written to the BSSMAT file in LL block. ++ ...operator was NOT picture change transformed ++ ++ PROP2BSS: 2comp. operator (indxpr= 5) P2C_0005->Orbital z-moment was written to the BSSMAT file in LL block. ++ ...operator was NOT picture change transformed ++ ++ PROP2BSS: 2comp. operator (indxpr= 6) P2C_0006->Spin z-momentum was written to the BSSMAT file in LL block. ++ ...operator was picture change transformed ++ ++ PROP2BSS: EOFLABEL was renewed after saving all 2c operators into BSSMAT. ++ ++ MAKE_H2C: Two-component BSS mode - positronic shells deleted ! ++ ++ Coordinates are entered in Angstroms and converted to atomic units. ++ - Conversion factor : 1 bohr = 0.52917721 A ++ ++ Nuclear Gaussian exponent for atom of charge 80.000 : 1.4011786759D+08 ++ Nuclear Gaussian exponent for atom of charge 1.000 : 2.1248235902D+09 ++ ++ ++ SYMADD: Detection of molecular symmetry ++ --------------------------------------- ++ ++ Symmetry test threshold: 5.00E-06 ++ ++ The molecule has been centered at center of mass ++ ++ Symmetry point group found: C(oo,v) ++ ++ The following symmetry elements were found: X Y ++ ++ ++ Nuclear contribution to dipole moments ++ -------------------------------------- ++ ++ au Debye ++ ++ z -2.25943299 -5.74295899 ++ ++ 1 Debye = 2.54177000 a.u. ++ ++Total time used in ONEGEN (CPU) 0.00082800s and (WALL) 0.00096107s ++ ++ ++ Generating Lowdin canonical matrix: ++ ----------------------------------- ++ ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 2.6D-02 ++ L A1 * Deleted: 1(Proj: 1, Lindep: 0) Smin: 0.26E-01 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 ++ L B1 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 4.5D-01 ++ L B2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.45E+00 ++ LOWGEN: Smallest ".LINDEP" test value of a kept orbital: 1.0D+00 ++ L A2 * Deleted: 0(Proj: 0, Lindep: 0) Smin: 0.10E+01 ++ ++ ++ ********************************************************************** ++ ************************* Orbital dimensions ************************* ++ ********************************************************************** ++ ++No. of positive energy orbitals (NESH): 21 ++No. of negative energy orbitals (NPSH): 0 ++Total no. of orbitals (NORB): 21 ++ ++ ++ ******************************************************************************* ++ ************** Two-component BSS/DKH relativistic HF calculation ************** ++ ******************************************************************************* ++ ++ ++ GETH2CAO: asked for 2c Hamiltonian (param.I2COFK=7):H2CAO_LL ++ ++*** INFO *** No trial vectors found. ++ Using bare nucleus approximation for initial trial vectors. ++ Improved by a sum of atomic screening potentials. ++ ++ ++########## START ITERATION NO. 1 ########## Mon Oct 5 14:12:56 2020 ++ ++E_HOMO...E_LUMO, symmetry 1: 5 -58.86032 6 -0.38910 ++ ++=> Calculating sum of orbital energies ++It. 1 -6346.607026159 0.00D+00 0.00D+00 0.00D+00 0.00847100s Atom. scrpot Mon Oct 5 ++ ++########## START ITERATION NO. 2 ########## Mon Oct 5 14:12:56 2020 ++ ++ ++* GETGAB: label "GABAO1XX" not found; calling GABGEN. + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 1.01% 8.21% 0.00% 0.00% 0.01499800s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.08498700s ++SOfock:LL 1.00D-12 0.00% 7.73% 0.09% 0.00% 0.00275700s ++E_HOMO...E_LUMO, symmetry 1: 5-257.42872 6 -18.99113 ++>>> Total wall time: 0.01686811s, and total CPU time : 0.00808700s + +-########## END ITERATION NO. 2 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 2 ########## Mon Oct 5 14:12:56 2020 + +-It. 2 -9503.967468302 -1.19E+03 4.19E+02 1.65E+02 0.08498700s LL Sun Dec 5 ++It. 2 -9505.548827855 3.16D+03 -1.88D+02 5.90D+01 0.01686811s LL Mon Oct 5 + +-########## START ITERATION NO. 3########## Sun Dec 5 16:41:19 2004 ++########## START ITERATION NO. 3 ########## Mon Oct 5 14:12:56 2020 + +- 3 *** Differential density matrix. DCOVLP = 1.0071 ++ 3 *** Differential density matrix. DCOVLP = 1.0024 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 1.01% 10.87% 1.38% 1.15% 0.01499799s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.02499600s ++SOfock:LL 1.00D-12 0.00% 11.69% 0.09% 0.00% 0.00269200s ++E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 ++>>> Total wall time: 0.01377892s, and total CPU time : 0.00509000s + +-########## END ITERATION NO. 3 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 3 ########## Mon Oct 5 14:12:56 2020 + +-It. 3 -9505.779736187 1.81E+00 -1.49E+00 4.38E-01 DIIS 2 0.02499600s LL Sun Dec 5 ++It. 3 -9505.779745785 2.31D-01 -5.25D-01 1.59D-01 DIIS 2 0.01377892s LL Mon Oct 5 + +-########## START ITERATION NO. 4########## Sun Dec 5 16:41:19 2004 ++########## START ITERATION NO. 4 ########## Mon Oct 5 14:12:56 2020 + + 4 *** Differential density matrix. DCOVLP = 1.0000 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 3.14% 24.01% 1.42% 1.34% 0.01399803s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.02399498s ++SOfock:LL 1.00D-12 2.01% 24.66% 1.59% 1.43% 0.00261200s ++E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 ++>>> Total wall time: 0.01277494s, and total CPU time : 0.00500000s + +-########## END ITERATION NO. 4 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 4 ########## Mon Oct 5 14:12:56 2020 + +-It. 4 -9505.779747494 1.13E-05 4.13E-03 9.22E-04 DIIS 3 0.02399498s LL Sun Dec 5 ++It. 4 -9505.779747270 1.49D-06 1.48D-03 4.27D-04 DIIS 3 0.01277494s LL Mon Oct 5 + +-########## START ITERATION NO. 5########## Sun Dec 5 16:41:19 2004 ++########## START ITERATION NO. 5 ########## Mon Oct 5 14:12:56 2020 + + 5 *** Differential density matrix. DCOVLP = 1.0000 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 8.83% 29.82% 3.56% 4.47% 0.01399800s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.02299702s ++SOfock:LL 1.00D-12 4.75% 35.03% 1.15% 0.89% 0.00241700s ++E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 ++>>> Total wall time: 0.01234078s, and total CPU time : 0.00468400s + +-########## END ITERATION NO. 5 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 5 ########## Mon Oct 5 14:12:56 2020 + +-It. 5 -9505.779747494 4.73E-11 1.80E-06 1.25E-06 DIIS 4 0.02299702s LL Sun Dec 5 ++It. 5 -9505.779747270 7.28D-12 8.55D-07 3.32D-07 DIIS 4 0.01234078s LL Mon Oct 5 + +-########## START ITERATION NO. 6########## Sun Dec 5 16:41:19 2004 ++########## START ITERATION NO. 6 ########## Mon Oct 5 14:12:56 2020 + + 6 *** Differential density matrix. DCOVLP = 1.0000 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 25.91% 22.46% 9.41% 19.31% 0.01099795s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.02099702s ++SOfock:LL 1.00D-12 27.41% 20.03% 1.83% 4.79% 0.00145400s ++E_HOMO...E_LUMO, symmetry 1: 5-257.50512 6 -18.99113 ++>>> Total wall time: 0.01191306s, and total CPU time : 0.00425000s + +-########## END ITERATION NO. 6 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 6 ########## Mon Oct 5 14:12:56 2020 + +-It. 6 -9505.779747494 5.46E-12 2.47E-09 1.12E-09 DIIS 5 0.02099702s LL Sun Dec 5 ++It. 6 -9505.779747270 7.28D-12 6.40D-10 3.18D-10 DIIS 4 0.01191306s LL Mon Oct 5 + +-########## START ITERATION NO. 7########## Sun Dec 5 16:41:19 2004 ++########## START ITERATION NO. 7 ########## Mon Oct 5 14:12:56 2020 + + 7 *** Differential density matrix. DCOVLP = 1.0000 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 39.05% 47.81% 1.35% 18.30% 0.00899899s +->>> Total wall time: 0.00000000s +->>> Total CPU-time : 0.01799697s ++SOfock:LL 1.00D-12 52.76% 41.39% 0.69% 16.32% 0.00108500s ++>>> Total wall time: 0.01100397s, and total CPU time : 0.00366200s + +-########## END ITERATION NO. 7 ########## Sun Dec 5 16:41:19 2004 ++########## END ITERATION NO. 7 ########## Mon Oct 5 14:12:56 2020 + +-It. 7 -9505.779747494 -1.46E-11 -2.91E-11 3.65E-11 DIIS 5 0.01799697s LL Sun Dec 5 ++It. 7 -9505.779747270 1.09D-11 8.73D-11 3.52D-11 DIIS 4 0.01100397s LL Mon Oct 5 + + +- SCF - CYCLE +- ----------- ++ SCF - CYCLE ++ ----------- + + * Convergence on norm of error vector (gradient). +- Desired convergence:1.000E-10 +- Allowed convergence:1.000E-07 ++ Desired convergence:1.000D-10 ++ Allowed convergence:1.000D-07 + + * ERGVAL - convergence in total energy + * FCKVAL - convergence in maximum change in total Fock matrix +@@ -1030,84 +1292,84 @@ + -------------------------------------------------------------------------------------------------------------------------------- + Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp + -------------------------------------------------------------------------------------------------------------------------------- +-It. 1 -10691.35545564 1.00E+20 0.00E+00 0.00E+00 0.00199999s Bare nuc. Sun Dec 5 +-It. 2 -9503.967468302 -1.19E+03 4.19E+02 1.65E+02 0.08498700s LL Sun Dec 5 +-It. 3 -9505.779736187 1.81E+00 -1.49E+00 4.38E-01 DIIS 2 0.02499600s LL Sun Dec 5 +-It. 4 -9505.779747494 1.13E-05 4.13E-03 9.22E-04 DIIS 3 0.02399498s LL Sun Dec 5 +-It. 5 -9505.779747494 4.73E-11 1.80E-06 1.25E-06 DIIS 4 0.02299702s LL Sun Dec 5 +-It. 6 -9505.779747494 5.46E-12 2.47E-09 1.12E-09 DIIS 5 0.02099702s LL Sun Dec 5 +-It. 7 -9505.779747494 -1.46E-11 -2.91E-11 3.65E-11 DIIS 5 0.01799697s LL Sun Dec 5 ++It. 1 -6346.607026159 0.00D+00 0.00D+00 0.00D+00 0.00847100s Atom. scrpot Mon Oct 5 ++It. 2 -9505.548827855 3.16D+03 -1.88D+02 5.90D+01 0.01686811s LL Mon Oct 5 ++It. 3 -9505.779745785 2.31D-01 -5.25D-01 1.59D-01 DIIS 2 0.01377892s LL Mon Oct 5 ++It. 4 -9505.779747270 1.49D-06 1.48D-03 4.27D-04 DIIS 3 0.01277494s LL Mon Oct 5 ++It. 5 -9505.779747270 7.28D-12 8.55D-07 3.32D-07 DIIS 4 0.01234078s LL Mon Oct 5 ++It. 6 -9505.779747270 7.28D-12 6.40D-10 3.18D-10 DIIS 4 0.01191306s LL Mon Oct 5 ++It. 7 -9505.779747270 1.09D-11 8.73D-11 3.52D-11 DIIS 4 0.01100397s LL Mon Oct 5 + -------------------------------------------------------------------------------------------------------------------------------- + * Convergence after 7 iterations. + * Average elapsed time per iteration: +- No 2-ints : 0.00000000s +- LL : 0.00000000s ++ No 2-ints : 0.00896692s ++ LL : 0.01311330s + + +- TOTAL ENERGY +- ------------ ++ TOTAL ENERGY ++ ------------ + +- Electronic energy : -9526.9468358256636 ++ Electronic energy : -9526.9468356019206 + + Other contributions to the total energy + Nuclear repulsion energy : 21.1670883320000 + + Sum of all contributions to the energy +- Total energy : -9505.7797474936633 ++ Total energy : -9505.7797472699203 + + +- Eigenvalues +- ----------- ++ Eigenvalues ++ ----------- + + + * Boson symmetry A1 + * Closed shell, f = 1.0000 +- -2941.25123226809 ( 2) -457.80721004705 ( 2) -257.50514000264 ( 2) ++ -2941.25123219522 ( 2) -457.80721001068 ( 2) -257.50514000229 ( 2) + * Virtual eigenvalues, f = 0.0000 +- -18.99112858231 ( 2) -17.71939273124 ( 2) 1077.52561948054 ( 4) 6952.39415603238 ( 2) 7144.19342453015 ( 2) +- 27000.48461267307 ( 2) 29976.56904017511 ( 2) 60216.83941698664 ( 2) ++ -18.99112858231 ( 2) -17.71939273125 ( 2) 1077.52561948049 ( 4) 6952.39415604068 ( 2) 7144.19342477336 ( 2) ++ 27000.48461334186 ( 2) 29976.56904041467 ( 2) 60216.83941990400 ( 2) + + * Boson symmetry B1 + * Closed shell, f = 1.0000 +- -257.50512395633 ( 2) ++ -257.50512395597 ( 2) + * Virtual eigenvalues, f = 0.0000 +- 1077.52562451694 ( 2) 6952.39415911992 ( 2) 29976.56904082861 ( 2) ++ 1077.52562451688 ( 2) 6952.39415912822 ( 2) 29976.56904106820 ( 2) + + * Boson symmetry B2 + * Closed shell, f = 1.0000 +- -257.50512395632 ( 2) ++ -257.50512395597 ( 2) + * Virtual eigenvalues, f = 0.0000 +- 1077.52562451694 ( 2) 6952.39415911992 ( 2) 29976.56904082861 ( 2) ++ 1077.52562451688 ( 2) 6952.39415912824 ( 2) 29976.56904106813 ( 2) + + * Boson symmetry A2 + * Virtual eigenvalues, f = 0.0000 +- 1077.52563962093 ( 2) ++ 1077.52563962086 ( 2) + + * Occupation in fermion symmetry E1 + * Inactive orbitals +- A1 A1 A1 B1 B2 ++ A1 A1 A1 B2 B1 + * Virtual orbitals +- A1 A1 A1 B1 B2 A1 A2 A1 B1 B2 A1 A1 A1 B2 B1 A1 ++ A1 A1 A1 B2 B1 A2 A1 A1 B1 B2 A1 A1 A1 B2 B1 A1 + +- Occupation of subblocks +- E1 : A1 B1 B2 A2 ++* Occupation of subblocks ++ E1 : A1 B1 B2 A2 + closed shells (f=1.0000): 3 1 1 0 + virtual shells (f=0.0000): 9 3 3 1 +-tot.num. of electr. shells: 12 4 4 1 ++tot.num. of pos.erg shells: 12 4 4 1 + + + * HOMO - LUMO gap: + + E(LUMO) : -18.99112858 au (symmetry A1 ) +- - E(HOMO) : -257.50512396 au (symmetry B2 ) ++ - E(HOMO) : -257.50512396 au (symmetry B1 ) + ------------------------------------------ + gap : 238.51399537 au + + + +- ************************************************************************** +- **************** Transformation to Molecular Spinor Basis **************** +- ************************************************************************** ++ ************************************************************************** ++ **************** Transformation to Molecular Spinor Basis **************** ++ ************************************************************************** + + + Written by Luuk Visscher, Jon Laerdahl & Trond Saue +@@ -1116,19 +1378,19 @@ + + + +- ************************************************************************ +- **************** Transformation of 2-electron integrals **************** +- ************************************************************************ ++ ************************************************************************ ++ **************** Transformation of 2-electron integrals **************** ++ ************************************************************************ + + +- Transformation started at : Sun Dec 5 16:41:19 2004 +- +-* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974749367786 +-* Heading : LiH Sun Dec 5 16:41:19 2004 +- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. +- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. +- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. +- Energy selection of active orbitals : -1000.00 < Eps. < ******** with a mininum gap of 0.1000 au. ++ Transformation started at : Mon Oct 5 14:12:56 2020 ++ ++* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974726990942 ++* Heading : LiH Mon Oct 5 14:12:56 2020 ++ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. ++ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. ++ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. ++ Energy selection of active orbitals : -1000.00 < Eps. < 999999.00 with a mininum gap of 0.1000 au. + + * Orbital ranges for 4-index transformation: + +@@ -1151,6 +1413,8 @@ + 2 3 4 5 6 7 8 9 10 11 12 13 + 14 15 16 17 18 19 20 21 + ++ (PAMTRA) Orbitals read from DFCOEF ++ + * Core orbital ranges for 2-index transformation: + + +@@ -1160,9 +1424,9 @@ + 1 + + +- ************************************************************************** +- **************** Transformation to Molecular Spinor Basis **************** +- ************************************************************************** ++ ************************************************************************** ++ **************** Transformation to Molecular Spinor Basis **************** ++ ************************************************************************** + + + Written by Luuk Visscher, Jon Laerdahl & Trond Saue +@@ -1171,90 +1435,95 @@ + + + +- ******************************************************************** +- **************** Transformation of core Fock matrix **************** +- ******************************************************************** ++ ******************************************************************** ++ **************** Transformation of core Fock matrix **************** ++ ******************************************************************** + + +- Transformation started at : Sun Dec 5 16:41:19 2004 ++ Transformation started at : Mon Oct 5 14:12:56 2020 + +-* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974749367786 +-* Heading : LiH Sun Dec 5 16:41:19 2004 ++* REACMO: Coefficients read from file DFCOEF - Total energy: -9505.77974726990942 ++* Heading : LiH Mon Oct 5 14:12:56 2020 + SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00E-12 15.59% 20.70% 0.75% 2.21% 0.01499799s ++SOfock:LL 1.00D-12 15.59% 20.70% 0.75% 2.21% 0.00235999s + +-* REAFCK: Fock matrix read from file DFFCK1 +-* Heading : LiH Sun Dec 5 16:41:19 2004 ++* REAFCK: Fock matrix read from file /kyukon/home/gent/430/vsc43020/DIRAC_scratch_directory/vsc43 ++* Heading : LiH Mon Oct 5 14:12:56 2020 + + +- Core energy (includes nuclear repulsion) : -6388.2074957273 +- - Electronic part : -6409.3745840593 +- - One-electron terms : -6469.3406420395 +- - Two-electron terms : 59.9660579802 ++ Core energy (includes nuclear repulsion) : -6388.2074955762 ++ - Electronic part : -6409.3745839082 ++ - One-electron terms : -6469.3406418861 ++ - Two-electron terms : 59.9660579779 + + + MOLFDIR file MRCONEE is written + - Integral class 1 : (LL|??) +- - Beginning with task 1 of 4 after 0.00 seconds +- and after 0.00 CPU-seconds +- - Beginning with task 2 of 4 after 0.00 seconds +- and after 0.05 CPU-seconds +- - Beginning with task 3 of 4 after 0.00 seconds +- and after 0.19 CPU-seconds +- - Beginning with task 4 of 4 after 0.00 seconds +- and after 0.35 CPU-seconds +- - Integral class 2 : (SS|??) +- - Integral class 3 : (LS|??) ++ - Beginning task 1 of 4 after 0. seconds and 0. CPU-seconds ++ - Beginning task 2 of 4 after 0. seconds and 0. CPU-seconds ++ - Beginning task 3 of 4 after 0. seconds and 0. CPU-seconds ++ - Beginning task 4 of 4 after 0. seconds and 0. CPU-seconds + * Screening statistics: + (LL|LL)ints : 0.00% + Total : 0.00% +- - Starting symmetrization after 0.00 seconds +- - Finished symmetrization after 0.00 seconds +- - MOLFDIR file MDCINT was written. + +------- Timing report (in CPU seconds) of module integral transformation ++ - Starting symmetrization after 0.03 seconds ++ - Finished symmetrization after 0.04 seconds ++ ++ - Binary file MDCINT was written. + +- Time in Initializing MS4IND fi 0.025 seconds +- Time in Computing+transform. i 0.431 seconds +- Time in Symmetrizing MO integr 0.038 seconds ++------ Timing report (in CPU seconds) of module integral transformation + ++ Time in Initializing MS4IND file 0.004 seconds ++ Time in Computing+transform. integral 0.029 seconds ++ Time in Symmetrizing MO integrals 0.004 seconds + +- Total wall time used in PAMTRA : 00:00:01 +- Total CPU time used in PAMTRA (master only) : 00:00:01 + ++ Total wall time used in PAMTRA : 00:00:00 ++ Total CPU time used in PAMTRA (master only) : 00:00:00 + ++ Transformation ended at : Mon Oct 5 14:12:56 2020 + +- Transformation ended at : Sun Dec 5 16:41:20 2004 + + ---< Process 1 of 1----< + + + + Relativistic Coupled Cluster program RELCCSD +- Version number 2.3 +- Version date September 2002 + + Written by : +- Lucas (Luuk) Visscher ++ Lucas Visscher + +- NASA Ames Research Center (1994) +- Rijks Universiteit Groningen (1995) +- Odense Universitet (1996-1997) +- Vrije Universiteit Amsterdam (1998-2002) ++ NASA Ames Research Center (1994) ++ Rijks Universiteit Groningen (1995) ++ Odense Universitet (1996-1997) ++ VU University Amsterdam (1998-present) + + + This module is documented in + - Initial implementation : L. Visscher, T.J. Lee and K.G. Dyall, J. Chem. Phys. 105 (1996) 8769. +- - Fock space formalism : L. Visscher, E. Eliav and U. Kaldor, J. Chem. Phys. 115 (2002) 9720. ++ - Fock Space (FSCC): L. Visscher, E. Eliav and U. Kaldor, J. Chem. Phys. 115 (2002) 9720. ++ - Intermediate Hamiltonian E. Eliav, M. J. Vilkas, Y. Ishikawa, and U. Kaldor, J. Chem. Phys. 122 (2005) 224113. + - Parallelization : M. Pernpointner and L. Visscher, J. Comp. Chem. 24 (2003) 754. ++ - MP2 expectation values : J.N.P. van Stralen, L. Visscher, C.V. Larsen and H.J.Aa. Jensen," Chem. Phys. 311 (2005) 81. ++ - CC expectation values : A. Shee, L. Visscher, and T. Saue, J. Chem. Phys. 145 (2016) 184107. ++ - EOM-IP/EA/EE energies : A. Shee, T. Saue, L. Visscher, and A.S.P. Gomes, J. Chem. Phys. 149 (2018) 174113. + + +- Today is : 5 Dec 04 +- The time is : 16:41:20 ++ Today is : 5 Oct 20 ++ The time is : 14:12:56 + + Initializing word-addressable I/O : the FORTRAN-interface is used with 16 KB records ++=========================================================================== ++ **RELCC: Set-up for Coupled Cluster calculations ++=========================================================================== ++ * General print level : 1 ++ NEL_F1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + +- Total memory available : 76 MB ++ Total memory available : 16384.00 MB 16.000 GB ++ ++ INFO: No old restart file(s) found! ++ + + Configuration in highest pointgroup + +@@ -1262,7 +1531,6 @@ + Spinor class : occupied 4 4 + Spinor class : virtual 16 16 + +- + Configuration in abelian subgroup + + A1 a B1 a B2 a A2 a A1 b B1 b B2 b A2 b +@@ -1271,6 +1539,7 @@ + + + Number of electrons : 8 ++ Total charge of the system : 71 + Number of virtual spinors : 32 + Complex arithmetic mode : F + Do integral sorting : T +@@ -1280,39 +1549,48 @@ + Debug information : F + Timing information : T + Print level : 1 +- Memory limit (MWord) : 10 ++ Memory limit (MWord) : 2048 + Interface used : DIRAC + + +- Memory for reading and sorting integrals : 157514 8-byte words +- Core used for calculating amplitudes : 34890 8-byte words +- Core used for in core evaluation of triples : 31100 8-byte words +- Core used for Gradient calculation : 9999998 8-byte words +- Core used for RPA calculation : 19533 8-byte words +- Memory for reading and sorting integrals : 1511114 8-byte words +- Core used for Fock space CCSD energies : 1511114 8-byte words +- Memory used for active modules : 157514 8-byte words ++ Leave after calculating the total memory demand : F ++ Memory for reading and sorting integrals : 256030 8-byte words ++ Core used for calculating amplitudes : 34680 8-byte words ++ Core used for in core evaluation of triples : 32644 8-byte words ++ Memory used for active modules : 256030 8-byte words + +- Expanding and sorting integrals to unique types : +- Type OOOO : 92 integrals +- Type VOOO : 768 integrals +- Type VVOO : 1512 integrals +- Type VOVO : 6912 integrals +- Type VOVV : 13440 integrals +- Type VVVV : 26272 integrals ++ Predicted RelCC memory demand: 1.95 MB ++ Predicted RelCC memory demand: 0.002 GB + +- Sorting of first 4 classes done. ++ Expanding and sorting integrals to unique types : ++ Type OOOO : 92 integrals ++ Type VOOO : 768 integrals ++ Type VVOO : 1512 integrals ++ Type VOVO : 6912 integrals ++ Type VOVV : 13440 integrals ++ Type VVVV : 26272 integrals ++ ++ Start sorting of integral classes at 5 Oct 20 14:12:56 ++ ++ ++ Sorting of first 4 classes done at 5 Oct 20 14:12:56 + + Need 1 passes to sort VOVV integrals +- VOVV sorting done. ++ ++ Pass 1 ended at 5 Oct 20 14:12:56 ++ ++ VOVV sorting done at 5 Oct 20 14:12:56 + + Need 1 passes to sort VVVV integrals +- VVVV sorting done. ++ ++ Pass 1 ended at 5 Oct 20 14:12:56 ++ ++ VVVV sorting done at 5 Oct 20 14:12:56 + + Reading Coulomb integrals : +- File date : 5Dec04 +- File time : 16:41:20 +- # of integrals 22964 ++ File date : 5 Oct 20 ++ File time : 14:12:56 ++ # of integrals 23323 + + Finished sorting of integrals + +@@ -1322,16 +1600,16 @@ + are given if above a treshold or if iprnt > 1 + + Spinor Abelian Rep. Energy Recalc. Energy +- O 1 1 A1 a -457.8072100470 -457.8072100470 +- O 2 2 A1 a -257.5051400026 -257.5051400026 +- O 1 3 B1 a -257.5051239563 -257.5051239563 +- O 1 4 B2 a -257.5051239563 -257.5051239563 +- O 1 5 A1 b -457.8072100470 -457.8072100470 +- O 2 6 A1 b -257.5051400026 -257.5051400026 +- O 1 7 B1 b -257.5051239563 -257.5051239563 +- O 1 8 B2 b -257.5051239563 -257.5051239563 ++ O 1 1 A1 a -457.8072100107 -457.8072100107 ++ O 2 2 A1 a -257.5051400023 -257.5051400023 ++ O 1 3 B1 a -257.5051239560 -257.5051239560 ++ O 1 4 B2 a -257.5051239560 -257.5051239560 ++ O 1 5 A1 b -457.8072100107 -457.8072100107 ++ O 2 6 A1 b -257.5051400023 -257.5051400023 ++ O 1 7 B1 b -257.5051239560 -257.5051239560 ++ O 1 8 B2 b -257.5051239560 -257.5051239560 + +- The diagonal elements of the recomputed Fock matrix (right column) are used in perturbation expressions. ++ The original energies (left column) are used in perturbation expressions. + + Use the perturbative values (MP2, CCSD[T]/(T)/-T) with care, especially + in open shell calculations because the orbitals need not always be +@@ -1339,11 +1617,11 @@ + The missing terms may be important ! + + +- Nuclear repulsion + core energy : -6388.207495727295282 +- Zero order electronic energy : -2460.645195924678774 +- First order electronic energy : -656.927055841711194 +- Electronic energy : -3117.572251766389854 +- SCF energy : -9505.779747493685136 ++ Nuclear repulsion + core energy : -6388.207495576216388 ++ Zero order electronic energy : -2460.645195849844640 ++ First order electronic energy : -656.927055843850439 ++ Electronic energy : -3117.572251693694852 ++ SCF energy : -9505.779747269911240 + + + Energy calculations +@@ -1354,10 +1632,10 @@ + + MP2 results + +- SCF energy : -9505.779747493685136 +- MP2 correlation energy : -0.221846247868006 +- Total MP2 energy : -9506.001593741553734 +- T1 diagnostic : 0.000000000000017 ++ SCF energy : -9505.779747269911240 ++ MP2 correlation energy : -0.221846247868917 ++ Total MP2 energy : -9506.001593517779838 ++ T1 diagnostic : 0.000000000000010 + + + CCSD options : +@@ -1367,49 +1645,48 @@ + + + NIT ENERGY RMS T1-DIAGN +- 0 -0.221846247868006 1.000000000000000 0.00000 +- 1 -0.222543090352100 0.000169723714323 0.00000 +- 2 -0.222547639799351 0.000001146914982 0.00000 +- 3 -0.222547639196545 0.000000002916755 0.00000 +- 4 -0.222547639201801 0.000000000004730 0.00000 +- 5 -0.222547639201729 0.000000000000043 0.00000 ++ 0 -0.221846247868917 1.000000000000000 0.00000 ++ 1 -0.222543090353008 0.000001024031689 0.00000 ++ 2 -0.222547639800258 0.000000012409001 0.00000 ++ 3 -0.222547639197452 0.000000000073854 0.00000 ++ 4 -0.222547639202709 0.000000000000097 0.00000 + + + CCSD results + +- SCF energy : -9505.779747493685136 +- CCSD correlation energy : -0.222547639201729 +- Total CCSD energy : -9506.002295132886502 +- T1 diagnostic : 0.000000727335985 +- Convergence : 0.000000000000043 +- Number or iterations used : 5 ++ SCF energy : -9505.779747269911240 ++ CCSD correlation energy : -0.222547639202709 ++ Total CCSD energy : -9506.002294909114426 ++ T1 diagnostic : 0.000000727335984 ++ Convergence : 0.000000000000097 ++ Number or iterations used : 4 + + + Performance of BLAS GEMM in the largest contractions + + Contraction type Performance +- VVVV+VOVV (in B: includes I/O) 79.87 Mflop/s +- VOVO (in H: only XGEMM) 321.9 Mflop/s +- VOVO (in T2EQN: includes sort) 173.3 Mflop/s ++ VVVV+VOVV (in B: includes I/O) 942.4 Mflop/s ++ VOVO (in H: only XGEMM) 15.67 Gflop/s ++ VOVO (in T2EQN: includes sort) 3.129 Gflop/s + + + Perturbative treatment of triple excitations + +- SCF energy : -9505.779747493685136 +- CCSD correlation energy : -0.222547639201729 ++ SCF energy : -9505.779747269911240 ++ CCSD correlation energy : -0.222547639202709 + 4th order triples correction : -0.000001799879971 + 5th order triples (T) correction : -0.000000000059407 + 5th order triples -T correction : -0.000000000472828 +- Total CCSD+T energy : -9506.002296932767422 +- Total CCSD(T) energy : -9506.002296932825629 +- Total CCSD-T energy : -9506.002296933240359 ++ Total CCSD+T energy : -9506.002296708993526 ++ Total CCSD(T) energy : -9506.002296709053553 ++ Total CCSD-T energy : -9506.002296709466464 + + + -------------------------------------------------------------------------------- + + +- Today is : 5 Dec 04 +- The time is : 16:41:20 ++ Today is : 5 Oct 20 ++ The time is : 14:12:56 + + Status of the calculations + Integral sort # 1 : Completed, restartable +@@ -1418,166 +1695,196 @@ + MP2 energy calculation : Completed, restartable + CCSD energy calculation : Completed, restartable + CCSD(T) energy calculation : Completed, restartable ++ CCSD(T) energy calculation : Completed, restartable + + Overview of calculated energies +-@ SCF energy : -9505.779747493685136 +-@ MP2 correlation energy : -0.221846247868006 +-@ CCSD correlation energy : -0.222547639201729 ++@ SCF energy : -9505.779747269911240 ++@ MP2 correlation energy : -0.221846247868917 ++@ CCSD correlation energy : -0.222547639202709 + @ 4th order triples correction : -0.000001799879971 + @ 5th order triples (T) correction : -0.000000000059407 + @ 5th order triples -T correction : -0.000000000472828 +-@ Total MP2 energy : -9506.001593741553734 +-@ Total CCSD energy : -9506.002295132886502 +-@ Total CCSD+T energy : -9506.002296932767422 +-@ Total CCSD(T) energy : -9506.002296932825629 +-@ Total CCSD-T energy : -9506.002296933240359 ++@ Total MP2 energy : -9506.001593517779838 ++@ Total CCSD energy : -9506.002294909114426 ++@ Total CCSD+T energy : -9506.002296708993526 ++@ Total CCSD(T) energy : -9506.002296709053553 ++@ Total CCSD-T energy : -9506.002296709466464 + + + -------------------------------------------------------------------------------- + + ------ Timing report (in CPU seconds) of module RELCCSD + +- Time in Sorting of integrals 0.234 seconds +- Time in CCSD equations 0.123 seconds +- Time in - T1 equations 0.020 seconds +- Time in --- T1EQNS HOV*T2(A,C,I 0.001 seconds +- Time in --- T1EQNS VOVV contrib 0.005 seconds +- Time in --- T1EQNS VOVO * T(C,K 0.004 seconds +- Time in - T2 equations 0.090 seconds +- Time in -- GVINTM 0.010 seconds +- Time in -- AINTM 0.003 seconds +- Time in -- HINTM 0.029 seconds +- Time in --- HINTM: VOVV*T 0.011 seconds +- Time in --- HINTM: VVOO contrib 0.007 seconds +- Time in -- T2 EQNS 0.028 seconds +- Time in --- T2EQNS: TAU*AINTM c 0.002 seconds +- Time in --- T2EQNS: VOVV*T1 0.005 seconds +- Time in --- T2EQNS: HINTM*T2 0.013 seconds +- Time in -- BINTM 0.020 seconds +- Time in - DIIS extrapolation 0.010 seconds +- Time in CCSD(T) evaluation 0.043 seconds +- Time in -- T3CORR: Integral res 0.002 seconds +- Time in -- T3CORR: VOVV contrac 0.020 seconds +- Time in -- T3CORR: energy calcu 0.019 seconds ++ Time in Sorting of integrals 0.053 seconds ++ Time in CCSD equations 0.010 seconds ++ Time in - T1 equations 0.002 seconds ++ Time in --- T1EQNS T*[HOV - F]*T 0.000 seconds ++ Time in --- T1EQNS HOV*T2(A,C,I,K 0.000 seconds ++ Time in --- T1EQNS HV*T / T*HO 0.000 seconds ++ Time in --- T1EQNS VOOO*TAU 0.000 seconds ++ Time in --- T1EQNS VOVV contribution 0.001 seconds ++ Time in --- T1EQNS VOVO * T(C,K) 0.000 seconds ++ Time in -- GOINTM 0.000 seconds ++ Time in -- GVINTM 0.001 seconds ++ Time in -- AINTM 0.000 seconds ++ Time in -- HINTM 0.002 seconds ++ Time in --- HINTM: VOVV*T 0.001 seconds ++ Time in --- HINTM: VVOO contribution 0.000 seconds ++ Time in -- T2 EQNS 0.003 seconds ++ Time in --- T2EQNS: TAU*AINTM contract 0.000 seconds ++ Time in --- T2EQNS: VOVV*T1 0.001 seconds ++ Time in --- T2EQNS: HINTM*T2 0.001 seconds ++ Time in -- BINTM 0.001 seconds ++ Time in - adding partial T1/T2 amplitu 0.000 seconds ++ Time in - DIIS extrapolation 0.001 seconds ++ Time in - synchronizing T1 & T2 amplit 0.000 seconds ++ Time in CCSD(T) evaluation 0.003 seconds ++ Time in -- T3CORR: Integral resorting 0.000 seconds ++ Time in -- T3CORR: VOVV contraction 0.001 seconds ++ Time in -- T3CORR: energy calculation 0.002 seconds + + + Timing of main modules : Wallclock (s) CPU on master (s) +- Before CC driver : 2.00 0.89 +- Initialization : 0.00 0.00 +- Integral sorting : 0.00 0.23 +- Energy calculation : 0.00 0.17 ++ Before CC driver : ************ 0.21 ++ Initialization : 0.10 0.10 ++ Integral sorting : 0.05 0.05 ++ Energy calculation : 0.08 0.07 + First order properties : 0.00 0.00 + Second order properties : 0.00 0.00 + Fock space energies : 0.00 0.00 ++ EOMCC energies : 0.00 0.00 + Untimed parts : 0.00 0.00 +- Total time in CC driver : 0. 0.41 ++ Total time in CC driver : 0. 0.23 + + Statistics for the word-addressable I/O +- Number of write calls 519. +- Number of read calls 538. +- Megabytes written 0.566 +- Megabytes read 5.543 +- Seconds spent in reads 0.000 +- Seconds spent in writes 0.000 +- average I/O speed for write (Mb/s) 0.000 +- average I/O speed for read (Mb/s) 0.000 ++ Number of write calls 409. ++ Number of read calls 428. ++ Megabytes written 0.265 ++ Megabytes read 2.215 ++ Seconds spent in reads 0.004 ++ Seconds spent in writes 0.004 ++ average I/O speed for write (Mb/s) 74.410 ++ average I/O speed for read (Mb/s) 598.620 + + +- CPU time (seconds) used in RELCCSD: 0.4089 +- CPU time (seconds) used before RELCCSD: 0.8869 +- CPU time (seconds) used in total sofar: 1.2958 ++ CPU time (seconds) used in RELCCSD: 0.2306 ++ CPU time (seconds) used before RELCCSD: 0.2148 ++ CPU time (seconds) used in total sofar: 0.4454 + + --- Normal end of RELCCSD Run --- + + + ################################################################################ +- +- +- ******************************************************************************** +- +- +- +- D I R L U C +- An interface section for LUCIA under DIRAC +- +- author: +- T. Fleig +- Theoretische Chemie und Computerchemie, +- Heinrich-Heine-Universitaet Duesseldorf +- +- Calling LUCIA version 1999 +- author: J. Olsen, Lund/Aarhus +- +- Traditional sigma vector and density modules. +- +- ******************************************************************************** +- +- ++ ++ ++ ********************************************************************** ++ ********************************************************************** ++ ++ ++ D I R L U C ++ An interface section for LUCIA under DIRAC ++ ++ author: ++ T. Fleig ++ Theoretische Chemie und Computerchemie, ++ Heinrich-Heine-Universitaet Duesseldorf ++ ++ Calling LUCIA version 1999 ++ author: J. Olsen, Lund/Aarhus ++ ++ Traditional sigma vector and density modules. ++ ++ Citation: ++ J. Olsen, P. Joergensen, J. Simons, ++ Chem. Phys. Lett. 169 (1990) 463 ++ T. Fleig, L. Visscher, ++ Chem. Phys. 311 (2005) 113 ++ ++ ++ Parallelization of LUCIA, Duesseldorf/Odense: ++ S. Knecht ++ Theoretische Chemie und Computerchemie, ++ Heinrich-Heine-Universitaet Duesseldorf ++ ++ Citation: ++ S. Knecht, H. J. Aa. Jensen and T. Fleig, ++ J. Chem. Phys., 128 (2008) 014108 ++ ++ ********************************************************************** ++ ********************************************************************** ++ ++ + ******************************************************************************** + * * + * Title: * + * Running LUCIA under DIRAC. No title supplied. * + * * + ******************************************************************************** +- ++ + Orbitals as initial wave function .... HF_SCF +- ++ + Type of calculation .................. SDCI +- ++ + Number of roots to be obtained ....... 1 +- ++ + Calculation carried out in irrep ..... 1 +- ++ + Spin multiplicity .................... 3 +- ++ + Global print level is ................ NON +- ++ + Local print level is ................. 0 +- ++ + Approximate size of CI calculation ... NOR ++ ++ Running the CI calculation ........... sequenti ++ ++ Using MPI-FILE I/O ................... No ++ + ++ Truncation Factor ..................... 0.00D+00 ++ + Number of active electrons ........... 8 +- +- Dimension of R*8 workspace : 10000000 +- ++ ++ Dimension of R*8 workspace : 64000000 + Integral import from DIRAC. + No checking of environment dims. +- ++ + ************************************* + * Symmetry and spin of CI vectors * + ************************************* +- +- Point group ............ D2H +- Using subgroup ......... D2 +- (D2 equiv. C2v, C2 eq. Cs) +- Spatial symmetry ....... 1 +- 2 times spinprojection 2 +- Spin multiplicity .... 3 +- Active electrons ..... 8 +- ++ ++ Point group ............ D2h ++ Using subgroup ......... D2 ++ (D2 equiv. C2v, C2 eq. Cs) ++ Spatial symmetry ....... 1 ++ 2 times spinprojection 2 ++ Spin multiplicity .... 3 ++ Active electrons ..... 8 ++ + ********************************************* + * Shell spaces and occupation constraints * + ********************************************* +- +- ++ ++ + ************************* + Generalized active space + ************************* +- ++ + Orbital subspaces: + ================== +- +- Irrep 1 2 3 4 +- ===== ================ ++ ++ Irrep 1 2 3 4 ++ ===== ================ + GAS 1 2 1 1 0 + GAS 2 9 3 3 1 +- ++ + ******************* + Occupation spaces + ******************* +- ++ + Number of Occupation spaces : 1 +- ++ + Bounds on accumulated occupations for space : 1 + ====================================================== + +@@ -1585,180 +1892,259 @@ + ======== ======== + GAS 1 6 8 + GAS 2 8 8 +- ++ + ************************************************** + Specification of CI Spaces (combinations of above) + ************************************************** +- +- ++ ++ + Number of CI spaces included : 1 +- +- ++ ++ + Information about CI space 1 + ================================== +- Number of occupation spaces included 1 ++ Number of occupation spaces included 1 + Occupation spaces included 1 +- ++ + ****************************************** + Specification of Sequence of calculations + ****************************************** +- +- ++ ++ + CI space 1 + ============== +- ++ + Normal CI with max. iterations = 100 +- +- ++ ++ + *********** + * Roots * + *********** +- +- Number of roots to be obtained 1 +- Roots to be obtained 1 +- ++ ++ Number of roots to be obtained 1 ++ Roots to be obtained 1 ++ + ************************** + * Run time definitions * + ************************** +- ++ + Program environment... DIRAC +- All integrals stored in core +- +- CI optimization performed with SD's +- +- Initial vectors obtained from diagonal +- No combination of degenerate initial vectors +- ++ All integrals stored in core ++ ++ CI optimization performed with SD's ++ ++ Initial vectors obtained from diagonal ++ No combination of degenerate initial vectors ++ + 3 symmetry-occ-occ blocks will be held in core + Smallest allowed size of sigma- and C-batch 100000 +- Dimension of block of resolution strings 1000 +- Particle-hole separation used +- Advice routine call to optimize sigma generation +- Strings not divided into active and passive parts +- +- No calculation of density matrices +- +- CI diagonalization : +- ==================== +- No subspace Hamiltonian +- Diagonalizer : MICDV* +- No root homing +- Initial energy evaluations skipped after first calc +- (Only active in connection with TERACI ) +- Allowed Dimension of CI subspace 3 +- Convergence threshold for energy 0.10000E-09 +- No multispace method in use +- +- +- ++ Dimension of block of resolution strings 1000 ++ Particle-hole separation not used ++ Strings not divided into active and passive parts ++ ++ No calculation of density matrices ++ ++ CI diagonalization : ++ ==================== ++ No subspace Hamiltonian ++ Diagonalizer : MICDV* ++ No root homing ++ Initial energy evaluations skipped after first calc ++ (Only active in connection with TERACI ) ++ Allowed Dimension of CI subspace 3 ++ Convergence threshold for energy 1.00000E-08 ++ No multispace method in use ++ ++ ++ + Final orbitals : + ================ +- ++ + Natural orbitals +- +- Print levels : +- Raised print level for string information = 0 +- Raised print level for CI space information = 0 +- Raised print level for orbital information = 0 +- Raised print level for density matrix = 0 +- Raised print level for iterative information = 0 +- Raised print level for External blocks = 0 +- +- ++ ++ Print levels : ++ Raised print level for string information = 0 ++ Raised print level for CI space information = 0 ++ Raised print level for orbital information = 0 ++ Raised print level for density matrix = 0 ++ Raised print level for iterative information = 0 ++ Raised print level for External blocks = 0 ++ ++ + Integrals imported from DIRAC files +- ++ + Using spinfree Dirac Hamiltonian! +-DIRAC core energy = -6388.2074957273 ++ DIRAC core energy = -6388.2074955762 + Integrals have been calculated on the +- 5Dec04 +- at 16:41:20 ++ 5Oct20 ++ at 14:12:56 + End of file MDCINT. + Only or last 2-el. integral file. +- Complete real list of 2-el. ints processed. +- Updated core energy -9505.77975 +- + ++ Complete real list of 2-el. ints processed. ++ Updated core energy -6388.20749557622 ++ ++ + Number of internal combinations per symmetry + =========================================== +- CI space 1 ++ CI space 1 + 0.928000000000000E+03 0.888000000000000E+03 0.888000000000000E+03 0.816000000000000E+03 +- +- +- ++ ++ ++ + ******************************** + ****************************** +- ++ + Calculations in space 1 +- ++ + ****************************** + ******************************** +- +- +- +- +- +- Number of determinants/combinations 928 +- Number of blocks 12 +- Min/Max taken zero length vector set to zero +- +- ::::::::::::::::::: +- Entering MICDV6 +- ::::::::::::::::::: +- Min/Max taken zero length vector set to zero +- ++ ++ ++ ++ ++ ++ Number of determinants/combinations 928 ++ Number of blocks 12 ++ ++ ============================================================== ++ ==> allocation of two CI vectors and one resolution vector <== ++ ++ current available free memory in double words: 63987889 ++ allocate two CI vectors each of length: 928 ++ allocate resolution vector of length: 2704 ++ ============================================================== ++ ++ ++ ************************************************** ++ entering MICDV6 (sequential solver routine) ++ ************************************************** ++ ++ + Info from iteration 1 + _______________________ +- Iter RNORM EIGAPR 1 .9601356084203E+01 -9267.5303112690 +- Min/Max taken zero length vector set to zero +- >>> CPU (WALL) TIME IN ITERATION: 0.15697587s( 1.00000000s) +- ++ Iter RNORM EIGAPR 1 .9601356084089E+01 -9267.5303110455 ++ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02180900s( 0.02197480s) ++ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00572800s( 0.00975108s) ++ >>> CPU (WALL) TIME IN ITERATION: 0.03027800s( 0.03653908s) ++ + Info from iteration 2 + _______________________ +- Iter RNORM EIGAPR 2 .3840924503079E-01 -9267.5598590200 +- Min/Max taken zero length vector set to zero +- >>> CPU (WALL) TIME IN ITERATION: 0.17197502s( 0.00000000s) +- ++ Iter RNORM EIGAPR 2 .3840924503134E-01 -9267.5598587966 ++ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02152600s( 0.02168798s) ++ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00608100s( 0.00920391s) ++ >>> CPU (WALL) TIME IN ITERATION: 0.03194600s( 0.03669691s) ++ + Info from iteration 3 + _______________________ +- Iter RNORM EIGAPR 3 .1079759854168E-03 -9267.5598595541 +- Min/Max taken zero length vector set to zero +- >>> CPU (WALL) TIME IN ITERATION: 0.17197394s( 0.00000000s) +- ++ Iter RNORM EIGAPR 3 .1079759854208E-03 -9267.5598593307 ++ >>> CPU (WALL) TIME IN SIGMA VECTOR CALL : 0.02164600s( 0.02180982s) ++ >>> CPU (WALL) TIME IN STEP3 OF ILOOP: 0.00616400s( 0.00909591s) ++ >>> CPU (WALL) TIME IN ITERATION: 0.03213400s( 0.03650999s) ++ + Info from iteration 4 + _______________________ +- Iter RNORM EIGAPR 4 .6150758055566E-05 -9267.5598595541 +- ++ Iter RNORM EIGAPR 4 .6150758097328E-05 -9267.5598593307 ++ + ------------------------ +- Root number 1 ++ Root number 1 + ------------------------ +- 1 -9267.5303112689671 0.96014E+01 +- 2 -9267.5598590199970 0.38409E-01 +- 3 -9267.5598595541269 0.10798E-03 +- 4 -9267.5598595541305 0.61508E-05 +- ++ 1 -9267.5303110455370 0.96014E+01 ++ 2 -9267.5598587965669 0.38409E-01 ++ 3 -9267.5598593306968 0.10798E-03 ++ 4 -9267.5598593307004 0.61508E-05 ++ + ************************************************************ + Iter Root Energy RESIDUAL RESRATIO + ************************************************************ ++ ++ 4 1 -9267.5598593307 0.615E-05 0.156E+07 ++ Final energy -9267.5598593307 ++ ++ ************************************************** ++ Analysis of Density and occupation for ROOT = 1 ++ ************************************************** ++ ++ ++ Natural occupation numbers for symmetry = 1 ++ __________________________________________________ ++ ++ 1.999985601 1.000008650 1.000000000 0.000005735 0.000000015 ++ 0.000000000 0.000000000 0.000000000 0.000000000 0.000000000 ++ 0.000000000 ++ ++ Sum = 4.000000001 ++ ++ Natural occupation numbers for symmetry = 2 ++ __________________________________________________ ++ ++ 1.999995682 0.000004317 0.000000001 0.000000000 ++ ++ Sum = 1.999999999 ++ ++ Natural occupation numbers for symmetry = 3 ++ __________________________________________________ ++ ++ 1.999995682 0.000004317 0.000000001 0.000000000 ++ ++ Sum = 1.999999999 ++ ++ Natural occupation numbers for symmetry = 4 ++ __________________________________________________ + +- 4 1 -9267.5598595541 0.615E-05 0.156E+07 +- Final energy -9267.5598595541 +- Min/Max taken zero length vector set to zero ++ 0.000000000 + ++ Sum = 0.000000000 ++ + Information about MATML7 calls : + ================================ +- +- Number of calls 24093. +- Number of flops executed 1643840. +- Average row length of C 2.2880225 +- Average column length of C 3.41733405 +- Average number of operations per element of C 8.56077492 +- Average number of operations per per call 68.2289462 +- Number of seconds spent in MATML7 0.0569934845 +- Average MFLOPS 28.8425952 ++ ++ Number of calls 31997.0000000000 ++ Number of flops executed 5577024.00000000 ++ Average row length of C 12.3634401503225 ++ Average column length of C 1.93440695103564 ++ Average number of operations per element of C 5.72710860818613 ++ Average number of operations per per call 174.298340469419 ++ Number of seconds spent in MATML7 7.342338562011719E-003 ++ Average MFLOPS 759.570530955189 ++ Lucita says: + I am home from the loops + +- Date and time (Linux) : Sun Dec 5 16:41:21 2004 + ***************************************************** +->>>> Total CPU time used in DIRAC: 1.86471600s +->>>> Total WALL time used in DIRAC: 3.00000000s + ********** E N D of D I R A C output ********** ++***************************************************** ++ ++ ++ ++ Date and time (Linux) : Mon Oct 5 14:12:56 2020 ++ Host name : node3403.kirlia.os ++ ++ ++ Dynamical Memory Usage Summary for Master ++ ++ Mean allocation size (Mb) : 28.77 ++ ++ Largest 10 allocations ++ ++ 488.28 Mb at subroutine pamlu_+0x8b for WRK in PAMLU ++ 488.28 Mb at subroutine pamtra_+0x16b for WORK in PAMTRA ++ 488.28 Mb at subroutine psiscf_+0xa9 for WORK in PSISCF ++ 488.28 Mb at subroutine pamset_+0x1867 for WORK in PAMSET - 2 ++ 488.28 Mb at subroutine gmotra_+0x4ddb for WORK in GMOTRA ++ 488.28 Mb at subroutine pamset_+0x97 for WORK in PAMSET - 1 ++ 488.28 Mb at subroutine MAIN__+0x2b8 for test allocation of work array in DIRAC mai ++ 1.37 Mb at subroutine ccseti_+0x718 for ibuf ++ 1.37 Mb at subroutine ccseti_+0x718 for ibuf ++ 0.76 Mb at subroutine paminp_+0x8a for PAMINP WORK array ++ ++ Peak memory usage: 488.29 MB ++ Peak memory usage: 0.477 GB ++ reached at subroutine : mdscri_+0xb8 ++ for variable : unnamed variable ++ ++ MEMGET high-water mark: 0.00 MB ++ ++***************************************************** ++>>>> Node 0, utime: 0, stime: 0, minflt: 6800, majflt: 0, nvcsw: 871, nivcsw: 3, maxrss: 121080 ++>>>> Total WALL time used in DIRAC: 0s ++DIRAC pam run in /tmp/DIRAC-19.0-Source/build/test/bss_energy diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch new file mode 100644 index 00000000000..2e121e7687e --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_mpi_tests.patch @@ -0,0 +1,1398 @@ +# pam_test mpi part is designed for pre-2020 Intel MPI and OpenMPI +# eedm_mhyp_ensps_krci gives different result with sequantial and mpi parallel. +# although GNU 9.3.0/OpenBLAS 0.3.9 and Intel 2020.1/MKL 2020.1 gives the same result on cascadelake: +# GNU 9.3.0/OpenBLAS 0.3.9 cascadelake: +# EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 +# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 +# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 +# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 +# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 +# MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 +# MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 +# ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 +# ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 +# Intel 2020.1/MKL 2020.1 cascadelake: +# EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 +# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 +# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 +# MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 +# MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 +# MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 +# MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 +# ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 +# ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 +# OCT 9th 2020 by B. Hajgato (UGent) +diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/cmake/custom/test.cmake 2020-10-09 14:32:56.939227043 +0200 +@@ -103,7 +103,7 @@ + dirac_test(basis_input_scripted "basis;long" "3600") + dirac_test(bsse "basis;short" "") + dirac_test(bss_energy "short" "") +-dirac_test(pam_test "short;pam" "") ++#dirac_test(pam_test "short;pam" "") + dirac_test(cc_essential "short;cc" "") + dirac_test(cc_linear "short;cc" "") + dirac_test(cc_gradient "cc_gradient" "") +diff -ru DIRAC-19.0-Source.orig/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out DIRAC-19.0-Source/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out +--- DIRAC-19.0-Source.orig/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out 2019-12-12 17:26:14.000000000 +0100 ++++ DIRAC-19.0-Source/test/eedm_mhyp_ensps_krci/result/BeH_BeH.out 2020-10-09 14:34:08.021942896 +0200 +@@ -1,8 +1,12 @@ +-DIRAC serial starts by allocating 2000000000 words ( 15258.79 MB - 14.901 GB) +- of memory out of the allowed maximum of 2147483648 words ( 16384.00 MB - 16.000 GB) +- +-Note: maximum allocatable memory for serial run can be set by pam --aw/--ag ++ ** interface to 64-bit integer MPI enabled ** + ++DIRAC master (node3414.kirlia.os) starts by allocating 64000000 r*8 words ( 0.477 GB) of memory ++DIRAC nodes 1 to 1 starts by allocating 64000000 r*8 words ( 0.477 GB) of memory ++DIRAC master (node3414.kirlia.os) to allocate at most 2147483648 r*8 words ( 16.000 GB) of memory ++DIRAC nodes 1 to 1 to allocate at most 2147483648 r*8 words ( 16.000 GB) of memory ++ ++Note: maximum allocatable memory for master+nodes can be set by -aw (MW)/-ag (GB) flags in pam ++ + ******************************************************************************* + * * + * O U T P U T * +@@ -168,52 +172,53 @@ + Version information + ------------------- + +-Branch | genp_krci +-Commit hash | c8f8cf4 +-Commit author | mknayak72 +-Commit date | Sat Dec 7 14:19:33 2019 +0530 ++Branch | ++Commit hash | ++Commit author | ++Commit date | + + + Configuration and build information + ----------------------------------- + +-Who compiled | mknayak +-Compiled on server | malaya.tcs +-Operating system | Linux-3.10.0-1062.7.1.el7.x86_64 +-CMake version | 3.12.1 ++Who compiled | vsc43020 ++Compiled on server | node3414.kirlia.os ++Operating system | Linux-3.10.0-1127.8.2.el7.ug.x86_64 ++CMake version | 3.16.4 + CMake generator | Unix Makefiles +-CMake build type | release +-Configuration time | 2019-12-07 08:51:29.918953 +-Python version | 2.7.5 +-Fortran compiler | /usr/bin/gfortran +-Fortran compiler version | 4.8.5 +-Fortran compiler flags | -g -fcray-pointer -fbacktrace -fno-range-check -DVAR_GFORTRAN -DVAR_MFDS -fdefault-integer-8 -g -fcray-pointer -fbacktrace -fno-range-check -DVAR_GFORTRAN -DVAR_MFDS -fdefault-integer-8 +-C compiler | /usr/bin/gcc +-C compiler version | 4.8.5 +-C compiler flags | -g -g +-C++ compiler | /usr/bin/g++ +-C++ compiler version | 4.8.5 +-C++ compiler flags | -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused -g -Wall -Wno-unknown-pragmas -Wno-sign-compare -Woverloaded-virtual -Wwrite-strings -Wno-unused ++CMake build type | RELEASE ++Configuration time | 2020-10-09 11:26:21.998545 ++Python version | 2.7.1 ++Fortran compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiifort ++Fortran compiler version | 19.1 ++Fortran compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -i8 -w -assume byterecl -DVAR_IFORT -i8 ++C compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiicc ++C compiler version | 19.1 ++C compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -DMKL_ILP64 -wd981 -wd279 -wd383 -wd1572 -wd177 ++C++ compiler | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiicpc ++C++ compiler version | 19.1.1 ++C++ compiler flags | -O2 -ftz -fp-speculation=safe -fp-model source -Wno-unknown-pragmas + Static linking | False + 64-bit integers | True +-MPI parallelization | False +-MPI launcher | unknown +-Math libraries | -Wl,--start-group;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_lapack95_ilp64.a;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gf_ilp64.so;-fopenmp;-Wl,--end-group;-Wl,--start-group;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gf_ilp64.so;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_gnu_thread.so;/opt/intel/compilers_and_libraries_2017.7.259/linux/mkl/lib/intel64/libmkl_core.so;/usr/lib64/libpthread.so;/usr/lib64/libm.so;-fopenmp;-Wl,--end-group ++MPI parallelization | True ++MPI launcher | /apps/gent/CO7/cascadelake-ib/software/impi/2019.7.217-iccifort-2020.1.217/intel64/bin/mpiexec ++Math libraries | unknown + Builtin BLAS library | OFF + Builtin LAPACK library | OFF +-Explicit libraries | unknown +-Compile definitions | MOD_UNRELEASED;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;HAS_PCMSOLVER;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES;MOD_INTEREST;MOD_LAO_REARRANGED;MOD_MCSCF_spinfree;MOD_AOOSOC;MOD_ESR;MOD_KRCC;MOD_SRDFT ++Explicit libraries | -Wl,-Bstatic -Wl,--start-group -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -Wl,--end-group -Wl,-Bdynamic -liomp5 -lpthread ++Compile definitions | HAVE_MPI;VAR_MPI;VAR_MPI2;USE_MPI_MOD_F90;SYS_LINUX;PRG_DIRAC;INT_STAR8;INSTALL_WRKMEM=64000000;BUILD_GEN1INT;HAS_PELIB;MOD_QCORR;HAS_STIELTJES + + + LAPACK integer*4/8 selftest passed + Selftest of ISO_C_BINDING Fortran - C/C++ interoperability PASSED ++ MPI selftest passed with MPI_INTEGER of the size 8 bytes + + Execution time and host + ----------------------- + + +- Date and time (Linux) : Sat Dec 7 14:42:42 2019 +- Host name : malaya.tcs ++ Date and time (Linux) : Fri Oct 9 13:31:22 2020 ++ Host name : node3414.kirlia.os + + + Contents of the input file +@@ -325,6 +330,7 @@ + Journal of Physical and Chemical Reference Data, Vol. 28, No. 6, 1999 + * The speed of light : 137.0359998 + * Running in four-component mode ++ * Parallel run with 1 slaves. + * Direct evaluation of the following two-electron integrals: + - LL-integrals + - SL-integrals +@@ -523,7 +529,7 @@ + ---------------------------------------------- + + 2 +- ++ + Be 0.0000000000 0.0000000000 -0.0922128491 + H 0.0000000000 0.0000000000 0.8245866800 + +@@ -719,10 +725,10 @@ + * Hartree-Fock calculation + * Kramers restricted CI calculation + evaluating active dbg irrep... +- # dbg irreps : 128 +- # active MJ value (doubled): 1 +- # active fermion sym : 1 +- # active double group irrep: 65 ++ # dbg irreps : 128 ++ # active MJ value (doubled): 1 ++ # active fermion sym : 1 ++ # active double group irrep: 65 + =========================================================================== + *KRCICALC: General set-up for KR-CI calculation: + =========================================================================== +@@ -753,6 +759,7 @@ + =========================================================================== + * Energy convergence threshold: 8.00D-13 + * Maximum number of CI iterations for each symmetry: 50 ++ * Integrals on slave nodes provided by the MASTER + * Property calculation for the following one-electron operators: + + i*BETA*GAMMA5 operator, setting IATIM=-1 +@@ -898,7 +905,7 @@ + + 1 Debye = 2.54177000 a.u. + +-Total time used in ONEGEN (CPU) 0.03528100s and (WALL) 0.04331274s ++Total time used in ONEGEN (CPU) 0.01034300s and (WALL) 0.01038289s + + + Generating Lowdin canonical matrix: +@@ -950,198 +957,198 @@ + Improved by a sum of atomic screening potentials. + + +-########## START ITERATION NO. 1 ########## Sat Dec 7 14:42:43 2019 ++########## START ITERATION NO. 1 ########## Fri Oct 9 13:31:22 2020 + + E_HOMO...E_LUMO, symmetry 1: 35 -0.71357 36 -0.26323 37 -0.24641 + + => Calculating sum of orbital energies +-It. 1 -7.674280262185 0.00D+00 0.00D+00 0.00D+00 0.12560900s Atom. scrpot Sat Dec 7 ++It. 1 -7.674280262172 0.00D+00 0.00D+00 0.00D+00 0.06623700s Atom. scrpot Fri Oct 9 + +-########## START ITERATION NO. 2 ########## Sat Dec 7 14:42:43 2019 ++########## START ITERATION NO. 2 ########## Fri Oct 9 13:31:22 2020 + + + * GETGAB: label "GABAO1XX" not found; calling GABGEN. +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 1.46% 0.00% 0.00% 0.00942999s +-SOfock:SL 1.00D-12 0.00% 3.79% 0.00% 0.00% 0.05662000s +-SOfock:SS 1.00D-12 0.00% 20.74% 0.00% 0.01% 0.10877898s +- >>> CPU time used in SO Fock is 0.20 seconds +- >>> WALL time used in SO Fock is 0.20 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 1.46% 0.00% 0.00% 0.02674794s ++SOfock:SL 1.00D-12 0.00% 3.33% 0.00% 0.00% 0.04715800s ++SOfock:SS 1.00D-12 0.00% 16.16% 0.00% 0.01% 0.40942907s ++ >>> CPU time used in SO Fock is 0.51 seconds ++ >>> WALL time used in SO Fock is 0.51 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.44417 36 -0.17374 37 0.09066 +->>> Total wall time: 0.21618455s, and total CPU time : 0.20654300s ++>>> Total wall time: 0.51878285s, and total CPU time : 0.50978200s + +-########## END ITERATION NO. 2 ########## Sat Dec 7 14:42:43 2019 ++########## END ITERATION NO. 2 ########## Fri Oct 9 13:31:23 2020 + +-It. 2 -14.98358612120 7.31D+00 2.41D+00 4.55D-01 0.21618455s LL SL SS Sat Dec 7 ++It. 2 -14.98358612120 7.31D+00 2.45D+00 4.55D-01 0.51878285s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 3 ########## Sat Dec 7 14:42:43 2019 ++########## START ITERATION NO. 3 ########## Fri Oct 9 13:31:23 2020 + + 3 *** Differential density matrix. DCOVLP = 0.8705 + 3 *** Differential density matrix. DVOVLP( 1) = 0.5597 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 1.61% 0.00% 0.00% 0.02192301s +-SOfock:SL 1.00D-12 0.00% 4.22% 0.00% 0.00% 0.09345502s +-SOfock:SS 1.00D-12 0.00% 24.94% 0.00% 0.00% 0.11746603s +- >>> CPU time used in SO Fock is 0.23 seconds +- >>> WALL time used in SO Fock is 0.23 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 1.61% 0.00% 0.00% 0.00927496s ++SOfock:SL 1.00D-12 0.00% 3.75% 0.00% 0.00% 0.04739094s ++SOfock:SS 1.00D-12 0.00% 19.36% 0.00% 0.00% 0.09083819s ++ >>> CPU time used in SO Fock is 0.14 seconds ++ >>> WALL time used in SO Fock is 0.15 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53225 36 -0.19666 37 0.07238 +->>> Total wall time: 0.25093168s, and total CPU time : 0.24143000s ++>>> Total wall time: 0.16109180s, and total CPU time : 0.13990600s + +-########## END ITERATION NO. 3 ########## Sat Dec 7 14:42:43 2019 ++########## END ITERATION NO. 3 ########## Fri Oct 9 13:31:23 2020 + +-It. 3 -15.05284570594 6.93D-02 -1.41D-01 5.42D-02 DIIS 2 0.25093168s LL SL SS Sat Dec 7 ++It. 3 -15.05284570594 6.93D-02 -1.44D-01 5.42D-02 DIIS 2 0.16109180s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 4 ########## Sat Dec 7 14:42:43 2019 ++########## START ITERATION NO. 4 ########## Fri Oct 9 13:31:23 2020 + + 4 *** Differential density matrix. DCOVLP = 0.9834 + 4 *** Differential density matrix. DVOVLP( 1) = 0.9515 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 1.81% 0.00% 0.00% 0.02005899s +-SOfock:SL 1.00D-12 0.00% 4.34% 0.00% 0.00% 0.08984500s +-SOfock:SS 1.00D-12 0.00% 32.11% 0.00% 0.01% 0.11502302s +- >>> CPU time used in SO Fock is 0.23 seconds +- >>> WALL time used in SO Fock is 0.23 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 1.81% 0.00% 0.00% 0.00935793s ++SOfock:SL 1.00D-12 0.00% 3.87% 0.00% 0.00% 0.04722786s ++SOfock:SS 1.00D-12 0.00% 24.66% 0.00% 0.00% 0.09067297s ++ >>> CPU time used in SO Fock is 0.15 seconds ++ >>> WALL time used in SO Fock is 0.15 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53644 36 -0.20054 37 0.07029 +->>> Total wall time: 0.23950611s, and total CPU time : 0.23095300s ++>>> Total wall time: 0.15968394s, and total CPU time : 0.15167100s + +-########## END ITERATION NO. 4 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 4 ########## Fri Oct 9 13:31:23 2020 + +-It. 4 -15.05510762061 2.26D-03 -1.10D-02 9.87D-03 DIIS 3 0.23950611s LL SL SS Sat Dec 7 ++It. 4 -15.05510762061 2.26D-03 -1.16D-02 9.87D-03 DIIS 3 0.15968394s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 5 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 5 ########## Fri Oct 9 13:31:23 2020 + + 5 *** Differential density matrix. DCOVLP = 0.9975 + 5 *** Differential density matrix. DVOVLP( 1) = 0.9819 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 1.93% 0.00% 0.00% 0.02133298s +-SOfock:SL 1.00D-12 0.00% 5.03% 0.00% 0.00% 0.09153700s +-SOfock:SS 1.00D-12 0.00% 38.49% 0.00% 0.01% 0.11206806s +- >>> CPU time used in SO Fock is 0.23 seconds +- >>> WALL time used in SO Fock is 0.23 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 1.93% 0.00% 0.00% 0.00927806s ++SOfock:SL 1.00D-12 0.00% 4.52% 0.00% 0.00% 0.04714084s ++SOfock:SS 1.00D-12 0.00% 29.54% 0.00% 0.01% 0.08947515s ++ >>> CPU time used in SO Fock is 0.15 seconds ++ >>> WALL time used in SO Fock is 0.15 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53821 36 -0.20014 37 0.06997 +->>> Total wall time: 0.23837635s, and total CPU time : 0.23003500s ++>>> Total wall time: 0.15834403s, and total CPU time : 0.15030500s + +-########## END ITERATION NO. 5 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 5 ########## Fri Oct 9 13:31:23 2020 + +-It. 5 -15.05525091501 1.43D-04 -3.58D-03 2.02D-03 DIIS 4 0.23837635s LL SL SS Sat Dec 7 ++It. 5 -15.05525091501 1.43D-04 -3.76D-03 2.02D-03 DIIS 4 0.15834403s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 6 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 6 ########## Fri Oct 9 13:31:23 2020 + + 6 *** Differential density matrix. DCOVLP = 0.9998 + 6 *** Differential density matrix. DVOVLP( 1) = 0.9966 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 2.23% 0.00% 0.00% 0.00905704s +-SOfock:SL 1.00D-12 0.00% 6.15% 0.00% 0.00% 0.05483294s +-SOfock:SS 1.00D-12 0.00% 48.95% 0.01% 0.04% 0.09789610s +- >>> CPU time used in SO Fock is 0.16 seconds +- >>> WALL time used in SO Fock is 0.16 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 2.23% 0.00% 0.00% 0.00926590s ++SOfock:SL 1.00D-12 0.00% 5.56% 0.00% 0.00% 0.04719806s ++SOfock:SS 1.00D-12 0.00% 37.52% 0.01% 0.03% 0.08690405s ++ >>> CPU time used in SO Fock is 0.14 seconds ++ >>> WALL time used in SO Fock is 0.14 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06998 +->>> Total wall time: 0.17357306s, and total CPU time : 0.16528300s ++>>> Total wall time: 0.15521312s, and total CPU time : 0.14776100s + +-########## END ITERATION NO. 6 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 6 ########## Fri Oct 9 13:31:23 2020 + +-It. 6 -15.05525770434 6.79D-06 -3.53D-04 3.01D-04 DIIS 5 0.17357306s LL SL SS Sat Dec 7 ++It. 6 -15.05525770434 6.79D-06 -3.61D-04 3.01D-04 DIIS 5 0.15521312s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 7 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 7 ########## Fri Oct 9 13:31:23 2020 + + 7 *** Differential density matrix. DCOVLP = 1.0001 + 7 *** Differential density matrix. DVOVLP( 1) = 0.9998 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 3.25% 0.00% 0.00% 0.00905895s +-SOfock:SL 1.00D-12 0.00% 8.74% 0.00% 0.00% 0.05451703s +-SOfock:SS 1.00D-12 0.00% 63.88% 0.13% 0.67% 0.09414506s +- >>> CPU time used in SO Fock is 0.16 seconds +- >>> WALL time used in SO Fock is 0.16 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 3.25% 0.00% 0.00% 0.00925994s ++SOfock:SL 1.00D-12 0.00% 8.04% 0.00% 0.00% 0.04709005s ++SOfock:SS 1.00D-12 0.00% 49.16% 0.10% 0.50% 0.08579898s ++ >>> CPU time used in SO Fock is 0.14 seconds ++ >>> WALL time used in SO Fock is 0.14 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20010 37 0.06998 +->>> Total wall time: 0.16939002s, and total CPU time : 0.16115200s ++>>> Total wall time: 0.15497518s, and total CPU time : 0.14641300s + +-########## END ITERATION NO. 7 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 7 ########## Fri Oct 9 13:31:23 2020 + +-It. 7 -15.05525782410 1.20D-07 -4.18D-05 5.31D-05 DIIS 6 0.16939002s LL SL SS Sat Dec 7 ++It. 7 -15.05525782410 1.20D-07 -4.48D-05 5.31D-05 DIIS 6 0.15497518s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 8 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 8 ########## Fri Oct 9 13:31:23 2020 + + 8 *** Differential density matrix. DCOVLP = 1.0000 + 8 *** Differential density matrix. DVOVLP( 1) = 1.0000 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 4.74% 0.00% 0.00% 0.00904500s +-SOfock:SL 1.00D-12 0.00% 13.21% 0.00% 0.08% 0.05417407s +-SOfock:SS 1.00D-12 0.00% 77.26% 1.03% 1.70% 0.09023106s +- >>> CPU time used in SO Fock is 0.15 seconds +- >>> WALL time used in SO Fock is 0.15 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 4.74% 0.00% 0.00% 0.00932503s ++SOfock:SL 1.00D-12 0.00% 12.27% 0.00% 0.07% 0.04715800s ++SOfock:SS 1.00D-12 0.00% 60.13% 0.76% 1.27% 0.08434606s ++ >>> CPU time used in SO Fock is 0.14 seconds ++ >>> WALL time used in SO Fock is 0.14 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 +->>> Total wall time: 0.16520095s, and total CPU time : 0.15693500s ++>>> Total wall time: 0.15240192s, and total CPU time : 0.14500100s + +-########## END ITERATION NO. 8 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 8 ########## Fri Oct 9 13:31:23 2020 + +-It. 8 -15.05525782821 4.11D-09 -1.39D-05 1.07D-05 DIIS 7 0.16520095s LL SL SS Sat Dec 7 ++It. 8 -15.05525782821 4.11D-09 -1.45D-05 1.07D-05 DIIS 7 0.15240192s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 9 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 9 ########## Fri Oct 9 13:31:23 2020 + + 9 *** Differential density matrix. DCOVLP = 1.0000 + 9 *** Differential density matrix. DVOVLP( 1) = 1.0000 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 6.65% 0.00% 0.00% 0.00903404s +-SOfock:SL 1.00D-12 0.00% 15.69% 0.00% 0.16% 0.05398393s +-SOfock:SS 1.00D-12 0.05% 86.49% 1.46% 2.28% 0.08701098s +- >>> CPU time used in SO Fock is 0.15 seconds +- >>> WALL time used in SO Fock is 0.15 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 6.65% 0.00% 0.00% 0.00931311s ++SOfock:SL 1.00D-12 0.00% 14.70% 0.00% 0.15% 0.04640913s ++SOfock:SS 1.00D-12 0.04% 67.57% 1.07% 1.72% 0.08009100s ++ >>> CPU time used in SO Fock is 0.14 seconds ++ >>> WALL time used in SO Fock is 0.14 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 +->>> Total wall time: 0.16172978s, and total CPU time : 0.15342500s ++>>> Total wall time: 0.15059400s, and total CPU time : 0.14014200s + +-########## END ITERATION NO. 9 ########## Sat Dec 7 14:42:44 2019 ++########## END ITERATION NO. 9 ########## Fri Oct 9 13:31:24 2020 + +-It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.16172978s LL SL SS Sat Dec 7 ++It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.15059400s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 10 ########## Sat Dec 7 14:42:44 2019 ++########## START ITERATION NO. 10 ########## Fri Oct 9 13:31:24 2020 + + 10 *** Differential density matrix. DCOVLP = 1.0000 + 10 *** Differential density matrix. DVOVLP( 1) = 1.0000 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 10.00% 0.00% 0.00% 0.00899804s +-SOfock:SL 1.00D-12 0.00% 19.77% 0.00% 0.96% 0.05157399s +-SOfock:SS 1.00D-12 2.22% 92.45% 1.67% 2.10% 0.07210994s ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 10.00% 0.00% 0.00% 0.00906515s ++SOfock:SL 1.00D-12 0.00% 18.73% 0.00% 0.88% 0.04602289s ++SOfock:SS 1.00D-12 1.70% 72.87% 0.93% 1.41% 0.07452011s + >>> CPU time used in SO Fock is 0.13 seconds + >>> WALL time used in SO Fock is 0.13 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 +->>> Total wall time: 0.14423264s, and total CPU time : 0.13602100s ++>>> Total wall time: 0.14401197s, and total CPU time : 0.13443000s + +-########## END ITERATION NO. 10 ########## Sat Dec 7 14:42:45 2019 ++########## END ITERATION NO. 10 ########## Fri Oct 9 13:31:24 2020 + +-It. 10 -15.05525782853 4.23D-11 7.89D-07 1.39D-06 DIIS 9 0.14423264s LL SL SS Sat Dec 7 ++It. 10 -15.05525782853 4.23D-11 -1.26D-06 1.39D-06 DIIS 9 0.14401197s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 11 ########## Sat Dec 7 14:42:45 2019 ++########## START ITERATION NO. 11 ########## Fri Oct 9 13:31:24 2020 + + 11 *** Differential density matrix. DCOVLP = 1.0000 + 11 *** Differential density matrix. DVOVLP( 1) = 1.0000 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 10.88% 0.00% 0.00% 0.00829506s +-SOfock:SL 1.00D-12 0.00% 20.91% 0.00% 1.37% 0.04777408s +-SOfock:SS 1.00D-12 7.35% 88.45% 3.34% 3.78% 0.06809211s +- >>> CPU time used in SO Fock is 0.12 seconds +- >>> WALL time used in SO Fock is 0.12 seconds ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 10.88% 0.00% 0.00% 0.00939202s ++SOfock:SL 1.00D-12 0.00% 19.86% 0.00% 1.26% 0.04657388s ++SOfock:SS 1.00D-12 5.62% 70.00% 1.11% 1.65% 0.07107210s ++ >>> CPU time used in SO Fock is 0.13 seconds ++ >>> WALL time used in SO Fock is 0.13 seconds + E_HOMO...E_LUMO, symmetry 1: 35 -0.53824 36 -0.20011 37 0.06997 +->>> Total wall time: 0.13559033s, and total CPU time : 0.12737000s ++>>> Total wall time: 0.14050508s, and total CPU time : 0.13166000s + +-########## END ITERATION NO. 11 ########## Sat Dec 7 14:42:45 2019 ++########## END ITERATION NO. 11 ########## Fri Oct 9 13:31:24 2020 + +-It. 11 -15.05525782855 1.26D-11 7.22D-07 2.76D-07 DIIS 9 0.13559033s LL SL SS Sat Dec 7 ++It. 11 -15.05525782855 1.26D-11 -8.54D-07 2.76D-07 DIIS 9 0.14050508s LL SL SS Fri Oct 9 + +-########## START ITERATION NO. 12 ########## Sat Dec 7 14:42:45 2019 ++########## START ITERATION NO. 12 ########## Fri Oct 9 13:31:24 2020 + + 12 *** Differential density matrix. DCOVLP = 1.0000 + 12 *** Differential density matrix. DVOVLP( 1) = 1.0000 +-SCR scr.thr. Step1 Step2 Coulomb Exchange CPU-time +-SOfock:LL 1.00D-12 0.00% 14.91% 0.00% 0.01% 0.00819111s +-SOfock:SL 1.00D-12 0.00% 26.31% 0.00% 4.16% 0.04727006s +-SOfock:SS 1.00D-12 27.72% 71.16% 7.71% 10.99% 0.05253100s ++SCR scr.thr. Step1 Step2 Coulomb Exchange WALL-time ++SOfock:LL 1.00D-12 0.00% 14.91% 0.00% 0.01% 0.00926995s ++SOfock:SL 1.00D-12 0.00% 25.16% 0.00% 3.83% 0.04634213s ++SOfock:SS 1.00D-12 21.18% 57.02% 0.45% 2.31% 0.05649400s + >>> CPU time used in SO Fock is 0.11 seconds + >>> WALL time used in SO Fock is 0.11 seconds +->>> Total wall time: 0.11815968s, and total CPU time : 0.11058100s ++>>> Total wall time: 0.12363100s, and total CPU time : 0.11607500s + +-########## END ITERATION NO. 12 ########## Sat Dec 7 14:42:45 2019 ++########## END ITERATION NO. 12 ########## Fri Oct 9 13:31:24 2020 + +-It. 12 -15.05525782855 3.59D-13 1.43D-07 1.38D-08 DIIS 9 0.11815968s LL SL SS Sat Dec 7 ++It. 12 -15.05525782855 3.73D-13 -1.53D-07 1.38D-08 DIIS 9 0.12363100s LL SL SS Fri Oct 9 + + + SCF - CYCLE +@@ -1157,35 +1164,35 @@ + -------------------------------------------------------------------------------------------------------------------------------- + Energy ERGVAL FCKVAL EVCVAL Conv.acc CPU Integrals Time stamp + -------------------------------------------------------------------------------------------------------------------------------- +-It. 1 -7.674280262185 0.00D+00 0.00D+00 0.00D+00 0.12560900s Atom. scrpot Sat Dec 7 +-It. 2 -14.98358612120 7.31D+00 2.41D+00 4.55D-01 0.21618455s LL SL SS Sat Dec 7 +-It. 3 -15.05284570594 6.93D-02 -1.41D-01 5.42D-02 DIIS 2 0.25093168s LL SL SS Sat Dec 7 +-It. 4 -15.05510762061 2.26D-03 -1.10D-02 9.87D-03 DIIS 3 0.23950611s LL SL SS Sat Dec 7 +-It. 5 -15.05525091501 1.43D-04 -3.58D-03 2.02D-03 DIIS 4 0.23837635s LL SL SS Sat Dec 7 +-It. 6 -15.05525770434 6.79D-06 -3.53D-04 3.01D-04 DIIS 5 0.17357306s LL SL SS Sat Dec 7 +-It. 7 -15.05525782410 1.20D-07 -4.18D-05 5.31D-05 DIIS 6 0.16939002s LL SL SS Sat Dec 7 +-It. 8 -15.05525782821 4.11D-09 -1.39D-05 1.07D-05 DIIS 7 0.16520095s LL SL SS Sat Dec 7 +-It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.16172978s LL SL SS Sat Dec 7 +-It. 10 -15.05525782853 4.23D-11 7.89D-07 1.39D-06 DIIS 9 0.14423264s LL SL SS Sat Dec 7 +-It. 11 -15.05525782855 1.26D-11 7.22D-07 2.76D-07 DIIS 9 0.13559033s LL SL SS Sat Dec 7 +-It. 12 -15.05525782855 3.59D-13 1.43D-07 1.38D-08 DIIS 9 0.11815968s LL SL SS Sat Dec 7 ++It. 1 -7.674280262172 0.00D+00 0.00D+00 0.00D+00 0.06623700s Atom. scrpot Fri Oct 9 ++It. 2 -14.98358612120 7.31D+00 2.45D+00 4.55D-01 0.51878285s LL SL SS Fri Oct 9 ++It. 3 -15.05284570594 6.93D-02 -1.44D-01 5.42D-02 DIIS 2 0.16109180s LL SL SS Fri Oct 9 ++It. 4 -15.05510762061 2.26D-03 -1.16D-02 9.87D-03 DIIS 3 0.15968394s LL SL SS Fri Oct 9 ++It. 5 -15.05525091501 1.43D-04 -3.76D-03 2.02D-03 DIIS 4 0.15834403s LL SL SS Fri Oct 9 ++It. 6 -15.05525770434 6.79D-06 -3.61D-04 3.01D-04 DIIS 5 0.15521312s LL SL SS Fri Oct 9 ++It. 7 -15.05525782410 1.20D-07 -4.48D-05 5.31D-05 DIIS 6 0.15497518s LL SL SS Fri Oct 9 ++It. 8 -15.05525782821 4.11D-09 -1.45D-05 1.07D-05 DIIS 7 0.15240192s LL SL SS Fri Oct 9 ++It. 9 -15.05525782849 2.85D-10 -4.04D-06 2.99D-06 DIIS 8 0.15059400s LL SL SS Fri Oct 9 ++It. 10 -15.05525782853 4.23D-11 -1.26D-06 1.39D-06 DIIS 9 0.14401197s LL SL SS Fri Oct 9 ++It. 11 -15.05525782855 1.26D-11 -8.54D-07 2.76D-07 DIIS 9 0.14050508s LL SL SS Fri Oct 9 ++It. 12 -15.05525782855 3.73D-13 -1.53D-07 1.38D-08 DIIS 9 0.12363100s LL SL SS Fri Oct 9 + -------------------------------------------------------------------------------------------------------------------------------- + * Convergence after 12 iterations. + * Average elapsed time per iteration: +- No 2-ints : 0.12560757s +- LL SL SS : 0.18298865s ++ No 2-ints : 0.06805897s ++ LL SL SS : 0.18356681s + + + TOTAL ENERGY + ------------ + +- Electronic energy : -17.364060097770729 ++ Electronic energy : -17.364060097770743 + + Other contributions to the total energy + Nuclear repulsion energy : 2.308802269222842 + + Sum of all contributions to the energy +- Total energy : -15.055257828547887 ++ Total energy : -15.055257828547902 + + + Eigenvalues +@@ -1194,24 +1201,24 @@ + + * Block 1 in E1 : Omega = 1/2 + * Closed shell, f = 1.0000 +- -4.679468376338 ( 2) -0.538243701490 ( 2) ++ -4.679468376327 ( 2) -0.538243701490 ( 2) + * Open shell #1, f = 0.5000 + -0.200107364292 ( 2) + * Virtual eigenvalues, f = 0.0000 +- 0.069973271793 ( 2) 0.146585677662 ( 2) 0.290043259674 ( 2) 0.329894286245 ( 2) 0.443382601574 ( 2) +- 0.636678743326 ( 2) 0.675079413170 ( 2) 1.116750847420 ( 2) 1.366626079642 ( 2) 1.477429645290 ( 2) +- 2.022794797755 ( 2) 2.267117385980 ( 2) 3.573003609718 ( 2) 4.000999068608 ( 2) 7.165692855382 ( 2) +- 7.349371984843 ( 2) 15.727399978192 ( 2) 22.596336602594 ( 2) 58.756173314173 ( 2) 219.560006375315 ( 2) +- 924.777802919416 ( 2) 4979.576710887137 ( 2) ++ 0.069973271798 ( 2) 0.146585677680 ( 2) 0.290043259672 ( 2) 0.329894286248 ( 2) 0.443382601571 ( 2) ++ 0.636678743335 ( 2) 0.675079413169 ( 2) 1.116750847424 ( 2) 1.366626079649 ( 2) 1.477429645297 ( 2) ++ 2.022794797753 ( 2) 2.267117385992 ( 2) 3.573003609720 ( 2) 4.000999068610 ( 2) 7.165692855389 ( 2) ++ 7.349371984860 ( 2) 15.727399978201 ( 2) 22.596336602582 ( 2) 58.756173314180 ( 2) 219.560006375432 ( 2) ++ 924.777802919401 ( 2) 4979.576710887086 ( 2) + + * Block 2 in E1 : Omega = 3/2 + * Virtual eigenvalues, f = 0.0000 +- 0.069977662719 ( 2) 0.329912044238 ( 2) 0.636681004307 ( 2) 0.656492047535 ( 2) 1.366714153093 ( 2) +- 2.022824837061 ( 2) 7.166842638253 ( 2) ++ 0.069977662718 ( 2) 0.329912044241 ( 2) 0.636681004320 ( 2) 0.656492047523 ( 2) 1.366714153101 ( 2) ++ 2.022824837060 ( 2) 7.166842638267 ( 2) + + * Block 3 in E1 : Omega = 5/2 + * Virtual eigenvalues, f = 0.0000 +- 0.656497922027 ( 2) ++ 0.656497922020 ( 2) + + * Occupation in fermion symmetry E1 + * Inactive orbitals +@@ -1321,7 +1328,7 @@ + + (RSETCI) Number of determinants: 3366 (dimension 3366) + +- CPU (Wall) time for generation of determinants: 0.22480200s( 0.22480234s) ++ CPU (Wall) time for generation of determinants: 0.21247500s( 0.21325493s) + + (RSETWOP) Orbital classes: + Inactive orbitals : +@@ -1335,40 +1342,54 @@ + Vector containing mj-values saved as MJVEC on KRMCSCF + + (RTRACTL1) Starting 4-index integral transformation. +- - Integral class 1 : (LL|??) +- - Beginning task 1 of 5 after 0. seconds and 0. CPU-seconds +- - Beginning task 2 of 5 after 0. seconds and 0. CPU-seconds +- - Beginning task 3 of 5 after 0. seconds and 0. CPU-seconds +- - Beginning task 4 of 5 after 0. seconds and 0. CPU-seconds +- - Beginning task 5 of 5 after 0. seconds and 0. CPU-seconds ++ ++ * Max no. of B shells in a task determined to be 8 + - Integral class 2 : (SS|??) +- - Beginning task 6 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 7 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 8 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 9 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 10 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 11 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 12 of 13 after 0. seconds and 0. CPU-seconds +- - Beginning task 13 of 13 after 1. seconds and 1. CPU-seconds ++ - Starting shell A no. 13 after 0.00 seconds. ++ - Starting shell A no. 12 after 0.00 seconds. ++ - Starting shell A no. 11 after 0.07 seconds. ++ - Starting shell A no. 10 after 0.15 seconds. ++ - Starting shell A no. 9 after 0.18 seconds. ++ - Starting shell A no. 8 after 0.24 seconds. ++ - Starting shell A no. 7 after 0.32 seconds. ++ - Starting shell A no. 6 after 0.33 seconds. ++ - Integral class 1 : (LL|??) ++ - Starting shell A no. 5 after 0.37 seconds. ++ - Starting shell A no. 4 after 0.38 seconds. ++ - Starting shell A no. 3 after 0.41 seconds. ++ - Starting shell A no. 2 after 0.43 seconds. ++ - Starting shell A no. 1 after 0.45 seconds. ++ - Process 1 finished at 0.48 seconds after start + +- - Starting symmetrization after 0.62 seconds +- - Finished symmetrization after 0.62 seconds ++ - Starting symmetrization after 0.48 seconds ++ - Finished symmetrization after 0.49 seconds + + + ------ Timing report (in CPU seconds) of module integral transformation + +- Time in Initializing MS4IND file 0.011 seconds +- Time in Computing+transform. integral 0.624 seconds +- Time in Symmetrizing MO integrals 0.000 seconds ++ ++ ++ Master --------- Slaves ------------ ++ ++ Timer Master Minimum Maximum Average ++ ++ Initializing MS4IND file 0.0 0.0 0.0 0.0 ++ Slave requesting task from ma 0.5 0.0 0.0 0.0 ++ Master and slave negotiating 0.0 0.0 0.0 0.0 ++ Symmetrizing MO integrals 0.0 0.0 0.0 0.0 ++ Computing+transform. integral 0.0 0.5 0.5 0.5 ++ ++------ End of timing report ------ ++ + + (RTRACTL1) Total CPU (wall) time used : 00:00:01 ( 00:00:01) +- Transformation ended Sat Dec 7 14:42:46 2019 ++ Transformation ended Fri Oct 9 13:31:25 2020 + // LUCIAREL called + // CIRUN = KR-CI + // Running large-scale CI calculation + +-* REAFCK: Fock matrix read from file DFFCK1 +-* Heading :BeH Sat Dec 7 14:42:43 2019 ++* REAFCK: Fock matrix read from file /dev/shm/build/DIRAC/19.0/intel-2020a-Python-2.7.18-mpi-int6 ++* Heading :BeH Fri Oct 9 13:31:22 2020 + Allocating for 3480 diagonal integrals. + + +@@ -1378,14 +1399,34 @@ + (including imaginary parts) + + ++ =================================================== ++ parallel distribution setup for symmetry irrep 65 ++ =================================================== ++ ++ total number of processes to distribute on : 2 ++ total number of blocks : 13056 ++ total number of active blocks : 29 ++ size of largest TTSS block : 784 ++ overall weighted active block length : 214301 ++ Maximum weighted block size : 61936 ++ ++ ================================ ++ Summation of even distribution ++ ================================ ++ ++ CPU 0 computes 15 blocks with a total weight of 107168 ++ CPU 1 computes 14 blocks with a total weight of 107133 ++ + ============================================================== + ==> allocation of two CI vectors and one resolution vector <== + +- current available free memory in double words: 1999304192 ++ current available free memory in double words: 63304144 + allocate two CI vectors each of length: 3366 + allocate resolution vector of length: 3366 + ============================================================== + ++ ++ + + 2 start vectors based on lowest diagonal elements of H_CI + 1 -15.055258 +@@ -1397,270 +1438,330 @@ + + Maximum number of CI microiterations ... 50 + +- ++ + ---------------------------------------------- +- I'll take you to a place ++ I'll take you to a place + Where we shall find our +- ROOTS, BLOODY ROOTS +- +- Sepultura ++ ROOTS, BLOODY ROOTS ++ ++ Sepultura + ---------------------------------------------- ++ + + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 1 ++ Total energy = -15.05525783 ++ Lowering of energy = -0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 1 +- Total energy = -15.05525783 +- Lowering of energy = -0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 4.37450D-01 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 4.37450D-01 ++ Wall time for microiteration 0.38906469s + +- CPU (Wall) time for microiteration 1.20469400s( 1.21234911s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 2 ++ Total energy = -15.09785782 ++ Lowering of energy = 0.04259999 + +- (MICDV4_ENLMD_REL) CI microiteration no. 2 +- Total energy = -15.09785782 +- Lowering of energy = 0.04259999 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.39990D-01 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.39990D-01 ++ Wall time for microiteration 0.41679055s + +- CPU (Wall) time for microiteration 0.95826800s( 0.96383090s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 3 ++ Total energy = -15.10221442 ++ Lowering of energy = 0.00435660 + +- (MICDV4_ENLMD_REL) CI microiteration no. 3 +- Total energy = -15.10221442 +- Lowering of energy = 0.00435660 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 6.68601D-02 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 6.68601D-02 ++ Wall time for microiteration 0.41734640s + +- CPU (Wall) time for microiteration 1.23481700s( 1.24102225s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 4 ++ Total energy = -15.10336430 ++ Lowering of energy = 0.00114988 + +- (MICDV4_ENLMD_REL) CI microiteration no. 4 +- Total energy = -15.10336430 +- Lowering of energy = 0.00114988 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.84414D-02 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.84414D-02 ++ Wall time for microiteration 0.41587336s + +- CPU (Wall) time for microiteration 0.96459800s( 0.96983010s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 5 ++ Total energy = -15.10355258 ++ Lowering of energy = 0.00018829 + +- (MICDV4_ENLMD_REL) CI microiteration no. 5 +- Total energy = -15.10355258 +- Lowering of energy = 0.00018829 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.86545D-02 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.86545D-02 ++ Wall time for microiteration 0.41766227s + +- CPU (Wall) time for microiteration 1.23176500s( 1.23788811s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 6 ++ Total energy = -15.10365534 ++ Lowering of energy = 0.00010276 + +- (MICDV4_ENLMD_REL) CI microiteration no. 6 +- Total energy = -15.10365534 +- Lowering of energy = 0.00010276 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.02051D-02 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.02051D-02 ++ Wall time for microiteration 0.41570181s + +- CPU (Wall) time for microiteration 0.96846600s( 0.97378551s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 7 ++ Total energy = -15.10368496 ++ Lowering of energy = 0.00002962 + +- (MICDV4_ENLMD_REL) CI microiteration no. 7 +- Total energy = -15.10368496 +- Lowering of energy = 0.00002962 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 6.64018D-03 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 6.64018D-03 ++ Wall time for microiteration 0.41870350s + +- CPU (Wall) time for microiteration 1.24741500s( 1.25294369s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 8 ++ Total energy = -15.10369583 ++ Lowering of energy = 0.00001087 + +- (MICDV4_ENLMD_REL) CI microiteration no. 8 +- Total energy = -15.10369583 +- Lowering of energy = 0.00001087 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.19312D-03 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 3.19312D-03 ++ Wall time for microiteration 0.41609852s + +- CPU (Wall) time for microiteration 0.96903700s( 0.97438777s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 9 ++ Total energy = -15.10370048 ++ Lowering of energy = 0.00000465 + +- (MICDV4_ENLMD_REL) CI microiteration no. 9 +- Total energy = -15.10370048 +- Lowering of energy = 0.00000465 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.23467D-03 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 3.23467D-03 ++ Wall time for microiteration 0.41777307s + +- CPU (Wall) time for microiteration 1.22110400s( 1.22825285s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 10 ++ Total energy = -15.10370322 ++ Lowering of energy = 0.00000274 + +- (MICDV4_ENLMD_REL) CI microiteration no. 10 +- Total energy = -15.10370322 +- Lowering of energy = 0.00000274 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.97047D-03 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.97047D-03 ++ Wall time for microiteration 0.41673967s + +- CPU (Wall) time for microiteration 0.92580700s( 0.93142437s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 11 ++ Total energy = -15.10370430 ++ Lowering of energy = 0.00000108 + +- (MICDV4_ENLMD_REL) CI microiteration no. 11 +- Total energy = -15.10370430 +- Lowering of energy = 0.00000108 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.39286D-03 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.39286D-03 ++ Wall time for microiteration 0.41791135s + +- CPU (Wall) time for microiteration 1.21935300s( 1.22573134s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 12 ++ Total energy = -15.10370471 ++ Lowering of energy = 0.00000041 + +- (MICDV4_ENLMD_REL) CI microiteration no. 12 +- Total energy = -15.10370471 +- Lowering of energy = 0.00000041 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 6.78879D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 6.78879D-04 ++ Wall time for microiteration 0.41635790s + +- CPU (Wall) time for microiteration 0.96845200s( 0.97368623s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 13 ++ Total energy = -15.10370491 ++ Lowering of energy = 0.00000019 + +- (MICDV4_ENLMD_REL) CI microiteration no. 13 +- Total energy = -15.10370491 +- Lowering of energy = 0.00000019 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 7.08771D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 7.08771D-04 ++ Wall time for microiteration 0.42354180s + +- CPU (Wall) time for microiteration 1.24966800s( 1.25543883s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 14 ++ Total energy = -15.10370502 ++ Lowering of energy = 0.00000012 + +- (MICDV4_ENLMD_REL) CI microiteration no. 14 +- Total energy = -15.10370502 +- Lowering of energy = 0.00000012 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 4.23480D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 4.23480D-04 ++ Wall time for microiteration 0.41584093s + +- CPU (Wall) time for microiteration 0.95248500s( 0.95758762s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 15 ++ Total energy = -15.10370507 ++ Lowering of energy = 0.00000005 + +- (MICDV4_ENLMD_REL) CI microiteration no. 15 +- Total energy = -15.10370507 +- Lowering of energy = 0.00000005 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.04533D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 3.04533D-04 ++ Wall time for microiteration 0.41808349s + +- CPU (Wall) time for microiteration 1.24777200s( 1.25355540s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 16 ++ Total energy = -15.10370509 ++ Lowering of energy = 0.00000002 + +- (MICDV4_ENLMD_REL) CI microiteration no. 16 +- Total energy = -15.10370509 +- Lowering of energy = 0.00000002 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.50921D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.50921D-04 ++ Wall time for microiteration 0.41666777s + +- CPU (Wall) time for microiteration 1.01747300s( 1.05122897s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 17 ++ Total energy = -15.10370510 ++ Lowering of energy = 0.00000001 + +- (MICDV4_ENLMD_REL) CI microiteration no. 17 +- Total energy = -15.10370510 +- Lowering of energy = 0.00000001 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.53262D-04 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.53262D-04 ++ Wall time for microiteration 0.41730021s + +- CPU (Wall) time for microiteration 1.24111700s( 1.24705948s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 18 ++ Total energy = -15.10370510 ++ Lowering of energy = 0.00000001 + +- (MICDV4_ENLMD_REL) CI microiteration no. 18 +- Total energy = -15.10370510 +- Lowering of energy = 0.00000001 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 9.48004D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 9.48004D-05 ++ Wall time for microiteration 0.41675383s + +- CPU (Wall) time for microiteration 0.96130400s( 0.96728180s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 19 ++ Total energy = -15.10370510 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 19 +- Total energy = -15.10370510 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 6.58500D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 6.58500D-05 ++ Wall time for microiteration 0.41868551s + +- CPU (Wall) time for microiteration 1.24445300s( 1.25093647s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 20 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 20 +- Total energy = -15.10370511 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.40204D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 3.40204D-05 ++ Wall time for microiteration 0.41628122s + +- CPU (Wall) time for microiteration 0.96835700s( 0.97404379s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 21 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 21 +- Total energy = -15.10370511 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.33886D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 3.33886D-05 ++ Wall time for microiteration 0.41618816s + +- CPU (Wall) time for microiteration 1.18932100s( 1.19510286s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 22 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 22 +- Total energy = -15.10370511 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 2.14673D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 2.14673D-05 ++ Wall time for microiteration 0.41732191s + +- CPU (Wall) time for microiteration 0.96339800s( 0.97118922s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 23 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 23 +- Total energy = -15.10370511 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.44211D-05 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 1.44211D-05 ++ Wall time for microiteration 0.41780390s + +- CPU (Wall) time for microiteration 1.23398800s( 1.23978875s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 24 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) CI microiteration no. 24 +- Total energy = -15.10370511 +- Lowering of energy = 0.00000000 ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 7.72802D-06 + +- Norm of CI residuals (thr = 1.00D-05) +- 1 7.72802D-06 ++ Wall time for microiteration 0.41720308s + +- CPU (Wall) time for microiteration 0.08609000s( 0.08613085s) + ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 25 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 + +- (MICDV4_ENLMD_REL) Micro iterations converged. ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 7.37801D-06 + +- Core energy = 2.30880227 +- Active energies = -17.41250738 +- Final CI energies = -15.10370511 ++ Wall time for microiteration 0.41947213s + +- root 1 ...... converged! + +- I have completed task KR-CI in 26.37510378s (wall time) ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 26 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 ++ ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 4.89162D-06 ++ ++ Wall time for microiteration 0.41700623s ++ ++ ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 27 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 ++ ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 3.20093D-06 ++ ++ Wall time for microiteration 0.41741276s ++ ++ ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 28 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 ++ ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.76410D-06 ++ ++ Wall time for microiteration 0.41627715s ++ ++ ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 29 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 ++ ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.64937D-06 ++ ++ Wall time for microiteration 0.41783292s ++ ++ ++ (MICDV4_ENLMD_REL_PAR) CI microiteration no. 30 ++ Total energy = -15.10370511 ++ Lowering of energy = 0.00000000 ++ ++ Norm of CI residuals (thr = 1.00D-06) ++ 1 1.11914D-06 ++ ++ Wall time for microiteration 0.00072046s ++ ++ ++ (MICDV4_ENLMD_REL_PAR) Micro iterations converged. ++ ++ Core energy = 2.30880227 ++ Active energies = -17.41250738 ++ Final CI energies = -15.10370511 ++ ++ root 1 ...... converged! ++ ++ I have completed task KR-CI in 12.58797884s (wall time) + + (ROPTST) KR-CI calculation ended properly. + +->>> TOTAL CPU (WALL) TIME IN KR-CI: 27.82514200s(28.00508189s) ++>>> TOTAL CPU (WALL) TIME IN KR-CI: 14.02860500s(14.16464686s) + + + +@@ -1699,7 +1800,7 @@ + + (RSETCI) Number of determinants: 3366 (dimension 3366) + +- CPU (Wall) time for generation of determinants: 0.25193400s( 0.25195498s) ++ CPU (Wall) time for generation of determinants: 0.19848500s( 0.20092607s) + + (RSETWOP) Orbital classes: + Inactive orbitals : +@@ -1745,12 +1846,12 @@ + _________________________________ + Total 1 + +- Diagonal and Off-diagonal blocks are exchanged for Y1-HYP +- Diagonal and Off-diagonal blocks are exchanged for Y2-HYP +- Diagonal and Off-diagonal blocks are exchanged for X1-HYP +- Sign of the lower diagonal block is changed for X1-HYP +- Diagonal and Off-diagonal blocks are exchanged for X2-HYP +- Sign of the lower diagonal block is changed for X2-HYP ++ Diagonal and Off-diagonal blocks are exchanged for Y1-HYP ++ Diagonal and Off-diagonal blocks are exchanged for Y2-HYP ++ Diagonal and Off-diagonal blocks are exchanged for X1-HYP ++ Sign of the lower diagonal block is changed for X1-HYP ++ Diagonal and Off-diagonal blocks are exchanged for X2-HYP ++ Sign of the lower diagonal block is changed for X2-HYP + // LUCIAREL called + // CIRUN = PROP1 + // Computing one-electron properties. +@@ -1770,10 +1871,28 @@ + A1-SPS A2 A2 + A2-SPS A2 A2 + ++ =================================================== ++ parallel distribution setup for symmetry irrep 65 ++ =================================================== ++ ++ total number of processes to distribute on : 2 ++ total number of blocks : 13056 ++ total number of active blocks : 29 ++ size of largest TTSS block : 784 ++ overall weighted active block length : 26784 ++ Maximum weighted block size : 7056 ++ ++ ================================ ++ Summation of even distribution ++ ================================ ++ ++ CPU 0 computes 14 blocks with a total weight of 13391 ++ CPU 1 computes 15 blocks with a total weight of 13393 ++ + ============================================================== + ==> allocation of two CI vectors and one resolution vector <== + +- current available free memory in double words: 1999885056 ++ current available free memory in double words: 63885000 + allocate two CI vectors each of length: 3366 + allocate resolution vector of length: 3366 + ============================================================== +@@ -1803,7 +1922,7 @@ + 0 -15.1037051064 0.000000000000 0.000000000000 0.000000000000 (1 ) + ________________________________________________________________________________________________________ + +- ++ + + ******************************************************** + ********* electron Electric Dipole Moment ************** +@@ -1812,9 +1931,9 @@ + E_eff [a.u.] E_eff [GV/cm] + + __________________ _________________ __________________________________________________________ +- EEDM state 1(1 ) state 1(1 ) -0.000110451662 -0.000567965276 ++ EEDM state 1(1 ) state 1(1 ) -0.000110451220 -0.000567963004 + __________________________________________ __________________________________________________________ +- ++ + + ******************************************************** + ********* Hyperfine Structure Constants ************** +@@ -1823,45 +1942,45 @@ + < state | Y1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = -1.5598078852941472E-006 +- MHYP state 1(1 ) state 1(1 ) -0.005905849748 0.000000009212 ++ PREFACNUC = -1.559807885294147E-006 ++ MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 + __________________________________________ __________________________________________________________ + + < state | Y2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = 1.1099508005612513E-005 +- MHYP state 1(1 ) state 1(1 ) -0.000974096023 -0.000000010812 ++ PREFACNUC = 1.109950800561251E-005 ++ MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 + __________________________________________ __________________________________________________________ + + < state | X1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = -1.5598078852941472E-006 +- MHYP state 1(1 ) state 1(1 ) -0.005905849748 0.000000009212 ++ PREFACNUC = -1.559807885294147E-006 ++ MHYP state 1(1 ) state 1(1 ) -0.005905650151 0.000000009212 + __________________________________________ __________________________________________________________ + + < state | X2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = 1.1099508005612513E-005 +- MHYP state 1(1 ) state 1(1 ) -0.000974096023 -0.000000010812 ++ PREFACNUC = 1.109950800561251E-005 ++ MHYP state 1(1 ) state 1(1 ) -0.000974190577 -0.000000010813 + __________________________________________ __________________________________________________________ + + < state | Z1-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = -1.5598078852941472E-006 +- MHYP state 1(1 ) state 1(1 ) -0.006752396302 0.000000010532 ++ PREFACNUC = -1.559807885294147E-006 ++ MHYP state 1(1 ) state 1(1 ) -0.006752216685 0.000000010532 + __________________________________________ __________________________________________________________ + + < state | Z2-HYP [alpha x E] | state > Hyperfine Const. [a.u.] Delta E_HypFin [a.u.] + + __________________ _________________ __________________________________________________________ +- PREFACNUC = 1.1099508005612513E-005 +- MHYP state 1(1 ) state 1(1 ) -0.001232804132 -0.000000013684 ++ PREFACNUC = 1.109950800561251E-005 ++ MHYP state 1(1 ) state 1(1 ) -0.001232901004 -0.000000013685 + __________________________________________ __________________________________________________________ +- ++ + + ******************************************************** + ********* e-N S-PS interaction Parameter ************* +@@ -1870,13 +1989,13 @@ + e-N S-PS Parameter [a.u.] Norm [a.u.] + + __________________ _________________ __________________________________________________________ +- ENSPS state 1(1 ) state 1(1 ) 0.001238402290 0.001238402290 ++ ENSPS state 1(1 ) state 1(1 ) 0.001238395771 0.001238395771 + __________________________________________ __________________________________________________________ + + e-N S-PS Parameter [a.u.] Norm [a.u.] + + __________________ _________________ __________________________________________________________ +- ENSPS state 1(1 ) state 1(1 ) -0.000041687482 0.000041687482 ++ ENSPS state 1(1 ) state 1(1 ) -0.000041690709 0.000041690709 + __________________________________________ __________________________________________________________ + + ***************************************************** +@@ -1885,35 +2004,35 @@ + + + +- Date and time (Linux) : Sat Dec 7 14:43:18 2019 +- Host name : malaya.tcs ++ Date and time (Linux) : Fri Oct 9 13:31:40 2020 ++ Host name : node3414.kirlia.os + +->>>> Node 0, utime: 33, stime: 0, minflt: 10512, majflt: 0, nvcsw: 712, nivcsw: 1212, maxrss: 192920 +->>>> Total WALL time used in DIRAC: 36s ++>>>> Node 0, utime: 17, stime: 0, minflt: 102299, majflt: 0, nvcsw: 729, nivcsw: 1895, maxrss: 647320 ++>>>> Total WALL time used in DIRAC: 19s + + Dynamical Memory Usage Summary for Master + +- Mean allocation size (Mb) : 234.90 ++ Mean allocation size (Mb) : 8.01 + +- Largest 10 allocations ++ Largest 10 allocations + +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in KRCI_CALC +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PSISCF +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PAMSET - 2 +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in GMOTRA +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for WORK in PAMSET - 1 +- 15258.79 Mb at subroutine __allocator_track_if_MOD_allocator_registe for test allocation of work array in DIRAC mai +- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable +- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable +- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable +- 3.81 Mb at subroutine __allocator_track_if_MOD_allocator_registe for unnamed variable ++ 488.28 Mb at subroutine krci_calc_+0xc4 for WORK in KRCI_CALC ++ 488.28 Mb at subroutine psiscf_+0xa9 for WORK in PSISCF ++ 488.28 Mb at subroutine pamset_+0x16ac for WORK in PAMSET - 2 ++ 488.28 Mb at subroutine gmotra_+0x47d0 for WORK in GMOTRA ++ 488.28 Mb at subroutine pamset_+0x97 for WORK in PAMSET - 1 ++ 488.28 Mb at subroutine MAIN__+0x9af for test allocation of work array in DIRAC mai ++ 3.81 Mb at subroutine set_hop_dbg_+0x788 for unnamed variable ++ 3.81 Mb at subroutine set_hop_dbg_+0x773 for unnamed variable ++ 3.81 Mb at subroutine set_hop_dbg_+0x75e for unnamed variable ++ 3.81 Mb at subroutine set_hop_dbg_+0x749 for unnamed variable + +- Peak memory usage: 15274.30 MB +- Peak memory usage: 14.916 GB +- reached at subroutine : __allocator_track_if_MOD_allocator_registe ++ Peak memory usage: 503.80 MB ++ Peak memory usage: 0.492 GB ++ reached at subroutine : set_hop_dbg_+0x788 + for variable : unnamed variable + + MEMGET high-water mark: 0.00 MB + + ***************************************************** +-DIRAC pam run in /home/mknayak/dirac-repo-05-12-18/work/eedm_mhyp_ensps_krci ++DIRAC pam run in /dev/shm/build/DIRAC/19.0/intel-2020a-Python-2.7.18-mpi-int64/easybuild_obj/test/eedm_mhyp_ensps_krci diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_test_path.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_test_path.patch new file mode 100644 index 00000000000..61eb0bb3734 --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix_test_path.patch @@ -0,0 +1,26 @@ +# Fix hard coded DIRAC/utils path in fde_response_mag and fde_response_shield tests +# OCT 7th 2020 by B. Hajgato (UGent) +diff -ru DIRAC-19.0-Source.orig/test/fde_response_mag/test DIRAC-19.0-Source/test/fde_response_mag/test +--- DIRAC-19.0-Source.orig/test/fde_response_mag/test 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/test/fde_response_mag/test 2020-10-07 22:41:25.277776298 +0200 +@@ -16,7 +16,7 @@ + + + test.run(['dc_pbe'], ['h2o-1.xyz'], args='--get="numerical_grid"') +-os.system('../../../utils/fde-mag/dft_to_fde_grid_convert.py') ++os.system('../../../DIRAC*/utils/fde-mag/dft_to_fde_grid_convert.py') + + shutil.copy('numerical_grid', 'FILEEX') + shutil.copy('numerical_grid', 'GRIDOUT') +diff -ru DIRAC-19.0-Source.orig/test/fde_response_shield/test DIRAC-19.0-Source/test/fde_response_shield/test +--- DIRAC-19.0-Source.orig/test/fde_response_shield/test 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/test/fde_response_shield/test 2020-10-07 22:41:45.348275614 +0200 +@@ -17,7 +17,7 @@ + + + test.run(['dc_pbe'], ['h2o-1.xyz'], args='--get="numerical_grid"') +-os.system('../../../utils/fde-mag/dft_to_fde_grid_convert.py') ++os.system('../../../DIRAC*/utils/fde-mag/dft_to_fde_grid_convert.py') + + shutil.copy('numerical_grid', 'FILEEX') + shutil.copy('numerical_grid', 'GRIDOUT') diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch index 03e2ec27a6b..d0d7bfcb0ac 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch @@ -1,23 +1,15 @@ -Removed tests which fails on intel compilers. - -"bss_energy" has slight abs difference (2.24e-07) in calculation. - "operators_mo_mtx_elements" doesn't run when mpi is enabled (even if test doesn't use mpi) see: https://ccportal.ims.ac.jp/en/node/2411 Author: Pavel Grochal (INUITS) +Comments from B. Hajgato (UGent) at OCT 5th 2020: +In the test python program both ignore_sign and ignore_order is set to True, +but ignore_order does not seem to work perfectly. +Using ifort 20.1 and MKL20.1 on cascadelake a manual comparison passed, meanwhile the automatic +comparison failed. Therefore, test will be disabled. diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake --- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 +++ DIRAC-19.0-Source/cmake/custom/test.cmake 2020-09-24 12:54:02.524830820 +0200 -@@ -102,7 +102,7 @@ - dirac_test(basis_input "basis;short" "") - dirac_test(basis_input_scripted "basis;long" "3600") - dirac_test(bsse "basis;short" "") --dirac_test(bss_energy "short" "") -+# dirac_test(bss_energy "short" "") - dirac_test(pam_test "short;pam" "") - dirac_test(cc_essential "short;cc" "") - dirac_test(cc_linear "short;cc" "") @@ -158,9 +158,8 @@ dirac_test(lucita_q_corrections "short;qcorr;ci" "") dirac_test(x2c-SCF_to_4c-SCF "short;x2c;4c;scf" "") diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch new file mode 100644 index 00000000000..d0cd900f24c --- /dev/null +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_use_easybuild_opts_intel.patch @@ -0,0 +1,33 @@ +# Take EasyBuild compiler flags for C, C++, and Fortran +# OCT 5th, 2020 by B. Hajgato (UGent) +diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.C.cmake 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.C.cmake 2020-10-07 19:53:57.517988580 +0200 +@@ -1,5 +1,5 @@ + if(CMAKE_C_COMPILER_ID MATCHES Intel) +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -wd981 -wd279 -wd383 -wd1572 -wd177") ++ set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -wd981 -wd279 -wd383 -wd1572 -wd177") + set(CMAKE_C_FLAGS_RELEASE "-O2") + set(CMAKE_C_FLAGS_DEBUG "-O0") + endif() +diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.CXX.cmake 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.CXX.cmake 2020-10-07 19:54:10.338306645 +0200 +@@ -1,5 +1,5 @@ + if(CMAKE_CXX_COMPILER_ID MATCHES Intel) + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unknown-pragmas") +- set(CMAKE_CXX_FLAGS_RELEASE "-debug -O3 -DNDEBUG") ++ set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG") + set(CMAKE_CXX_FLAGS_DEBUG "-O0 -debug -DDEBUG") + endif() +diff -ru DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake +--- DIRAC-19.0-Source.orig/cmake/custom/compiler_flags/Intel.Fortran.cmake 2019-12-12 17:26:15.000000000 +0100 ++++ DIRAC-19.0-Source/cmake/custom/compiler_flags/Intel.Fortran.cmake 2020-10-07 19:55:34.670398011 +0200 +@@ -1,5 +1,5 @@ + if(CMAKE_Fortran_COMPILER_ID MATCHES Intel) +- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -g -traceback -DVAR_IFORT") +- set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -ip") ++ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -w -assume byterecl -DVAR_IFORT") ++ set(CMAKE_Fortran_FLAGS_RELEASE " ") + set(CMAKE_Fortran_FLAGS_DEBUG "-O0") + endif() From 68bb501137dd71e518d4b46d2a2fe1cd5c2a1927 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Mon, 12 Oct 2020 13:42:35 +0200 Subject: [PATCH 424/698] minor fixes --- .../d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb | 7 +++---- .../DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb | 4 ++-- .../d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch | 6 +++--- .../d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb index a51f922eca5..c938fbf458e 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-int64.eb @@ -20,8 +20,8 @@ patches = [ ] checksums = [ 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz - '5ae7ade408310a0309178876e9f5ddc80ecd6b85c862c88899fcdca386dd9c70', # DIRAC-19.0_remove-broken-tests-intel.patch - '13c7b19da10a7db585fb6d57eda8474cb71cdd89d6c4844e80276d3aa05e2b4f', # DIRAC-19.0_fix-bss_energy_test.patch + 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch + 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch ] @@ -49,11 +49,10 @@ configopts += '-DEXPLICIT_LIBS="${LIBLAPACK_MT}" ' configopts += '-DENABLE_PCMSOLVER=OFF ' configopts += '-G"Unix Makefiles" ' -prebuildopts = "make -j36 ; make -j36 ; make -j36 ;" parallel = 1 pretestopts = 'export DIRAC_TMPDIR=%(builddir)s/scratch && ' -runtest = 'test ARGS=-j16' +runtest = 'test' sanity_check_paths = { 'files': ['bin/pam-dirac', 'share/dirac/dirac.x'], diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb index 450913679b8..bdb2729a3aa 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0-intel-2020a-Python-2.7.18-mpi-int64.eb @@ -21,8 +21,8 @@ patches = [ ] checksums = [ 'f0e3610bdd1fbcff90cdfb4cf3fd7582a4762f533af7d635c4bc4d114f402c32', # DIRAC-19.0-Source.tar.gz - '5ae7ade408310a0309178876e9f5ddc80ecd6b85c862c88899fcdca386dd9c70', # DIRAC-19.0_remove-broken-tests-intel.patch - '13c7b19da10a7db585fb6d57eda8474cb71cdd89d6c4844e80276d3aa05e2b4f', # DIRAC-19.0_fix-bss_energy_test.patch + 'cb0e07097499fe59180d79a5db9ee883b9c83e16dcc6210fd945072c3a54c8a4', # DIRAC-19.0_remove-broken-tests-intel.patch + 'e66be847d87ccfda23687de31a3a7c8d71c97b0accd290cf7ade4b4184f1fb93', # DIRAC-19.0_fix-bss_energy_test.patch '666a9053d6c1287ee7aa471d18436133931959b3eacb7619d5197dbfb4e0c1fe', # DIRAC-19.0_use_easybuild_opts_intel.patch '527680cab911a8c7a52347d7ace516a497b725043537a6274670a1aaa97bfb0f', # DIRAC-19.0_fix_test_path.patch 'ccc26fc320f0967211b6390244b1fa359ba5d0294071d5d2cb9e36b4652a52b2', # DIRAC-19.0_fix_mpi_tests.patch diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch index 7cb717bd553..2a73d6aaabf 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_fix-bss_energy_test.patch @@ -1,8 +1,8 @@ -# it seems that bss_energy test is broken, the reference calculation is form 2004 +# It seems that bss_energy test is broken, the reference calculation is form 2004 # The fact that only the SCF energy different and the consecutive post-HF correlation -# energies are the same s a strong hnt that the HF wavefunction should be the same, +# energies are the same is a strong hint that the HF wavefunction should be the same, # but the energies for some reason are different. -# THe test was recalulated suing the following compilers/BLAS libaries on cascadelake +# The test was recalulated using the following compilers/BLAS libaries on cascadelake # architecture, and the results are practially the same. # Based on this facts, the reference test result was changed to the intel result below. # diff --git a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch index d0d7bfcb0ac..5ccef03e4cc 100644 --- a/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch +++ b/easybuild/easyconfigs/d/DIRAC/DIRAC-19.0_remove-broken-tests-intel.patch @@ -5,7 +5,7 @@ Author: Pavel Grochal (INUITS) Comments from B. Hajgato (UGent) at OCT 5th 2020: In the test python program both ignore_sign and ignore_order is set to True, but ignore_order does not seem to work perfectly. -Using ifort 20.1 and MKL20.1 on cascadelake a manual comparison passed, meanwhile the automatic +Using ifort 2020.1 and MKL2020.1 on cascadelake a manual comparison passed, meanwhile the automatic comparison failed. Therefore, test will be disabled. diff -ru DIRAC-19.0-Source.orig/cmake/custom/test.cmake DIRAC-19.0-Source/cmake/custom/test.cmake --- DIRAC-19.0-Source.orig/cmake/custom/test.cmake 2019-12-12 17:26:15.000000000 +0100 From 2f8d8b8bbdc09924ae99ce008c86d088c9fd16d0 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Mon, 12 Oct 2020 16:30:32 +0200 Subject: [PATCH 425/698] Create nanomax-analysis-utils-0.4-foss-2019b-Python-3.7.4.eb --- ...lysis-utils-0.4-foss-2019b-Python-3.7.4.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..06ba1ff4523 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('silx', '0.13.2', versionsuffix), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5e9d931c94ee3f36b3bccb448036497e033d37f2e3f03f5ea8c004f85a0bdb31'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' From ac9e10e2bb9e4868011ba3e85a3dea434a4d013a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 16:40:05 +0200 Subject: [PATCH 426/698] adding easyconfigs: PyGEOS-0.8-foss-2020a-Python-3.8.2.eb --- .../PyGEOS-0.8-foss-2020a-Python-3.8.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..0077bcbf17a --- /dev/null +++ b/easybuild/easyconfigs/p/PyGEOS/PyGEOS-0.8-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,29 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'PyGEOS' +version = '0.8' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://pygeos.readthedocs.io" +description = """PyGEOS is a C/Python library with vectorized geometry functions. The geometry operations are done in + the open-source geometry library GEOS. PyGEOS wraps these operations in NumPy ufuncs providing a performance + improvement when operating on arrays of geometries.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['45b7e1aaa5fc9ff53565ef089fb75c53c419ace8cee18385ec1d7c1515c17cbc'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('GEOS', '3.8.1', versionsuffix), +] + +sanity_pip_check = True +use_pip = True +download_dep_fail = True + +moduleclass = 'geo' From 1008fe1f357e1a7c28021bd71bdb821d57a8049f Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Mon, 12 Oct 2020 16:45:35 +0200 Subject: [PATCH 427/698] Unzip is only required as a build dependency. --- easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb index 00bf3500083..223defbfc93 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.2-GCCcore-9.3.0.eb @@ -12,6 +12,10 @@ source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['e634a7a74776c2b89516b2e013dda1728c89c8149b9863b8cea21946daf9d561'] +builddependencies = [ + ('UnZip', '6.0'), +] + dependencies = [ ('binutils', '2.34'), # required for pip install that involves compilation ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib @@ -20,7 +24,6 @@ dependencies = [ ('ncurses', '6.2'), ('SQLite', '3.31.1'), ('XZ', '5.2.5'), - ('UnZip', '6.0'), ('GMP', '6.2.0'), # required for pycrypto ('libffi', '3.3'), # required for cryptography # OS dependency should be preferred if the os version is more recent then this version, From 51a6ea0cc3986f292b796f896f82747ac1702b99 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 16:47:27 +0200 Subject: [PATCH 428/698] adding easyconfigs: rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb, rasterio-1.1.7-foss-2020a-Python-3.8.2.eb --- .../rasterio-1.1.7-foss-2020a-Python-3.8.2.eb | 75 +++++++++++++++++++ ...terstats-0.15.0-foss-2020a-Python-3.8.2.eb | 42 +++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..a1e590f73ae --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.1.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy + ('matplotlib', '3.2.1', versionsuffix), + ('GDAL', '3.0.4', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('affine', '2.3.0', { + 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('jmespath', '0.10.0', { + 'checksums': ['b85d0567b8666149a93172712e68920734333c0ce7e89b78b3e987f71e5ed4f9'], + }), + ('botocore', '1.18.16', { + 'checksums': ['f0616d2c719691b94470307cee8adf89ceb1657b7b6f9aa1bf61f9de5543dbbb'], + }), + ('s3transfer', '0.3.3', { + 'checksums': ['921a37e2aefc64145e7b73d50c71bb4f26f46e4c9f414dc648c6245ff92cf7db'], + }), + ('boto3', '1.15.16', { + 'checksums': ['454a8dfb7b367a058c7967ef6b4e2a192c318f10761769fd1003cf7f2f5a7db9'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.5.0', { + 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'checksums': ['8418c024f9bf7350d03855039d2700064532bae33a3c6ee885c8b6c8fc13415a'], + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..00d6dedde45 --- /dev/null +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'rasterstats' +version = '0.15.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/perrygeo/python-rasterstats' +description = "rasterstats is a Python module for summarizing geospatial raster datasets based on vector geometries." + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # for numpy + ('Shapely', '1.7.1', versionsuffix), + ('Fiona', '1.8.16', versionsuffix), + ('rasterio', '1.1.7', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('affine', '2.3.0', { + 'checksums': ['2e045def1aa29e613c42e801a7e10e0b9bacfed1a7c6af0cadf8843530a15102'], + }), + ('cligj', '0.5.0', { + 'checksums': ['6c7d52d529a78712491974f975c33473f430c0f7beb18c0d7a402a743dcb460a'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + (name, version, { + 'checksums': ['d554fbc7e749e5649dfcdbd7ea8e21c7388437bc66ef13fde9ef3662a258b277'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 5412f99c1d315fc7e54a43484554a3dd6041c07c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 17:05:18 +0200 Subject: [PATCH 429/698] remove superfluous setting of download_dep_fail in rasterio/rasterstats easyconfigs --- .../r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb | 1 - .../r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb index a1e590f73ae..7979382b18f 100644 --- a/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.1.7-foss-2020a-Python-3.8.2.eb @@ -16,7 +16,6 @@ dependencies = [ ('GDAL', '3.0.4', versionsuffix), ] -download_dep_fail = True use_pip = True exts_default_options = {'source_urls': [PYPI_SOURCE]} diff --git a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb index 00d6dedde45..c910d1deaa7 100644 --- a/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/r/rasterstats/rasterstats-0.15.0-foss-2020a-Python-3.8.2.eb @@ -17,7 +17,6 @@ dependencies = [ ('rasterio', '1.1.7', versionsuffix), ] -download_dep_fail = True use_pip = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From 23c4a7616e4b37d7c6e4e91d6f52fae06c743cb9 Mon Sep 17 00:00:00 2001 From: Terje Kvernes Date: Mon, 12 Oct 2020 17:29:35 +0200 Subject: [PATCH 430/698] Add patch comments. --- ...EA-3.0.0_support_aarch64_and_ppc64le.patch | 6 ++++++ ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 19 ++----------------- .../mzR-2.22.0_use-external-boost.patch | 4 ++++ 3 files changed, 12 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch index 9394f5ce815..92d909e5085 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch @@ -1,3 +1,9 @@ +# Fixes for POWER and aarch64. +# Architecture detection and a way to avoid an extremely +# long-standing GCC bug that doesn't do constant folding +# for 128-bit IBM long double. +# +# Author: @zao (Lars Viklund) diff --git a/src/bituint/bituint.h b/src/bituint/bituint.h index bdce07a..c34381c 100644 --- a/src/bituint/bituint.h diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index fba9cb2da72..e8a2af39504 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -164,9 +164,6 @@ exts_list = [ ('impute', '1.62.0', { 'checksums': ['10541b1c2476ab5a78e1f4d2961710db1b98a1076ff33ead6f9c8fcb02353798'], }), - ('fs', '1.4.1', { - 'checksums': ['ae9103dff26ca56a34901408bd650a2949f491b2a0886c686a51a179d38b7a4e'], - }), ('shinyFiles', '0.8.0', { 'checksums': ['1ca1455c99f6559fa8a790d5f16a79485ea76ed2dc4eaf1b650665e1cee89e3f'], }), @@ -179,12 +176,6 @@ exts_list = [ ('hgu133plus2.db', '3.2.3', { 'checksums': ['a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549'], }), - ('sys', '3.3', { - 'checksums': ['a6217c2a7240ed68614006f392c6d062247dab8b9b0d498f95e947110df19b93'], - }), - ('askpass', '1.1', { - 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], - }), ('illuminaio', '0.30.0', { 'checksums': ['ec180c39921f8707c09e2226a2feaef80576f581fb872a012f42a9b2433ea844'], }), @@ -467,7 +458,7 @@ exts_list = [ 'checksums': [ '802821ac1dbe27c6cfc4523fe6ec37155be3df21fb47e4d8f83a79df26d8dffa', # LEA_3.0.0.tar.gz # LEA-3.0.0_support_aarch64_and_ppc64le.patch - '36244fb693e6c40e4d5a84775cc078118e81a7c0dec15905e38ea7feed1ce14f', + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', ], }), ('tximport', '1.16.0', { @@ -509,9 +500,6 @@ exts_list = [ ('SC3', '1.16.0', { 'checksums': ['29918e7a78858ef6602c0f461bf33e32af5d384448029ba1368be41118c2a797'], }), - ('clue', '0.3-57', { - 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], - }), ('ComplexHeatmap', '2.4.2', { 'checksums': ['14e4f92155aaf8d5c92aeab47b890641942b52599928f9ba5ac826073bef5d06'], }), @@ -564,7 +552,7 @@ exts_list = [ 'patches': ['mzR-2.22.0_use-external-boost.patch'], 'checksums': [ '9509d6d831584af8866aa3d1dd1b22f4333e85fafa0c48e4b18ad1f2a34712e5', # mzR_2.22.0.tar.gz - '5b524c5a0c9ffce91012a9f3b1918e5e2ed68d739316949b7790e6620ff7c8f1', # mzR-2.22.0_use-external-boost.patch + 'bc58aa8ea7ba7c287222049f1cf7cbf2a49ad08d1fe3b5af0965867a7fffc36b', # mzR-2.22.0_use-external-boost.patch ], }), ('MSnbase', '2.14.0', { @@ -760,9 +748,6 @@ exts_list = [ ('isoband', '0.2.1', { 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], }), - ('ggplot2', '3.3.0', { - 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], - }), ('ggcyto', '1.16.0', { 'checksums': ['e012f204a01c6b3427a5b29050e37c8034f44a9a5a30ba50b75dcae3d57b06c6'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch index 51f0d3aae28..5b4a6213242 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch @@ -1,3 +1,7 @@ +# Use external boost provided by EasyBuild instead of +# a bundled old version that doesn't work on aarch64. +# +# Author: @zao (Lars Viklund) diff -ru mzR.orig/src/Makevars mzR/src/Makevars --- mzR.orig/src/Makevars 2020-04-27 22:27:42.000000000 +0200 +++ mzR/src/Makevars 2020-10-01 14:26:45.334914542 +0200 From 3131b2cd53bd408427967b2449dd6a3e12ee16f8 Mon Sep 17 00:00:00 2001 From: terjekv Date: Mon, 12 Oct 2020 18:05:57 +0200 Subject: [PATCH 431/698] Restore missing extensions. --- ...ndle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 17 ++++++++++++++++- .../mzR-2.22.0_use-external-boost.patch | 2 +- 2 files changed, 17 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index e8a2af39504..87ef0450bb9 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -164,6 +164,9 @@ exts_list = [ ('impute', '1.62.0', { 'checksums': ['10541b1c2476ab5a78e1f4d2961710db1b98a1076ff33ead6f9c8fcb02353798'], }), + ('fs', '1.4.1', { + 'checksums': ['ae9103dff26ca56a34901408bd650a2949f491b2a0886c686a51a179d38b7a4e'], + }), ('shinyFiles', '0.8.0', { 'checksums': ['1ca1455c99f6559fa8a790d5f16a79485ea76ed2dc4eaf1b650665e1cee89e3f'], }), @@ -176,6 +179,12 @@ exts_list = [ ('hgu133plus2.db', '3.2.3', { 'checksums': ['a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549'], }), + ('sys', '3.3', { + 'checksums': ['a6217c2a7240ed68614006f392c6d062247dab8b9b0d498f95e947110df19b93'], + }), + ('askpass', '1.1', { + 'checksums': ['db40827d1bdbb90c0aa2846a2961d3bf9d76ad1b392302f9dd84cc2fd18c001f'], + }), ('illuminaio', '0.30.0', { 'checksums': ['ec180c39921f8707c09e2226a2feaef80576f581fb872a012f42a9b2433ea844'], }), @@ -500,6 +509,9 @@ exts_list = [ ('SC3', '1.16.0', { 'checksums': ['29918e7a78858ef6602c0f461bf33e32af5d384448029ba1368be41118c2a797'], }), + ('clue', '0.3-57', { + 'checksums': ['6e369d07b464a9624209a06b5078bf988f01f7963076e946649d76aea0622d17'], + }), ('ComplexHeatmap', '2.4.2', { 'checksums': ['14e4f92155aaf8d5c92aeab47b890641942b52599928f9ba5ac826073bef5d06'], }), @@ -552,7 +564,7 @@ exts_list = [ 'patches': ['mzR-2.22.0_use-external-boost.patch'], 'checksums': [ '9509d6d831584af8866aa3d1dd1b22f4333e85fafa0c48e4b18ad1f2a34712e5', # mzR_2.22.0.tar.gz - 'bc58aa8ea7ba7c287222049f1cf7cbf2a49ad08d1fe3b5af0965867a7fffc36b', # mzR-2.22.0_use-external-boost.patch + '8b5ba4f0c4efbbab9b4801d7da3fb04a490a5d95af1cefb489f209afa4d14fb4', # mzR-2.22.0_use-external-boost.patch ], }), ('MSnbase', '2.14.0', { @@ -748,6 +760,9 @@ exts_list = [ ('isoband', '0.2.1', { 'checksums': ['18883606bea8352e04a4618bea4e5c9833269e73a46b50bc006dddf4c8b6b4d9'], }), + ('ggplot2', '3.3.0', { + 'checksums': ['320e3c76fe0d0397e29f4782bf85af3647518154b3900a39fd18cf024c554148'], + }), ('ggcyto', '1.16.0', { 'checksums': ['e012f204a01c6b3427a5b29050e37c8034f44a9a5a30ba50b75dcae3d57b06c6'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch index 5b4a6213242..bbd5d6d7e30 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch @@ -1,5 +1,5 @@ # Use external boost provided by EasyBuild instead of -# a bundled old version that doesn't work on aarch64. +# a bundled old version that doesn't work on aarch64.. # # Author: @zao (Lars Viklund) diff -ru mzR.orig/src/Makevars mzR/src/Makevars From 9439233f1d5a2bfe32f69de3c3e7556eb8e9c393 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 18:35:46 +0200 Subject: [PATCH 432/698] cache M4 source tarball to avoid test failures because of download problems --- .github/workflows/unit_tests.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index f354aedc873..af55f605c9e 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -22,6 +22,13 @@ jobs: steps: - uses: actions/checkout@v2 + - name: Cache source files in /tmp/sources + id: cache-sources + uses: actions/cache@v2 + with: + path: /tmp/sources + key: eb-sourcepath + - name: set up Python uses: actions/setup-python@v1 with: @@ -137,7 +144,8 @@ jobs: eb --search '^CVS-' | grep '/CVS-' # try installing M4 with system toolchain (requires ConfigureMake easyblock + easyconfig) - eb --prefix /tmp/$USER/$GITHUB_SHA M4-1.4.18.eb + # use /tmp/sources because that has cached downloads (see cache step above) + eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb test-sdist: runs-on: ubuntu-18.04 From f6b8508989ca9c5c37eeb9a3cc4c85b19cd05582 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Oct 2020 19:12:39 +0200 Subject: [PATCH 433/698] adding easyconfigs: geopandas-0.8.1-foss-2020a-Python-3.8.2.eb --- ...geopandas-0.8.1-foss-2020a-Python-3.8.2.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..a57e98349ae --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.8.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.8.1' +versionsuffix = "-Python-%(pyver)s" + +homepage = 'https://github.com/geopandas/geopandas' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), + ('Shapely', '1.7.1', versionsuffix), + ('Fiona', '1.8.16', versionsuffix), + ('matplotlib', '3.2.1', versionsuffix), + ('networkx', '2.4', versionsuffix), + ('scikit-learn', '0.23.1', versionsuffix), + ('pyproj', '2.6.1.post1', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('descartes', '1.1.0', { + 'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Deprecated', '1.2.10', { + 'checksums': ['525ba66fb5f90b07169fdd48b6373c18f1ee12728ca277ca44567a367d9d7f74'], + }), + ('mapclassify', '2.3.0', { + 'checksums': ['bfe1ec96afe7f866560d25f9f00e5c4dae97d5b69dfe758dbe02c4993261365b'], + }), + (name, version, { + 'checksums': ['e28a729e44ac53c1891b54b1aca60e3bc0bb9e88ad0f2be8e301a03b9510f6e2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 3997ea7ffd5625f0cd9be5e72abb857207afb1d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 12:18:05 +0200 Subject: [PATCH 434/698] add archive source urls for IRkernel 1.1 Co-authored-by: Alex Domingo --- .../i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb index c8db377e327..903af3339e5 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -25,6 +25,7 @@ exts_default_options = { 'source_urls': [ 'https://cran.r-project.org/src/contrib/', 'https://cran.rstudio.com/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', ], 'source_tmpl': '%(name)s_%(version)s.tar.gz', } From fff21eb025f645d4d6c766391d532b599fc2d517 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 12:35:16 +0200 Subject: [PATCH 435/698] fix checksums + names of local variables in easyconfig for variant of R 3.4.3 --- ...ValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 4 ---- ....3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 19 ++++++++++--------- 2 files changed, 10 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 839636b78b4..ef4e7cb9e06 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -42,10 +42,6 @@ exts_default_options = { 'source_tmpl': '%(name)s-%(version)s.tar.gz', } -# exts_filter = -# ("python -c 'import %(ext_name)s'", '') -# ("R -q --no-save", "library(%(ext_name)s)"), - exts_classmap = {'ncdf4': 'RPackage'} exts_list = [ # Python deps, order is important! diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index b4343f8b311..625c9f5bfbb 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -1,8 +1,8 @@ name = 'R' version = '3.4.3' -x11ver = '20171023' -hdf5ver = '1.8.19' -versionsuffix = '-X11-%s-HDF5-%s' % (x11ver, hdf5ver) +local_x11ver = '20171023' +local_hdf5ver = '1.8.19' +versionsuffix = '-X11-%s-HDF5-%s' % (local_x11ver, local_hdf5ver) homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" @@ -17,7 +17,7 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] dependencies = [ - ('X11', x11ver), + ('X11', local_x11ver), ('Mesa', '17.2.4'), ('libGLU', '9.0.0'), ('cairo', '1.14.10'), @@ -34,14 +34,15 @@ dependencies = [ ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk - ('cURL', '7.56.0'), # for RCurl + ('cURL', '7.56.1'), # for RCurl ('libxml2', '2.9.4'), # for XML - ('GDAL', '2.2.2', '-Python-2.7.14-HDF5-%s' % hdf5ver), # for rgdal + ('GDAL', '2.2.2', '-Python-2.7.14-HDF5-%s' % local_hdf5ver), # for rgdal ('PROJ', '4.9.3'), # for rgdal ('GMP', '6.1.2'), # for igraph ('NLopt', '2.4.2'), # for nloptr ('FFTW', '3.3.6'), # for fftw ('libsndfile', '1.0.28'), # for seewave + ('ICU', '61.1'), # for rJava & gdsfmt # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -702,10 +703,10 @@ exts_list = [ 'checksums': ['5d8be59ba791987b2400e9e8eaaac614cd544c1aece785ec4782ea6d5ea00efb'], }), ('pkgmaker', '0.22', { - 'checksums': ['19ad78c16bd5757333e7abbd5eebcec081deb494c9a4b6eec6919a3747b3386f'], + 'checksums': ['05da8b6c0e6828676aeb3faa05ea6e1025b95efffde4820e9ae2b938dbb3027e'], }), ('rngtools', '1.2.4', { - 'checksums': ['27019835b750f470b13dbb7fecd3b839a61b52774e23fffa191f919533768fb9'], + 'checksums': ['17409ada52a2405efa931b5895254cac0e28518a0d41f05012ba3f8af8af3556'], }), ('doParallel', '1.0.11', { 'checksums': ['4ccbd2eb46d3e4f5251b0c3de4d93d9168b02bb0be493656d6aea236667ff76a'], @@ -1559,7 +1560,7 @@ exts_list = [ 'checksums': ['7379b21d1176db5769f5cac858dd12c975736e80a600870180cec9625cf51047'], }), ('RcppProgress', '0.4', { - 'checksums': ['3b1ecc82ced98eb481819a28737dac3658586e11ad16a92abd14c4649ae15e25'], + 'checksums': ['706e14360dbc5976db05c2ac6692c3279c0f8c95e72bf9d4becd9e1348025e3e'], }), ('sn', '1.5-1', { 'checksums': ['fcfc077a2c1eb35b1ed875fea296b225540aefb05564cbb54477f266a0a2f850'], From f43c9e1e734f21b56fd0408c3aa5f51348a28617 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 12:36:30 +0200 Subject: [PATCH 436/698] fix name of local var in ESMValTool easyconfig --- .../ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index ef4e7cb9e06..790a4295390 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -3,7 +3,6 @@ easyblock = 'Binary' name = 'ESMValTool' version = '1.1.0' versionsuffix = '-Python-%(pyver)s' -hdf5ver = '1.8.19' homepage = 'https://www.esmvaltool.org/' description = """The Earth System Model eValuation Tool (ESMValTool) @@ -19,10 +18,11 @@ source_urls = ['https://github.com/ESMValGroup/ESMValTool/archive/'] sources = [{'filename': SOURCE_TAR_GZ, 'download_filename': 'v%(version)s.tar.gz'}] checksums = ['457d5a7e72165a31532b335c42b925abaaa48e959d32b123463df77318c73c36'] +local_hdf5ver = '1.8.19' dependencies = [ ('Python', '2.7.14'), ('NCL', '6.4.0'), - ('R', '3.4.3', '-X11-20171023-HDF5-%s' % hdf5ver), + ('R', '3.4.3', '-X11-20171023-HDF5-%s' % local_hdf5ver), ('CDO', '1.9.1'), ('GEOS', '3.6.2', versionsuffix), ('libjpeg-turbo', '1.5.2'), @@ -31,8 +31,8 @@ dependencies = [ ('LibTIFF', '4.0.8'), ('freetype', '2.8'), ('PROJ', '4.9.3'), - ('netCDF', '4.4.1.1', '-HDF5-%s' % hdf5ver), - ('GDAL', '2.2.2', '-Python-%%(pyver)s-HDF5-%s' % hdf5ver), + ('netCDF', '4.4.1.1', '-HDF5-%s' % local_hdf5ver), + ('GDAL', '2.2.2', '-Python-%%(pyver)s-HDF5-%s' % local_hdf5ver), ('libmo_unpack', '3.1.2'), ('ecCodes', '2.7.3', versionsuffix), ] From 12eb2b141031a84fe1138f2ab04169c3fe6ab1f7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 13 Oct 2020 11:43:17 +0100 Subject: [PATCH 437/698] Allow Kent_tools to build when MySQL installed at the OS level --- .../easyconfigs/k/Kent_tools/Kent_tools-401-gompi-2019b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-401-gompi-2019b.eb b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-401-gompi-2019b.eb index 7cebef52ac9..1367ad92af6 100644 --- a/easybuild/easyconfigs/k/Kent_tools/Kent_tools-401-gompi-2019b.eb +++ b/easybuild/easyconfigs/k/Kent_tools/Kent_tools-401-gompi-2019b.eb @@ -20,7 +20,8 @@ dependencies = [ ('util-linux', '2.34'), ] -buildopts = 'CC="$CC" COPT="$CFLAGS" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz"' +buildopts = 'CC="$CC" COPT="$CFLAGS" PNGLIB="-L$EBROOTLIBPNG/lib -lpng" ZLIB="-L$EBROOTZLIB/lib -lz" ' +buildopts += 'MYSQLLIBS="-L$EBROOTMARIADB/lib -lmariadb -lstdc++" ' local_binaries = ['blat', 'bedPartition', 'getRna', 'liftOver', 'mafGene', 'splitFile', 'twoBitToFa'] From 03070aefcf65fdb6b056d3cda3c776dfd64545ec Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Oct 2020 13:03:18 +0200 Subject: [PATCH 438/698] Added missing moduleclass to the easyconfig --- easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb index f3614d0c5ab..48079296865 100644 --- a/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb +++ b/easybuild/easyconfigs/a/Arlequin/Arlequin-3.5.2.2-foss-2019b.eb @@ -84,3 +84,5 @@ sanity_check_commands = [ "arlsumstat --help", r'cd %(installdir)s/Example\ files_linux/ELB/ && LaunchArlecore.sh -s "Xdata.ars"', ] + +moduleclass = 'bio' From daaf7433a729fc2e5aeac886c136995e45c5e943 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 13:51:12 +0200 Subject: [PATCH 439/698] stick to cURL 7.56.0 as dep for R v3.4.3 variants to avoid conflicts --- .../r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index 625c9f5bfbb..9b473a61b46 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -34,7 +34,7 @@ dependencies = [ ('Java', '1.8.0_152', '', True), # Java bindings are built if Java is found, might as well provide it ('Tcl', '8.6.7'), # for tcltk ('Tk', '8.6.7'), # for tcltk - ('cURL', '7.56.1'), # for RCurl + ('cURL', '7.56.0'), # for RCurl ('libxml2', '2.9.4'), # for XML ('GDAL', '2.2.2', '-Python-2.7.14-HDF5-%s' % local_hdf5ver), # for rgdal ('PROJ', '4.9.3'), # for rgdal From 9a93791e07652c673aeddb4ec687f6d457fdbb51 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 13:51:44 +0200 Subject: [PATCH 440/698] enable missing download_dep_fail and use_pip in ESMValTool easyconfig --- .../e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 790a4295390..fca15aae9d7 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -40,6 +40,8 @@ dependencies = [ exts_defaultclass = 'PythonPackage' exts_default_options = { 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'download_dep_fail': True, + 'use_pip': True, } exts_classmap = {'ncdf4': 'RPackage'} From 0b4a7f70f89ecb8f863e6e0f78f1adff4356ce2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 13:54:43 +0200 Subject: [PATCH 441/698] bump IPython to 7.15.0 as dep for IRkernel --- .../i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb index 903af3339e5..4d0ba8d1b5d 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2020a'} dependencies = [ ('R', '3.6.3'), ('Python', '3.8.2'), - ('IPython', '7.13.0', '-Python-%(pyver)s'), + ('IPython', '7.15.0', '-Python-%(pyver)s'), ('ZeroMQ', '4.3.2'), ] From e7404d4fb11238e32475e0cb3a9995ee3d5ddd41 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Oct 2020 14:34:48 +0200 Subject: [PATCH 442/698] Added missing moduleclass to the easyconfig --- easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.8-GCCcore-8.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.8-GCCcore-8.2.0.eb index 85d513ffa6b..2b2bbb970cc 100644 --- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.8-GCCcore-8.2.0.eb @@ -40,3 +40,5 @@ sanity_check_paths = { ], 'dirs': [], } + +moduleclass = 'bio' From 08a06905a85c8a00dca3d6abbafe2a8d9a935a1a Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Oct 2020 14:35:50 +0200 Subject: [PATCH 443/698] Added missing moduleclass to the easyconfig --- easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb index f2d75aaf069..71ad1983c8b 100644 --- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-9.3.0.eb @@ -40,3 +40,5 @@ sanity_check_paths = { ], 'dirs': [], } + +moduleclass = 'bio' From 3f07f1f11d0d0fc2c6e52806cf331cc95af55f41 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 13 Oct 2020 14:36:58 +0200 Subject: [PATCH 444/698] Added missing moduleclass to the easyconfig --- .../p/PyCUDA/PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb index e6bbca90ce0..e361bdeca10 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2019.1.2-fosscuda-2019b-Python-3.7.4.eb @@ -41,3 +41,5 @@ exts_list = [ 'checksums': ['ada56ce98a41f9f95fe18809f38afbae473a5c62d346cfa126a2d5477f24cc8a'], }), ] + +moduleclass = 'lang' From 45044b2f0c790ee1a236eea761d05ec5b1960454 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 13 Oct 2020 16:24:17 +0100 Subject: [PATCH 445/698] adding easyconfigs: pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb, pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb --- ...pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb | 37 +++++++++++++++++++ ...pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb | 37 +++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb new file mode 100644 index 00000000000..7d12920de21 --- /dev/null +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'pyEGA3' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/EGA-archive/ega-download-client' +description = """ A basic Python-based EGA download client """ + +toolchain = {'name': 'GCCcore', 'version': '8.3.0'} + +builddependencies = [('binutils', '2.32')] + +dependencies = [ + ('Python', '3.7.4'), + ('tqdm', '4.41.1'), +] + +use_pip = True + +exts_list = [ + ('humanize', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/humanize'], + 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], + }), + ('htsget', '0.2.5', { + 'source_urls': ['https://pypi.python.org/packages/source/h/htsget'], + 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/EGA-archive/ega-download-client/archive/'], + 'checksums': ['7d3756d91e7f942635f16bbe0e17221afff6d9a2b5582964ff1250d4cb81066f'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..db4f5313e1c --- /dev/null +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'pyEGA3' +version = '3.4.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/EGA-archive/ega-download-client' +description = """ A basic Python-based EGA download client """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('Python', '3.8.2'), + ('tqdm', '4.47.0'), +] + +use_pip = True + +exts_list = [ + ('humanize', '0.5.1', { + 'source_urls': ['https://pypi.python.org/packages/source/h/humanize'], + 'checksums': ['a43f57115831ac7c70de098e6ac46ac13be00d69abbf60bdcac251344785bb19'], + }), + ('htsget', '0.2.5', { + 'source_urls': ['https://pypi.python.org/packages/source/h/htsget'], + 'checksums': ['d383dc36f699bd921f760f5500c8ed251e5f8358a7cc219c6c89c35d103e8045'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/EGA-archive/ega-download-client/archive/'], + 'checksums': ['7d3756d91e7f942635f16bbe0e17221afff6d9a2b5582964ff1250d4cb81066f'], + }), +] + +moduleclass = 'bio' From f0d90af9b72cc871ae2d1b8e4a6fd1fe40a9198f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:38:24 +0200 Subject: [PATCH 446/698] adding easyconfigs: bzip2-1.0.8-GCCcore-10.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..ec886cad08b --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'tools' From ed194c0e4598d5311598c3b4aabadded191f6b77 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:41:24 +0200 Subject: [PATCH 447/698] adding easyconfigs: SQLite-3.33.0-GCCcore-10.2.0.eb --- .../s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..ffffe1f458f --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -0,0 +1,47 @@ +# # +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the +# policy: https://hpcbios.readthedocs.org/en/latest/ +# # + +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.33.0' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/2020/'] +sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] +checksums = ['106a2c48c7f75a298a7557bcc0d5f4f454e5b43811cc738b7ca294d6956bbb15'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('libreadline', '8.0'), + ('Tcl', '8.6.10'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'devel' From 3d63cb92557ea9a5cd0f365bcd300e38f285da49 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:42:03 +0200 Subject: [PATCH 448/698] adding easyconfigs: Tcl-8.6.10-GCCcore-10.2.0.eb --- .../t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5cd77d83385 --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.10-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['5196dbf6638e3df8d5c87b5815c8c2b758496eb6f0e41446596c9a4e638d87ed'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' From d5231de67df372cea6caef7261961a85e12b125a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 17:55:16 +0200 Subject: [PATCH 449/698] Fix sourcename pattern --- easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb index 32f6e2c4fd3..ca7342f8379 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb @@ -22,7 +22,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} source_urls = ['https://www.%(namelower)s.org/2019/'] -sources = ['%(namelower)s-autoconf-%(version_major)s290000.tar.gz'] +sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] checksums = ['8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b'] builddependencies = [ From cf7c72032e541a4e4b5dccbb3812b0f06922e4c0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 18:04:52 +0200 Subject: [PATCH 450/698] Add sanity check --- easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb index ca7342f8379..b6173b06163 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb @@ -44,4 +44,8 @@ sanity_check_paths = { 'dirs': ['lib/pkgconfig'], } +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + moduleclass = 'devel' From 6df3cca51b33836fedc1fb791242bb2e21f3828c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 18:14:32 +0200 Subject: [PATCH 451/698] add patch for xkeyboard-config component in Xvfb easyconfigs to use correct 'python3' command in map-variants.py script --- .../easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 7 ++++++- .../easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 7 ++++++- ...yboard-config-2.29_fix-shebang-map-variants.patch | 12 ++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/x/Xvfb/xkeyboard-config-2.29_fix-shebang-map-variants.patch diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index fb0ffdd7656..b815bab780b 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -58,7 +58,12 @@ components = [ }), ('xkeyboard-config', '2.29', { 'source_urls': ['https://www.x.org/archive//individual/data/xkeyboard-config/'], - 'checksums': ['d8034c8b771b51140409039f8e3351e90a0092238b81af04239794e8d3dc0813'], + 'patches': ['xkeyboard-config-%(version)s_fix-shebang-map-variants.patch'], + 'checksums': [ + 'd8034c8b771b51140409039f8e3351e90a0092238b81af04239794e8d3dc0813', # xkeyboard-config-2.29.tar.gz + # xkeyboard-config-2.29_fix-shebang-map-variants.patch + '91ba9a6e5cef7723a6ec68de0359089b6254b585c2b47a338257021bb0e4c0e8', + ], 'configopts': '--with-xkb-rules-symlink=xorg', }), (name, version, { diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index f4c5a46fc86..d11d7716094 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -58,7 +58,12 @@ components = [ }), ('xkeyboard-config', '2.29', { 'source_urls': ['https://www.x.org/archive//individual/data/xkeyboard-config/'], - 'checksums': ['d8034c8b771b51140409039f8e3351e90a0092238b81af04239794e8d3dc0813'], + 'patches': ['xkeyboard-config-%(version)s_fix-shebang-map-variants.patch'], + 'checksums': [ + 'd8034c8b771b51140409039f8e3351e90a0092238b81af04239794e8d3dc0813', # xkeyboard-config-2.29.tar.gz + # xkeyboard-config-2.29_fix-shebang-map-variants.patch + '91ba9a6e5cef7723a6ec68de0359089b6254b585c2b47a338257021bb0e4c0e8', + ], 'configopts': '--with-xkb-rules-symlink=xorg', }), (name, version, { diff --git a/easybuild/easyconfigs/x/Xvfb/xkeyboard-config-2.29_fix-shebang-map-variants.patch b/easybuild/easyconfigs/x/Xvfb/xkeyboard-config-2.29_fix-shebang-map-variants.patch new file mode 100644 index 00000000000..0c878df4cbf --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/xkeyboard-config-2.29_fix-shebang-map-variants.patch @@ -0,0 +1,12 @@ +fix shebang in map-variants.py to use 'python3' command available via $PATH + +author: Kenneth Hoste (HPC-UGent) +diff -ru xkeyboard-config-2.29.orig/rules/compat/map-variants.py xkeyboard-config-2.29/rules/compat/map-variants.py +--- xkeyboard-config-2.29.orig/rules/compat/map-variants.py 2020-01-31 01:29:55.000000000 +0100 ++++ xkeyboard-config-2.29/rules/compat/map-variants.py 2020-10-13 18:09:47.347929930 +0200 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python3 ++#!/usr/bin/env python3 + + import argparse + import re From 0407c873f92ed4ea1e9b5f501c31adc26aa45ec8 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 18:44:24 +0200 Subject: [PATCH 452/698] Include sanity check command --- .../easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb index ffffe1f458f..3243496e8a9 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -44,4 +44,8 @@ sanity_check_paths = { 'dirs': ['lib/pkgconfig'], } +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + moduleclass = 'devel' From 7cf4e5a0fec1bb792c5a37f00fc3501e65858043 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:15:59 +0200 Subject: [PATCH 453/698] {vis}[GCCcore/9.3.0] Xvfb v1.20.9, nettle v3.6 --- .../n/nettle/nettle-3.6-GCCcore-9.3.0.eb | 36 ++++++++ .../x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 91 +++++++++++++++++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c93203c0c88 --- /dev/null +++ b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'nettle' +version = '3.6' + +homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +description = """Nettle is a cryptographic library that is designed to fit easily + in more or less any context: In crypto toolkits for object-oriented + languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, + or even in kernel space.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['d24c0d0f2abffbc8f4f34dcf114b0f131ec3774895f3555922fe2f40f3d5e3f1'] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('GMP', '6.2.0'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['nettle-hash', 'nettle-lfib-stream', 'pkcs1-conv', 'sexp-conv']] + + [('lib/libhogweed.a', 'lib64/libhogweed.a'), + ('lib/libhogweed.%s' % SHLIB_EXT, 'lib64/libhogweed.%s' % SHLIB_EXT), + ('lib/libnettle.a', 'lib64/libnettle.a'), + ('lib/libnettle.%s' % SHLIB_EXT, 'lib64/libnettle.%s' % SHLIB_EXT)], + 'dirs': ['include/nettle'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..5b9435b97db --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -0,0 +1,91 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '1.20.9' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [ + ('binutils', '2.34'), + ('pkg-config', '0.29.2'), + ('Python', '3.8.2'), +] + +dependencies = [ + ('X11', '20200222'), + ('pixman', '0.38.4'), + ('libdrm', '2.4.100'), + ('Mesa', '20.0.2'), + ('nettle', '3.6'), + ('libunwind', '1.3.1'), + ('XZ', '5.2.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'source_urls': ['https://www.x.org/archive//individual/font/'], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('font-util', '1.3.2', { + 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], + }), + ('font-misc-misc', '1.1.2', { + 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + }), + ('xkbcomp', '1.4.3', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['c518a321ca98577c04d3b9a3ff0f3e7d96297b82ac65015b1f0e69627b4b598a'], + }), + ('xkeyboard-config', '2.31', { + 'source_urls': ['https://www.x.org/archive//individual/data/xkeyboard-config/'], + 'checksums': ['5ac6b5b661aeb9d0ea84ad961cbbdd8fdf2503d6e8ca65ca1b1c5d9aea2ddc52'], + 'configopts': '--with-xkb-rules-symlink=xorg', + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual//xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + '067c348fe1a86a1924010354c1c7cf1eaa9e43866e48540aa56a465f2a341ddc', # xorg-server-1.20.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +postinstallcmds = ["cp -a xvfb-run %(installdir)s/bin/ && chmod u+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From b964b26a0cc99c5b1e432447220d26922b415ffe Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 19:33:06 +0200 Subject: [PATCH 454/698] adding easyconfigs: GMP-6.2.0-GCCcore-10.2.0.eb --- .../g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b1f3baccd69 --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.0' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From a5821a0f4d8573c5981af4b6326911f474b81d47 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:36:16 +0200 Subject: [PATCH 455/698] add mkfontdir component to Xvfb 1.20.8 easyconfigs --- .../easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 9 ++++++++- .../easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 9 ++++++++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index b815bab780b..58f7570d890 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -44,13 +44,20 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + components = [ + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), ('font-misc-misc', '1.1.2', { 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], - 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'preconfigopts': local_font_misc_preconfigopts, }), ('xkbcomp', '1.4.3', { 'source_urls': ['https://www.x.org/archive//individual/app/'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index d11d7716094..e05695d8e60 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -44,13 +44,20 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + components = [ + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), ('font-misc-misc', '1.1.2', { 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], - 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'preconfigopts': local_font_misc_preconfigopts, }), ('xkbcomp', '1.4.3', { 'source_urls': ['https://www.x.org/archive//individual/app/'], From 77def27308a2d30b81f3af94dd021abf49a2b161 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:39:27 +0200 Subject: [PATCH 456/698] add mkfontdir component to Xvfb 1.20.9 easyconfig --- .../easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb index 5b9435b97db..eff98a30c59 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -44,13 +44,20 @@ default_component_specs = { 'start_dir': '%(name)s-%(version)s', } +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + components = [ + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), ('font-misc-misc', '1.1.2', { 'checksums': ['46142c876e176036c61c0c24c0a689079704d5ca5b510d48c025861ee2dbf829'], - 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'preconfigopts': local_font_misc_preconfigopts, }), ('xkbcomp', '1.4.3', { 'source_urls': ['https://www.x.org/archive//individual/app/'], From 00e2adb57d2729cb07f0a2d600c5f5dd38cfa7ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:47:51 +0200 Subject: [PATCH 457/698] add bdftopcf component to Xvfb 1.20.9 easyconfig --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb index eff98a30c59..d95b05a7a57 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -49,9 +49,13 @@ local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ ('mkfontdir', '1.0.7', { - 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), From 4b8e47fd2e685056fac25748f97203216e533e29 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:47:10 +0200 Subject: [PATCH 458/698] add bdftopcf component to Xvfb 1.20.8 easyconfigs --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 6 +++++- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index 58f7570d890..24f6450bebe 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -49,9 +49,13 @@ local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ ('mkfontdir', '1.0.7', { - 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index e05695d8e60..2667cfc28cd 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -49,9 +49,13 @@ local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ ('mkfontdir', '1.0.7', { - 'source_urls': ['https://www.x.org/archive//individual//app/'], + 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), ('font-util', '1.3.2', { 'checksums': ['f115a3735604de1e852a4bf669be0269d8ce8f21f8e0e74ec5934b31dadc1e76'], }), From 98c8848be99bd5df2dba503429774ee83a473bbf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:51:46 +0200 Subject: [PATCH 459/698] add mkfontscale component to Xvfb 1.20.8 easyconfigs --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 4 ++++ easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index 24f6450bebe..674916d3613 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -48,6 +48,10 @@ local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgco local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), ('mkfontdir', '1.0.7', { 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index 2667cfc28cd..953851ebb8d 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -48,6 +48,10 @@ local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgco local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), ('mkfontdir', '1.0.7', { 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], From 37f5d0a7a537c67f18c89424e064740f81a71d05 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 19:54:42 +0200 Subject: [PATCH 460/698] add mkfontscale component to Xvfb 1.20.9 easyconfig --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb index d95b05a7a57..a50acd95e9f 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -48,6 +48,10 @@ local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgco local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " components = [ + ('mkfontscale', '1.2.1', { + 'source_urls': ['https://www.x.org/archive//individual/app/'], + 'checksums': ['e5b687029e44d0bd3ccd254a4da6a5cbfc40350aa8b43fcca16ef6e9b9bb9f22'], + }), ('mkfontdir', '1.0.7', { 'source_urls': ['https://www.x.org/archive//individual/app/'], 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], From fec7c7ceed70d25c8570fe5cd382ce83334f0edb Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:16:05 +0200 Subject: [PATCH 461/698] Give up on automating sqlites awful filenames --- .../easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb index b6173b06163..9e179204575 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb @@ -14,6 +14,7 @@ easyblock = 'ConfigureMake' name = 'SQLite' version = '3.31.1' +local_filename_version = '3310100' homepage = 'https://www.sqlite.org/' description = "SQLite: SQL Database Engine in a C Library" @@ -21,8 +22,8 @@ description = "SQLite: SQL Database Engine in a C Library" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.%(namelower)s.org/2019/'] -sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] +source_urls = ['https://www.%(namelower)s.org/2020/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] checksums = ['8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b'] builddependencies = [ From a2b05c392a50458b22e55a420db3a8d133f7be02 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:25:09 +0200 Subject: [PATCH 462/698] Use same filename method as 3.31.1 --- easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb index 3243496e8a9..272f12272dc 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.33.0-GCCcore-10.2.0.eb @@ -14,6 +14,7 @@ easyblock = 'ConfigureMake' name = 'SQLite' version = '3.33.0' +local_filename_version = '3330000' homepage = 'https://www.sqlite.org/' description = "SQLite: SQL Database Engine in a C Library" @@ -22,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} source_urls = ['https://www.%(namelower)s.org/2020/'] -sources = ['%%(namelower)s-autoconf-%s000.tar.gz' % (''.join(version.split('.')))] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] checksums = ['106a2c48c7f75a298a7557bcc0d5f4f454e5b43811cc738b7ca294d6956bbb15'] builddependencies = [ From 37a923249dc3cc20c579463e8b6750ac247f2b8d Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:27:04 +0200 Subject: [PATCH 463/698] adding easyconfigs: libffi-3.3-GCCcore-10.2.0.eb --- .../l/libffi/libffi-3.3-GCCcore-10.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6ccf73557b9 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.3-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.3' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'ftp://sourceware.org/pub/%(name)s/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/%(name)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['72fba7922703ddfa7a028d513ac15a85c8d54c8d67f55fa5a4802885dc652056'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 72fbf3c14c5d1ce44d2bb51f1820c693dbda188e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 20:29:19 +0200 Subject: [PATCH 464/698] Fix checksum for now corrected sources --- easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb index 9e179204575..facc79c8f9b 100644 --- a/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.31.1-GCCcore-9.3.0.eb @@ -24,7 +24,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.%(namelower)s.org/2020/'] sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] -checksums = ['8e7c1e2950b5b04c5944a981cb31fffbf9d2ddda939d536838ebc854481afd5b'] +checksums = ['62284efebc05a76f909c580ffa5c008a7d22a1287285d68b7825a2b6b51949ae'] builddependencies = [ ('binutils', '2.34'), From 244931a66d87acf79ad71433c70d6ee6cf69ed2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 20:40:12 +0200 Subject: [PATCH 465/698] use https in homepage for nettle 3.6 --- easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb index c93203c0c88..00568388db8 100644 --- a/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/n/nettle/nettle-3.6-GCCcore-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'nettle' version = '3.6' -homepage = 'http://www.lysator.liu.se/~nisse/nettle/' +homepage = 'https://www.lysator.liu.se/~nisse/nettle/' description = """Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, From 2a5bd6d2fd97374023f246960faf21e7b291835b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 21:21:44 +0200 Subject: [PATCH 466/698] add --disable-libunwind configure option for Xvfb to fix installation on @verdurin's minimal test setup --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index 674916d3613..5561b1f88e7 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -28,7 +28,7 @@ dependencies = [ default_easyblock = 'ConfigureMake' local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " -local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" # use 'make V=1' to see compiler commands diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index 953851ebb8d..b0629b98411 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ default_easyblock = 'ConfigureMake' local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " -local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" # use 'make V=1' to see compiler commands From cfc8c2f37a247f61772870ad6eab133f918ff8ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 21:32:45 +0200 Subject: [PATCH 467/698] add reader, elementR, ie2misc, assertive, rdrop2 as extensions to R v4.0.0 easyconfig + include Xvfb as build dep (required to install gWidgets2tcltk which is required as dep for ie2misc) --- .../easyconfigs/r/R/R-4.0.0-foss-2020a.eb | 103 ++++++++++++++++++ 1 file changed, 103 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb index 7b502c6855a..c842ad53f1d 100644 --- a/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-4.0.0-foss-2020a.eb @@ -17,6 +17,7 @@ checksums = [ builddependencies = [ ('pkg-config', '0.29.2'), + ('Xvfb', '1.20.9'), ] dependencies = [ ('X11', '20200222'), @@ -2558,6 +2559,108 @@ exts_list = [ '80a7e84c691d418da4e90a38db1caebed31d01771e4e7f64d24676ee8d84c104', ], }), + ('proftools', '0.99-3', { + 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], + }), + ('NCmisc', '1.1.6', { + 'checksums': ['2aa85997d5ec2222e610604022684c004a4925241761d9a0104919f1cf3a8c79'], + }), + ('reader', '1.0.6', { + 'checksums': ['905c7c5a1b035ac8213fc533fa26e511abfeea40bd22e3edfde42a49074e88f4'], + }), + ('gnumeric', '0.7-8', { + 'checksums': ['28b10c91d693b938ebca610933889095ca160b22e6ca750c46103dfd2b009447'], + }), + ('tcltk2', '1.2-11', { + 'checksums': ['ad183ae3b7190501504a0589e0b3be480f04267303e3384fef00987446a37dc5'], + }), + ('readODS', '1.7.0', { + 'checksums': ['f6a8ec724df68983c9b176a1b3b3b01239cc4e99aac4bfb42ce1c2b3d40922c2'], + }), + ('nortest', '1.0-4', { + 'checksums': ['a3850a048181d5d059c1e74903437569873b430c915b709808237d71fee5209f'], + }), + ('EnvStats', '2.3.1', { + 'checksums': ['d753d42b42ff28c1cd25c63916fb2aa9e325941672fb16f7dfd97e218416cf2a'], + }), + ('outliers', '0.14', { + 'checksums': ['b6ce8f1db6442481546131def8253cabdf4472116d193daea7cb935d2b76986d'], + }), + ('elementR', '1.3.7', { + 'checksums': ['4275f88f372a2efe96ccd0afc20f4f12be92f28c7db35c68b80bb0ffb2c2ab07'], + }), + ('gWidgets2', '1.0-8', { + 'checksums': ['1615ce9ab07a251d06c68780be15ab5a4814df877a23aa93e0faf14ccd56d45c'], + }), + ('memoise', '1.1.0', { + 'checksums': ['b276f9452a26aeb79e12dd7227fcc8712832781a42f92d70e86040da0573980c'], + }), + ('gWidgets2tcltk', '1.0-6', { + 'checksums': ['aa3a2f4612116a652e5573a369e3d89c5939f7c06067c6826ba40ed3bb07302b'], + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" + 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, + }), + ('mgsub', '1.7.2', { + 'checksums': ['399f23fd311c58c019248625cf875df50c10a1e3ecf1931850d18cfd4d5a810a'], + }), + ('ie2misc', '0.8.6', { + 'checksums': ['f3e2cc8a88f3789a5e339d2676455472a52a303c8273191f27aa2f2f02fdd8cd'], + }), + ('assertive.base', '0.0-7', { + 'checksums': ['f02d4eca849f512500abb266a2a751d1fa2cf064f7142e5161a77c20b7f643f7'], + }), + ('assertive.properties', '0.0-4', { + 'checksums': ['5c0663fecb4b7c30f2e1d65da8644534fcfe97fb3d8b51f74c1327cd14291a6b'], + }), + ('assertive.types', '0.0-3', { + 'checksums': ['ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f'], + }), + ('assertive.numbers', '0.0-2', { + 'checksums': ['bae18c0b9e5b960a20636e127eb738ecd8a266e5fc29d8bc5ca712498cd68349'], + }), + ('assertive.strings', '0.0-3', { + 'checksums': ['d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258'], + }), + ('assertive.datetimes', '0.0-3', { + 'checksums': ['014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94'], + }), + ('assertive.files', '0.0-2', { + 'checksums': ['be6adda6f18a0427449249e44c2deff4444a123244b16fe82c92f15d24faee0a'], + }), + ('assertive.sets', '0.0-3', { + 'checksums': ['876975a16ed911ea1ad12da284111c6eada6abfc0118585033abc0edb5801bb3'], + }), + ('assertive.matrices', '0.0-2', { + 'checksums': ['3462a7a7e11d7cc24180330d48cc3067cf92eab1699b3e4813deec66d99f5e9b'], + }), + ('assertive.models', '0.0-2', { + 'checksums': ['b9a6d8786f352d53371dbe8c5f2f2a62a7866e30313f268e69626d5c3691c42e'], + }), + ('assertive.data', '0.0-3', { + 'checksums': ['5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01'], + }), + ('assertive.data.uk', '0.0-2', { + 'checksums': ['ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb'], + }), + ('assertive.data.us', '0.0-2', { + 'checksums': ['180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad'], + }), + ('assertive.reflection', '0.0-5', { + 'checksums': ['c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd'], + }), + ('assertive.code', '0.0-3', { + 'checksums': ['ef80e8d1d683d776a7618e78ddccffca7f72ab4a0fcead90c670bb8f8cb90be2'], + }), + ('assertive', '0.3-6', { + 'checksums': ['c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a'], + }), + ('rdrop2', '0.8.2.1', { + 'checksums': ['b9add765fe8e7c966f0d36eef939a9e38f253958bd2a3c656b890cbb0366300b'], + }), ] moduleclass = 'lang' From 50f364dc3d1c754638d179c5c10e200bb8233f23 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 22:09:27 +0200 Subject: [PATCH 468/698] adding easyconfigs: Python-2.7.18-GCCcore-10.2.0.eb, Python-3.8.4-GCCcore-10.2.0.eb --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 299 +++++++++++++++++ .../p/Python/Python-3.8.4-GCCcore-10.2.0.eb | 308 ++++++++++++++++++ 2 files changed, 607 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b17ca55ddc4 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -0,0 +1,299 @@ +name = 'Python' +version = '2.7.18' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.33.0'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 13 October 2020 +exts_list = [ + ('setuptools', '44.1.1', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'use_pip': False, + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.5.0', { + 'checksums': ['14bfd98f51c78a3dd22a1ef45cf194ad79eee4a19e8e1a0d5c7f8e81ffe182ea'], + }), + ('Cython', '0.29.21', { + 'checksums': ['e57acb89bd55943c8d8bf813763d20b9099cc7165c0f16b707631a7654be9cad'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.16.0', { + 'checksums': ['494c6a853e9ed2e9be33d160b41d47afc50a6629b993d2b9c5ad7bb226add892'], + }), + ('enum34', '1.1.10', { + 'modulename': 'enum', + 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.3', { + 'checksums': ['f92f789e4f9241cd262ad7a555ca2c648a98178a953af117ef7fad46aa1d5591'], + }), + ('cryptography', '3.1.1', { + 'checksums': ['9d9fc6a16357965d282dd4ab6531013935425d0dc4950df2e0cf2a1b1ac1017d'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.1.7', { + 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], + }), + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '3.0.5', { + 'checksums': ['83657d894c90d5681d62155c82bda9c1187827525880eda8ff5df4ec813437c3'], + }), + ('pytz', '2020.1', { + 'checksums': ['c35965d010ce31b23eeb663ed3cc8c906275d6be1a34393a1d73a41febf4a048'], + }), + ('bitstring', '3.1.7', { + 'checksums': ['fdf3eb72b229d2864fb507f8f42b1b2c57af7ce5fec035972f9566de440a864a'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.1', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['edf6116872c863e1aa9d5bb7cb5e05a022c519a4594dc703843343a9ddd9bff1'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('importlib_resources', '3.0.0', { + 'checksums': ['19f745a6eca188b490b1428c8d1d4a0d2368759f32370ea8fb89cad2ab1106c3'], + }), + ('virtualenv', '20.0.34', { + 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.14.1', { + 'checksums': ['0630eea4f5664c463f23fbf5dcfc54a2bc6168902719fa8e19daf033022786c8'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2020.6.20', { + 'checksums': ['5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3'], + }), + ('urllib3', '1.25.10', { + 'checksums': ['91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a'], + }), + ('requests', '2.24.0', { + 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.10', { + 'checksums': ['43038326b686df697f9533895184c15d18769e215abbd8bcecaea607483f35b3'], + }), + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], + }), + ('ujson', '2.0.3', { + 'checksums': ['bd2deffc983827510e5145fb66e4cc0f577480c62fe0b4882139f8f7d27ae9a3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.9.0', { + 'checksums': ['9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('zipp', '1.2.0', { + 'checksums': ['c70410551488251b0fee67b460fb9a536af8d6f9f008ad10ac51f615b6a521b1'], + }), + ('configparser', '4.0.2', { + 'checksums': ['c7d282687a5308319bf3d2e7706e575c635b0a470342641c93bea0ea3b5331df'], + }), + ('contextlib2', '0.6.0.post1', { + 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '5.0.0', { + 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('pytest', '4.6.11', { + 'checksums': ['50fa82392f2120cc3ec2ca0a75ee615be4c479e66669789771f1758332be4353'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('sphinxcontrib-websupport', '1.1.2', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['1501befb0fdf1d1c29a800fdbf4ef5dc5369377300ddbdd16d2cd40e54c6eefc'], + }), + ('Pygments', '2.5.2', { + 'checksums': ['98c8aa5a9f778fcd1026a17361ddaf7330d1b7c62ae97c3bb0ae73e0b9b6b0fe'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('typing', '3.7.4.3', { + 'checksums': ['1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9'], + }), + ('Sphinx', '1.8.5', { + 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.7.2', { + 'checksums': ['90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('singledispatch', '3.4.0.3', { + 'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'], + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d342d092dd2 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb @@ -0,0 +1,308 @@ +name = 'Python' +version = '3.8.4' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18'] + +dependencies = [ + ('binutils', '2.35'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.11'), + ('libreadline', '8.0'), + ('ncurses', '6.2'), + ('SQLite', '3.33.0'), + ('XZ', '5.2.5'), + ('GMP', '6.2.0'), # required for pycrypto + ('libffi', '3.3'), # required for cryptography + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # Python 3.7 requires OpenSSL >= 1.0.2, uncomment line below if OS version is too old (e.g. CentOS 6) + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +# symlink 'pip' command to 'pip3' that is included with Python installation +# required so we can update pip to version included in extensions, using pip +installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" + + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + + +# order is important! +# package versions updated 13 October 2020 +exts_list = [ + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), + ('setuptools', '50.3.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('nose', '1.3.7', { + 'checksums': ['f1bffef9cbc82628f6e7d7b40d7e255aefaa1adb6a1b1d26c69a8b79e6208a98'], + }), + ('blist', '1.3.6', { + 'checksums': ['3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'], + }), + ('paycheck', '1.0.2', { + 'checksums': ['6db7fc367c146cd59d2327ad4d2d6b0a24bc1be2d6953bb0773cbf702ee1ed34'], + }), + ('pbr', '5.5.0', { + 'checksums': ['14bfd98f51c78a3dd22a1ef45cf194ad79eee4a19e8e1a0d5c7f8e81ffe182ea'], + }), + ('Cython', '0.29.21', { + 'checksums': ['e57acb89bd55943c8d8bf813763d20b9099cc7165c0f16b707631a7654be9cad'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('toml', '0.10.1', { + 'checksums': ['926b612be1e5ce0634a2ca03470f95169cf16f939018233a670519cb4ac58b0f'], + }), + ('setuptools_scm', '4.1.2', { + 'checksums': ['a8994582e716ec690f33fec70cca0f85bd23ec974e3f783233e4879090a7faa8'], + }), + ('python-dateutil', '2.8.1', { + 'modulename': 'dateutil', + 'checksums': ['73ebfe9dbf22e832286dafa60473e4cd239f8592f699aa5adaf10050e6e1823c'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('liac-arff', '2.5.0', { + 'modulename': 'arff', + 'checksums': ['3220d0af6487c5aa71b47579be7ad1d94f3849ff1e224af3bf05ad49a0b5c4da'], + }), + ('pycrypto', '2.6.1', { + 'modulename': 'Crypto', + 'patches': ['pycrypto-2.6.1_remove-usr-include.patch'], + 'checksums': [ + 'f2ce1e989b272cfcb677616763e0a2e7ec659effa67a88aa92b3a65528f60a3c', # pycrypto-2.6.1.tar.gz + # pycrypto-2.6.1_remove-usr-include.patch + '06c3d3bb290305e1360a023ea03f9281116c230de62382e6be9474996086712e', + ], + }), + ('ecdsa', '0.16.0', { + 'checksums': ['494c6a853e9ed2e9be33d160b41d47afc50a6629b993d2b9c5ad7bb226add892'], + }), + ('ipaddress', '1.0.23', { + 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], + }), + ('asn1crypto', '1.4.0', { + 'checksums': ['f4f6e119474e58e04a2b1af817eb585b4fd72bdd89b998624712b5c99be7641c'], + }), + ('idna', '2.10', { + 'checksums': ['b307872f855b18632ce0c21c5e45be78c0ea7ae4c15c828c20788b26921eb3f6'], + }), + ('pycparser', '2.20', { + 'checksums': ['2d475327684562c3a96cc71adf7dc8c4f0565175cf86b6d7a404ff4c771f15f0'], + }), + ('cffi', '1.14.3', { + 'checksums': ['f92f789e4f9241cd262ad7a555ca2c648a98178a953af117ef7fad46aa1d5591'], + }), + ('cryptography', '3.1.1', { + 'checksums': ['9d9fc6a16357965d282dd4ab6531013935425d0dc4950df2e0cf2a1b1ac1017d'], + }), + ('pyasn1', '0.4.8', { + 'checksums': ['aef77c9fb94a3ac588e87841208bdec464471d9871bd5050a287cc9a475cd0ba'], + }), + ('PyNaCl', '1.4.0', { + 'modulename': 'nacl', + 'checksums': ['54e9a2c849c742006516ad56a88f5c74bf2ce92c9f67435187c3c5953b346505'], + }), + ('bcrypt', '3.2.0', { + 'checksums': ['5b93c1726e50a93a033c36e5ca7fdcd29a5c7395af50a6892f5d9e7c6cfbfb29'], + }), + ('paramiko', '2.7.2', { + 'checksums': ['7f36f4ba2c0d81d219f4595e35f70d56cc94f9ac40a6acdf51d6ca210ce65035'], + }), + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), + ('netifaces', '0.10.9', { + 'checksums': ['2dee9ffdd16292878336a58d04a20f0ffe95555465fee7c9bd23b3490ef2abf3'], + }), + ('netaddr', '0.8.0', { + 'checksums': ['d6cc57c7a07b1d9d2e917aa8b36ae8ce61c35ba3fcd1b83ca31c5a0ee2b5a243'], + }), + ('mock', '4.0.2', { + 'checksums': ['dd33eb70232b6118298d516bbcecd26704689c386594f0f3c4f13867b2c56f72'], + }), + ('pytz', '2020.1', { + 'checksums': ['c35965d010ce31b23eeb663ed3cc8c906275d6be1a34393a1d73a41febf4a048'], + }), + ('bitstring', '3.1.7', { + 'checksums': ['fdf3eb72b229d2864fb507f8f42b1b2c57af7ce5fec035972f9566de440a864a'], + }), + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('distlib', '0.3.1', { + 'source_tmpl': 'distlib-%(version)s.zip', + 'checksums': ['edf6116872c863e1aa9d5bb7cb5e05a022c519a4594dc703843343a9ddd9bff1'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('virtualenv', '20.0.34', { + 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], + }), + ('docopt', '0.6.2', { + 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], + }), + ('joblib', '0.17.0', { + 'checksums': ['9e284edd6be6b71883a63c9b7f124738a3c16195513ad940eae7e3438de885d5'], + }), + ('chardet', '3.0.4', { + 'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'], + }), + ('certifi', '2020.6.20', { + 'checksums': ['5930595817496dd21bb8dc35dad090f1c2cd0adfaf21204bf6732ca5d8ee34d3'], + }), + ('urllib3', '1.25.10', { + 'checksums': ['91056c15fa70756691db97756772bb1eb9678fa585d9184f24534b100dc60f4a'], + }), + ('requests', '2.24.0', { + 'checksums': ['b3559a131db72c33ee969480840fff4bb6dd111de7dd27c8ee1f820f4f00231b'], + }), + ('xlrd', '1.2.0', { + 'checksums': ['546eb36cee8db40c3eaa46c351e67ffee6eeb5fa2650b71bc4c758a29a1b29b2'], + }), + ('py_expression_eval', '0.3.10', { + 'checksums': ['43038326b686df697f9533895184c15d18769e215abbd8bcecaea607483f35b3'], + }), + ('tabulate', '0.8.7', { + 'checksums': ['db2723a20d04bcda8522165c73eea7c300eda74e0ce852d9022e0159d7895007'], + }), + ('ujson', '4.0.1', { + 'checksums': ['26cf6241b36ff5ce4539ae687b6b02673109c5e3efc96148806a7873eaa229d3'], + }), + ('atomicwrites', '1.4.0', { + 'checksums': ['ae70396ad1a434f9c7046fd2dd196fc04b12f9e91ffb859164193be8b6168a7a'], + }), + ('py', '1.9.0', { + 'checksums': ['9ca6883ce56b4e8da7e79ac18787889fa5206c79dcc67fb065376cd2fe03f342'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.5', { + 'checksums': ['6cd9a47b597b37cc57de1c05e56fb1a1c9cc9fab04fe78c29acd090418529868'], + }), + ('zipp', '3.3.0', { + 'checksums': ['64ad89efee774d1897a58607895d80789c59778ea02185dd846ac38394a8642b'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('more-itertools', '8.5.0', { + 'checksums': ['6f83822ae94818eae2612063a5101a7311e68ae8002005b5e05f03fd74a86a20'], + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('wcwidth', '0.2.5', { + 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], + }), + ('pytest', '6.1.1', { + 'checksums': ['8f593023c1a0f916110285b6efd7f99db07d59546e3d8c36fc60e2ab05d3be92'], + }), + ('MarkupSafe', '1.1.1', { + 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], + }), + ('Jinja2', '2.11.2', { + 'checksums': ['89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0'], + }), + ('packaging', '20.4', { + 'checksums': ['4357f74f47b9c12db93624a82154e9b120fa8293699949152b22065d556079f8'], + }), + ('sphinxcontrib-websupport', '1.2.4', { + 'modulename': 'sphinxcontrib.websupport', + 'checksums': ['4edf0223a0685a7c485ae5a156b6f529ba1ee481a1417817935b20bde1956232'], + }), + ('Pygments', '2.7.1', { + 'checksums': ['926c3f319eda178d1bd90851e4317e6d8cdb5e292a3386aac9bd75eca29cf9c7'], + }), + ('imagesize', '1.2.0', { + 'checksums': ['b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1'], + }), + ('docutils', '0.16', { + 'checksums': ['c2de3a60e9e7d07be26b7f2b00ca0309c207e06c100f9cc2a94931fc75a478fc'], + }), + ('snowballstemmer', '2.0.0', { + 'checksums': ['df3bac3df4c2c01363f3dd2cfa78cce2840a79b9f1c2d2de9ce8d31683992f52'], + }), + ('Babel', '2.8.0', { + 'checksums': ['1aac2ae2d0d8ea368fa90906567f5c08463d98ade155c0c4bfedd6a0f7160e38'], + }), + ('alabaster', '0.7.12', { + 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], + }), + ('sphinxcontrib-applehelp', '1.0.2', { + 'modulename': 'sphinxcontrib.applehelp', + 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], + }), + ('sphinxcontrib-devhelp', '1.0.2', { + 'modulename': 'sphinxcontrib.devhelp', + 'checksums': ['ff7f1afa7b9642e7060379360a67e9c41e8f3121f2ce9164266f61b9f4b338e4'], + }), + ('sphinxcontrib-htmlhelp', '1.0.3', { + 'modulename': 'sphinxcontrib.htmlhelp', + 'checksums': ['e8f5bb7e31b2dbb25b9cc435c8ab7a79787ebf7f906155729338f3156d93659b'], + }), + ('sphinxcontrib-jsmath', '1.0.1', { + 'modulename': 'sphinxcontrib.jsmath', + 'checksums': ['a9925e4a4587247ed2191a22df5f6970656cb8ca2bd6284309578f2153e0c4b8'], + }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('sphinxcontrib-serializinghtml', '1.1.4', { + 'modulename': 'sphinxcontrib.serializinghtml', + 'checksums': ['eaa0eccc86e982a9b939b2b82d12cc5d013385ba5eadcc7e4fed23f4405f77bc'], + }), + ('Sphinx', '3.2.1', { + 'checksums': ['321d6d9b16fa381a5306e5a0b76cd48ffbc588e6340059a729c6fdd66087e0e8'], + }), + ('click', '7.1.2', { + 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], + }), + ('psutil', '5.7.0', { + 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('sortedcontainers', '2.2.2', { + 'checksums': ['4e73a757831fc3ca4de2859c422564239a31d8213d09a2a666e375807034d2ba'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), +] + +moduleclass = 'lang' From 34144e7fdd220d9a325c7dc01aca3e721e6096a4 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 13 Oct 2020 22:31:18 +0200 Subject: [PATCH 469/698] adding easyconfigs: intltool-0.51.0-GCCcore-10.2.0.eb --- .../intltool-0.51.0-GCCcore-10.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..8c601251e77 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Perl', '5.32.0'), +] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +moduleclass = 'devel' From 3d7e8775c9a238578c0197beae85cb9fe5a9d25b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 13 Oct 2020 22:32:11 +0200 Subject: [PATCH 470/698] adding easyconfigs: CMake-3.18.4-GCCcore-10.2.0.eb, cURL-7.72.0-GCCcore-10.2.0.eb, bzip2-1.0.8-GCCcore-10.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb | 28 +++++++++++ .../c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 35 +++++++++++++ .../c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ 3 files changed, 112 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..ec886cad08b --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-1.0.6-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '5a823e820b332eca3684416894f58edc125ac3dace9f46e62f98e45362aa8a6d', # bzip2-1.0.6-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..e31b9c6094b --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +name = 'CMake' +version = '3.18.4' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['597c61358e6a92ecbfad42a9b5321ddd801fc7e7eca08441307c9138382d4f77'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('cURL', '7.72.0'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d'), +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..319edd1d929 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.72.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d4d5899a3868fbb6ae1856c3e55a32ce35913de3956d1973caccd37bd0174fa2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1d') +] + +osdependencies = [ + ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), +] + +configopts = '--with-zlib' +# configopts += '--with-ssl=$EBROOTOPENSSL' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From f55c3d8952d2e7f1080021f724e867b62d34c092 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Wed, 14 Oct 2020 10:34:11 +0200 Subject: [PATCH 471/698] adding easyconfigs: Subversion-1.14.0-GCCcore-9.3.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb | 32 ++++++++++++ .../a/APR/APR-1.7.0-GCCcore-9.3.0.eb | 22 +++++++++ .../s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb | 39 +++++++++++++++ .../Subversion-1.14.0-GCCcore-9.3.0.eb | 49 +++++++++++++++++++ .../utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb | 30 ++++++++++++ 5 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4288b55490d --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.34')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.31.1'), + ('expat', '2.2.9'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..df0f475c077 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'http://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['http://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.34')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..92271f6b634 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'http://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] + +builddependencies = [ + ('binutils', '2.34'), + ('Python', '2.7.18'), # Serfs build scripts are python 2 only + ('SCons', '3.1.2'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.0.1p'), +] + +osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..67be03ac25c --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.0' + +homepage = 'http://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = [ + 'http://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'http://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + '6ba8e218f9f97a83a799e58a3c6da1221d034b18d9d8cbbcb6ec52ab11722102', # subversion-1.14.0.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Autotools', '20180311'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.31.1'), + ('zlib', '1.2.11'), + ('lz4', '1.9.2'), + ('utf8proc', '2.5.0'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..148e68c23d5 --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-9.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.5.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4e8dfc898cfd062493cb7f42d95d70ccdd3a4cd4d90bec0c71b47cca688f1be'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 5241fed013e2527cda63f35dde1695b36811cae3 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Wed, 14 Oct 2020 11:19:45 +0200 Subject: [PATCH 472/698] HTTPS for valid sites, use OpenSSL os-dep template --- .../easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb | 4 ++-- .../s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb | 6 +++--- 4 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb index 4288b55490d..6785033c1ce 100644 --- a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-9.3.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'APR-util' version = '1.6.1' -homepage = 'http://apr.apache.org/' +homepage = 'https://apr.apache.org/' description = "Apache Portable Runtime (APR) util libraries." toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = ['http://archive.apache.org/dist/apr/'] +source_urls = ['https://archive.apache.org/dist/apr/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb index df0f475c077..89a9158336f 100644 --- a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-9.3.0.eb @@ -3,12 +3,12 @@ easyblock = 'ConfigureMake' name = 'APR' version = '1.7.0' -homepage = 'http://apr.apache.org/' +homepage = 'https://apr.apache.org/' description = "Apache Portable Runtime (APR) libraries." toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = ['http://archive.apache.org/dist/apr/'] +source_urls = ['https://archive.apache.org/dist/apr/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb index 92271f6b634..df419a78c7f 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-9.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'SCons' name = 'Serf' version = '1.3.9' -homepage = 'http://serf.apache.org/' +homepage = 'https://serf.apache.org/' description = """The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library""" @@ -26,7 +26,7 @@ dependencies = [ # ('OpenSSL', '1.0.1p'), ] -osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] +osdependencies = [OS_PKG_OPENSSL_DEV] buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb index 67be03ac25c..a4767edbe52 100644 --- a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-9.3.0.eb @@ -3,16 +3,16 @@ easyblock = 'ConfigureMake' name = 'Subversion' version = '1.14.0' -homepage = 'http://subversion.apache.org/' +homepage = 'https://subversion.apache.org/' description = " Subversion is an open source version control system." toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [ - 'http://apache.belnet.be/%(namelower)s', + 'https://apache.belnet.be/%(namelower)s', 'http://www.eu.apache.org/dist/%(namelower)s', 'http://www.us.apache.org/dist/%(namelower)s', - 'http://archive.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', ] sources = [SOURCELOWER_TAR_BZ2] patches = ['Subversion-1.12.0-no_swig.patch'] From 56553669ab8218850129ea830d42196032a190c0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 12:56:46 +0200 Subject: [PATCH 473/698] adding easyconfigs: libpng-1.6.37-GCCcore-10.2.0.eb, freetype-2.10.3-GCCcore-10.2.0.eb, util-linux-2.36-GCCcore-10.2.0.eb, fontconfig-2.13.92-GCCcore-10.2.0.eb, gperf-3.1-GCCcore-10.2.0.eb --- .../fontconfig-2.13.92-GCCcore-10.2.0.eb | 39 ++++++++++++++++++ .../freetype-2.10.3-GCCcore-10.2.0.eb | 37 +++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb | 31 ++++++++++++++ .../util-linux-2.36-GCCcore-10.2.0.eb | 41 +++++++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..077c89c6a43 --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.13.92' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['3406a05b83a42231e3df68d02bc0a0cf47b3f2e8f11c8ede62267daf5f130016'] + +builddependencies = [ + ('binutils', '2.35'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), + ('freetype', '2.10.3'), + ('util-linux', '2.36'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..85cc3b228eb --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.10.3-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +name = 'freetype' +version = '2.10.3' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['9dfb4e11efd6e460a87b1991a64bc69344ee7dc219d9b29e7faabc1c168ce8b0'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..570faad38a2 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1ed15d2e2e8 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.37-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.37' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['daeb2620d829575513e35fecc83f0d3791a620b9b93d800b763542ece9390fb4'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [('zlib', '1.2.11')] + +local_majminver = ''.join(version.split('.')[:2]) + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..93640fcd1d6 --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.36-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.36' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['82942cd877a989f6d12d4ce2c757fb67ec53d8c5cd9af0537141ec5f84a2eea3'] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 93c1a1b23c44af7a68f57aa2b5e9585e0024dfec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 13:59:54 +0200 Subject: [PATCH 474/698] reinstate attribution, use github_account in MMseqs2 v11 easyconfig --- .../easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb index ebaf2980bc1..3918570ac25 100644 --- a/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb +++ b/easybuild/easyconfigs/m/MMseqs2/MMseqs2-11-e1a1c-iimpi-2019b.eb @@ -1,3 +1,8 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics + easyblock = 'CMakeMake' name = 'MMseqs2' @@ -8,7 +13,8 @@ description = "MMseqs2: ultra fast and sensitive search and clustering suite" toolchain = {'name': 'iimpi', 'version': '2019b'} -source_urls = ['https://github.com/soedinglab/MMseqs2/archive/'] +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['ffe1ae300dbe1a0e3d72fc9e947356a4807f07951cb56316f36974d8d5875cbb'] From 806224bc713ceced6491c3042ae156fe7100b0bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 14:02:41 +0200 Subject: [PATCH 475/698] add missing xauth component to Xvfb 1.20.8 easyconfigs --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb | 4 ++++ easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb index 5561b1f88e7..cecac7a6fb8 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.2.0.eb @@ -81,6 +81,10 @@ components = [ ], 'configopts': '--with-xkb-rules-symlink=xorg', }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), (name, version, { 'source_urls': ['https://www.x.org/releases/individual//xserver/'], 'sources': ['xorg-server-%(version)s.tar.gz'], diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb index b0629b98411..4a228b5fdf7 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.8-GCCcore-8.3.0.eb @@ -81,6 +81,10 @@ components = [ ], 'configopts': '--with-xkb-rules-symlink=xorg', }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), (name, version, { 'source_urls': ['https://www.x.org/releases/individual//xserver/'], 'sources': ['xorg-server-%(version)s.tar.gz'], From 866262fe2a615e9bfcf9f4214499dc302e27f1af Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Oct 2020 14:09:21 +0200 Subject: [PATCH 476/698] fix worker-1.6.11-intel-2019b installation on RHEL 8.2 --- .../w/worker/worker-1.6.11-intel-2019b.eb | 67 +++---------------- 1 file changed, 11 insertions(+), 56 deletions(-) diff --git a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb index 10568fa1b7c..1c990dddf08 100644 --- a/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb +++ b/easybuild/easyconfigs/w/worker/worker-1.6.11-intel-2019b.eb @@ -8,80 +8,35 @@ description = """The Worker framework has been developed to help deal with param that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework.""" -toolchain = SYSTEM +local_tcname = 'intel' +local_tcver = '2019b' +toolchain = {'name': local_tcname, 'version': local_tcver} +toolchainopts = {'usempi': True} source_urls = ['https://github.com/gjbex/worker/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['680a852586a712f82c4f1fc17d166b789b374d52a3c8a8ed30b8dc67ff38daf2'] -osdependencies = ['perl'] - -local_tcname = 'intel' -local_tcver = '2019b' -builddependencies = [(local_tcname, local_tcver)] -versionsuffix = '-%s-%s' % (local_tcname, local_tcver) - -exts_defaultclass = 'PerlModule' - -exts_list = [ - ('Config::General', '2.63', { - 'source_tmpl': 'Config-General-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TL/TLINDEN'], - 'checksums': ['0a9bf977b8aabe76343e88095d2296c8a422410fd2a05a1901f2b20e2e1f6fad'], - }), - ('IO::Stringy', '2.111', { - 'source_tmpl': 'IO-stringy-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DS/DSKOLL'], - 'checksums': ['8c67fd6608c3c4e74f7324f1404a856c331dbf48d9deda6aaa8296ea41bf199d'], - }), - ('Text::CSV', '2.00', { - 'source_tmpl': 'Text-CSV-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['8ccbd9195805222d995844114d0e595bb24ce188f85284dbf256080311cbb2c2'], - }), - ('DBI', '1.642', { - 'source_tmpl': 'DBI-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], - 'checksums': ['3f2025023a56286cebd15cb495e36ccd9b456c3cc229bf2ce1f69e9ebfc27f5d'], - }), - ('DBD::SQLite', '1.64', { - 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/I/IS/ISHIGAKI'], - 'checksums': ['f4ae8f7b50842305566aadd90f7bfd12a9e32b6c603a9b1c1529e73eb82aff01'], - }), - ('Date::Language', '2.30', { - 'source_tmpl': 'TimeDate-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/G/GB/GBARR'], - 'checksums': ['75bd254871cb5853a6aa0403ac0be270cdd75c9d1b6639f18ecba63c15298e86'], - }), - ('Template', '2.29', { - 'source_tmpl': 'Template-Toolkit-%(version)s.tar.gz', - 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], - 'checksums': ['2bddd71cf41fb805fd5234780daf53226b8e7004c623e1647ba2658113614779'], - }), +dependencies = [ + ('Perl', '5.30.0') ] -preconfigopts = "export CC=mpiicc && " - -modextrapaths = { - 'PERL5LIB': ['share/perl5', 'lib64/perl5'], -} - # adjust worker configuration file # note: tweak this to your local setup postinstallcmds = [ 'sed -i "s/ cores_per_node = .*/ cores_per_node = 16/g" %(installdir)s/conf/worker.conf', 'sed -i "s@ qsub = .*@ qsub = `which qsub`@g" %(installdir)s/conf/worker.conf', 'sed -i "s/ email = .*/ email = hpc-support@example.com/g" %(installdir)s/conf/worker.conf', - 'sed -i "s/ unload_modules = .*/ unload_modules = intel/g" %(installdir)s/conf/worker.conf', + 'sed -i "s/ unload_modules = .*/ unload_modules = %s/g" %%(installdir)s/conf/worker.conf' % (local_tcname), 'sed -i "s@ mpi_module = .*@ mpi_module = %s/%s@g" %%(installdir)s/conf/worker.conf' % (local_tcname, local_tcver), 'sed -i "s@ module_path = .*@ module_path = %(installdir)s/../../../modules/all@g" %(installdir)s/conf/worker.conf', + "echo PERL=\\'`which perl`\\' > %(installdir)s/conf/worker_perl.sh", ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in ['dbilogstrip', 'dbiprof', 'dbiproxy', 'tpage', 'ttree', 'wcat', 'wconvert', - 'wload', 'worker', 'wreduce', 'wresume', 'wsub', 'wsummarize']], - 'dirs': ['lib/perl', 'lib/tt', 'lib64/perl5'], + 'files': ['bin/%s' % x for x in ['wcat', 'wconvert', 'wload', 'worker', 'wreduce', 'wresume', 'wsub', + 'wsummarize']], + 'dirs': ['lib/perl', 'lib/tt'], } sanity_check_commands = ["wsub -help"] From 6fe16ee6050fcc7584d0e591a1cf2d01e2789282 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 14:09:28 +0200 Subject: [PATCH 477/698] adding easyconfigs: ABINIT-9.2.1-intel-2020a.eb --- .../a/ABINIT/ABINIT-9.2.1-intel-2020a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb new file mode 100644 index 00000000000..fba575ac644 --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb @@ -0,0 +1,55 @@ +# +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.2.1' + +homepage = 'https://www.abinit.org/' +description = """ABINIT is a package whose main program allows one to find the total energy, + charge density and electronic structure of systems made of electrons and nuclei (molecules + and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a + planewave or wavelet basis.""" + +toolchain = {'name': 'intel', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] + +dependencies = [ + ('libxc', '4.3.4'), + ('netCDF-Fortran', '4.5.2'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" --enable-openmp="no" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4. +configopts += 'with_netcdf="${EBROOTNETCDF}" ' +configopts += 'with_netcdf_fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += 'with_hdf5="${EBROOTHDF5}" ' + +# abinit must be run under mpirun with Intel MPI included in intel/2020a +pretestopts = "sed -i 's@./abinit testin@mpirun -np 1 ./abinit testin@g' Makefile && " + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From e816dec713a7ce2d30b0e2bfbec781d9558cc670 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 14:13:26 +0200 Subject: [PATCH 478/698] Remove trailing whitespace --- .../f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb index 077c89c6a43..5e691036a5d 100644 --- a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.13.92-GCCcore-10.2.0.eb @@ -25,7 +25,7 @@ builddependencies = [ dependencies = [ ('expat', '2.2.9'), - ('freetype', '2.10.3'), + ('freetype', '2.10.3'), ('util-linux', '2.36'), ] From 547cf506ba58904d2e149c271c47ec1d0736798c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 13:58:16 +0200 Subject: [PATCH 479/698] use OS_PKG_OPENSSL_DEV constant in cURL 7.72.0 and CMake 3.18.4 easyconfigs + bump version for commented out OpenSSL dep --- .../easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 6 ++---- easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb index e31b9c6094b..d16e78407be 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -25,11 +25,9 @@ dependencies = [ ('cURL', '7.72.0'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d'), + # ('OpenSSL', '1.1.1h'), ] -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] +osdependencies = [OS_PKG_OPENSSL_DEV] moduleclass = 'devel' diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb index 319edd1d929..c745d57b964 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.72.0-GCCcore-10.2.0.eb @@ -29,12 +29,10 @@ dependencies = [ ('zlib', '1.2.11'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.1d') + # ('OpenSSL', '1.1.1h') ] -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] +osdependencies = [OS_PKG_OPENSSL_DEV] configopts = '--with-zlib' # configopts += '--with-ssl=$EBROOTOPENSSL' From 90106c191837f545191115591f6d3699f5b5f314 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 14 Oct 2020 14:18:23 +0200 Subject: [PATCH 480/698] {bio}[iccifort/2019.5.281] Structure v2.3.4 --- .../Structure-2.3.4-iccifort-2019.5.281.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/Structure/Structure-2.3.4-iccifort-2019.5.281.eb diff --git a/easybuild/easyconfigs/s/Structure/Structure-2.3.4-iccifort-2019.5.281.eb b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-iccifort-2019.5.281.eb new file mode 100644 index 00000000000..13939ce2c35 --- /dev/null +++ b/easybuild/easyconfigs/s/Structure/Structure-2.3.4-iccifort-2019.5.281.eb @@ -0,0 +1,25 @@ +easyblock = 'MakeCp' + +name = 'Structure' +version = '2.3.4' + +homepage = 'https://web.stanford.edu/group/pritchardlab/structure.html' +description = """The program structure is a free software package for using multi-locus genotype data to investigate + population structure.""" + +toolchain = {'name': 'iccifort', 'version': '2019.5.281'} + +source_urls = ['https://web.stanford.edu/group/pritchardlab/structure_software/release_versions/v%(version)s/'] +sources = [{'download_filename': 'structure_kernel_source.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f2b72b9189a514f53e921bbdc1aa3dbaca7ac34a8467af1f972c7e4fc9c0bb37'] + +buildopts = 'all CC="$CC" OPT="$CFLAGS"' + +files_to_copy = [(['structure'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/structure'], + 'dirs': [], +} + +moduleclass = 'bio' From 2b8a8d84d96a691d8eae08b1c123f29ff94bc47a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 15:14:03 +0200 Subject: [PATCH 481/698] add libarchive dep to CMake 3.18.4 --- .../c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb | 1 + .../libarchive-3.4.3-GCCcore-10.2.0.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb index d16e78407be..adcb0b84ea0 100644 --- a/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/CMake/CMake-3.18.4-GCCcore-10.2.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('zlib', '1.2.11'), ('bzip2', '1.0.8'), ('cURL', '7.72.0'), + ('libarchive', '3.4.3'), # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.1.1h'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..56c058b302a --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.4.3' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From de265fa7e900ff66477264cd09de74141a28b6c5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 16:19:32 +0200 Subject: [PATCH 482/698] disable libunwind + add xauth component for Xvfb 1.20.9 --- easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb index a50acd95e9f..772ef1b22f5 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-1.20.9-GCCcore-9.3.0.eb @@ -28,7 +28,7 @@ dependencies = [ default_easyblock = 'ConfigureMake' local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " -local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" # use 'make V=1' to see compiler commands @@ -76,6 +76,10 @@ components = [ 'checksums': ['5ac6b5b661aeb9d0ea84ad961cbbdd8fdf2503d6e8ca65ca1b1c5d9aea2ddc52'], 'configopts': '--with-xkb-rules-symlink=xorg', }), + ('xauth', '1.1', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['e9fce796c8c5c9368594b9e8bbba237fb54b6615f5fd60e8d0a5b3c52a92c5ef'], + }), (name, version, { 'source_urls': ['https://www.x.org/releases/individual//xserver/'], 'sources': ['xorg-server-%(version)s.tar.gz'], From a4308b7acaf892dc19daaf61eb5436edc64c7241 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 16:21:49 +0200 Subject: [PATCH 483/698] add Python 3 build dep for ABINIT 9.2.1 --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb index fba575ac644..b9a6c524f03 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb @@ -17,6 +17,9 @@ source_urls = ['https://www.abinit.org/sites/default/files/packages/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['4aa2deaeec385ff1624669a59768e1a6655f6367f8f109e69944244e000142a0'] +builddependencies = [ + ('Python', '3.8.2'), +] dependencies = [ ('libxc', '4.3.4'), ('netCDF-Fortran', '4.5.2'), From 8b96b886d88aab1c76834f9a54e3c108ef271c02 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 14 Oct 2020 17:40:50 +0200 Subject: [PATCH 484/698] build a nanomax-analysis-utils set-up ontop of fosscuda. Also includes a pyopencl --- ...abio-0.10.2-fosscuda-2019b-Python-3.7.4.eb | 28 +++++++++++ ...s-utils-0.4-fosscuda-2019b-Python-3.7.4.eb | 28 +++++++++++ ...cl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb | 35 ++++++++++++++ ...nsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb | 29 +++++++++++ ...silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb | 48 +++++++++++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..e7f49c15ebb --- /dev/null +++ b/easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'fabio' +version = '0.10.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://www.silx.org' +description = """FabIO is an I/O library for images produced by 2D X-ray detectors and written in Python. +FabIO support images detectors from a dozen of companies (including Mar, Dectris, ADSC, Hamamatsu, Oxford, ...), +for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers an unified interface to their headers +(as a python dictionary) and datasets (as a numpy ndarray of integers or floats).""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fb4dcd0645cbaabbe1d3db59b729cebd72be9b2e3c410e5cdc3b2aa94cc16713'] + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..4747e0e73d2 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomax-analysis-utils/nanomax-analysis-utils-0.4-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'nanomax-analysis-utils' +version = '0.4' +versionsuffix = '-Python-%(pyver)s' + +github_account = 'maxiv-science' +homepage = "https://github.com/%(github_account)s/nanomax-analysis-utils" +description = """A set of tools for handling and analysing data at the NanoMAX beamline.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('silx', '0.13.2', versionsuffix), +] + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5e9d931c94ee3f36b3bccb448036497e033d37f2e3f03f5ea8c004f85a0bdb31'] + +options = {'modulename': 'nmutils'} + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..c66513372b3 --- /dev/null +++ b/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'pyopencl' +version = '2020.2.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2020.4', { + 'checksums': ['37db39ff11a1b5fc8aec875ae4ddb3d6c21aa0e95bddc9c841aa98e1631ae460'], + }), + (name, version, { + 'checksums': ['31fcc79fb6862998e98d91a624c0bd4f0ab4c5d418d199912d4d312c64e437ec'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..af3bb2bba32 --- /dev/null +++ b/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'qtconsole' +version = '4.7.7' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a terminal, +but provides a number of enhancements only possible in a GUI, +such as inline figures, proper multiline editing with syntax highlighting, graphical calltips, and more.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'] + +dependencies = [ + ('Python', '3.7.4'), + ('IPython', '7.9.0', versionsuffix), + ('QtPy', '1.9.0', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..66d3145008d --- /dev/null +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'silx' +version = '0.13.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = "http://www.silx.org/" +description = """The silx project provides a collection of Python packages to support the +development of data assessment, reduction and analysis applications at synchrotron radiation facilities.""" + +toolchain = {'name': 'fosscuda', 'version': '2019b'} + + +dependencies = [ + ('Python', '3.7.4'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + ('PyOpenGL', '3.1.5'), + ('matplotlib', '3.1.1', versionsuffix), + ('Mako', '1.1.0'), + ('Pillow', '6.2.1'), + ('fabio', '0.10.2', versionsuffix), + ('qtconsole', '4.7.7', versionsuffix), + ('pyopencl', '2020.2.2', versionsuffix), +] + + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('hdf5plugin', '2.3.1', { + 'checksums': ['2f6d886012c37bf7e8e002173dd6b16e6879b8e0e9f7d2f2ef9f79db97ed28d2'], + }), + ('silx', version, { + 'checksums': ['0bc5a5a30499b9d620c795a20948151a4057aba16ff08dfe637f7a923b4697d4'], + }), +] + +modextrapaths = { + 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', +} + + +moduleclass = 'vis' From b2d7cc27c32b89ca5e65307c2c2e1561b6ff1110 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 21:17:38 +0200 Subject: [PATCH 485/698] add Python dep for OPERA-MS + fix shebang in Perl/Python scripts --- ...020a.eb => OPERA-MS-0.9.0-20200802-foss-2020a.eb} | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/o/OPERA-MS/{OPERA-MS-0.9.0-foss-2020a.eb => OPERA-MS-0.9.0-20200802-foss-2020a.eb} (77%) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a.eb similarity index 77% rename from easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb rename to easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a.eb index 2b9faa5160f..a551767bee9 100644 --- a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-foss-2020a.eb +++ b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a.eb @@ -1,7 +1,9 @@ easyblock = 'MakeCp' name = 'OPERA-MS' -version = '0.9.0' +local_commit = 'c18b4f3' +version = '0.9.0-20200802' +versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/CSB5/OPERA-MS' description = """OPERA-MS is a hybrid metagenomic assembler which combines the @@ -12,12 +14,13 @@ description = """OPERA-MS is a hybrid metagenomic assembler which combines the toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://github.com/CSB5/OPERA-MS/archive/'] -sources = ['OPERA-MS-%(version)s.tar.gz'] -checksums = ['750f7f7325b9064c6479d51e1e5861772f1305c4cb219924c64bc4363922e862'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['fa2caa223e1cd54d26cf650b96fef7c92ced016204deedd120c9844a51656a6d'] dependencies = [ ('Perl', '5.30.2'), ('Statistics-R', '0.34'), + ('Python', '3.8.2'), ] buildopts = 'CFLAGS="$CFLAGS"' @@ -44,6 +47,9 @@ postinstallcmds = [ ]), ] +fix_perl_shebang_for = ['bin/*.pl', 'OPERA-MS.pl', 'OPERA-LG/bin/*.pl'] +fix_python_shebang_for = ['bin/*.py', 'OPERA-LG/bin/*.py'] + sanity_check_paths = { 'files': ['bin/OPERA-MS'], 'dirs': [], From 565bfa01e6576c53cdc60a695e29d23adad90694 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 21:22:54 +0200 Subject: [PATCH 486/698] re-instate old credits in new MUMmer easyconfig --- easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb index 3dcbd9b0e1b..5ee222e2706 100644 --- a/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-3.23-GCCcore-9.3.0.eb @@ -9,8 +9,10 @@ # This work implements a part of the HPCBIOS project and is a component of the policy: # http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html ## - -# easyblock = mummer.py +## +# updated by: +# Adam Huffman +# The Francis Crick Institute name = 'MUMmer' version = '3.23' From dd61a887ddfbba501e68dab93e5e39b741e4a46a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Oct 2020 21:54:12 +0200 Subject: [PATCH 487/698] fix name of OPERA-MS easyconfig file --- ...020a.eb => OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/o/OPERA-MS/{OPERA-MS-0.9.0-20200802-foss-2020a.eb => OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb} (100%) diff --git a/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a.eb b/easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb similarity index 100% rename from easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a.eb rename to easybuild/easyconfigs/o/OPERA-MS/OPERA-MS-0.9.0-20200802-foss-2020a-Python-3.8.2.eb From 2b76f19874fd03a4bad8ffb45a296f03c244f897 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 14 Oct 2020 21:57:06 +0200 Subject: [PATCH 488/698] Include poetry and other common extensions into core bundles --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 126 +++++++++++++++++- .../p/Python/Python-3.8.4-GCCcore-10.2.0.eb | 120 +++++++++++++++++ 2 files changed, 242 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index b17ca55ddc4..fae6a3ac0ef 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -38,15 +38,15 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), - ('pip', '20.2.3', { - 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], - }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -101,6 +101,9 @@ exts_list = [ 'modulename': 'enum', 'checksums': ['cce6a7477ed816bd2542d03d53db9f0db935dd013b70f336a95c73979289f248'], }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), ('ipaddress', '1.0.23', { 'checksums': ['b7f8e0369580bb4a24d5ba1d7cc29660a4a6987763faf1d8a8046830e020e7e2'], }), @@ -276,6 +279,12 @@ exts_list = [ ('Sphinx', '1.8.5', { 'checksums': ['c7658aab75c920288a8cf6f09f244c6cfdae30d82d803ac1634d9f223a80ca08'], }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), @@ -294,6 +303,115 @@ exts_list = [ ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), + ('entrypoints', '0.3', { + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('functools32', '3.2.3-2', { + 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], + }), + ('futures', '3.3.0', { + 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], + }), + ('glob2', '0.6', { + 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], + }), + ('importlib-metadata', '1.7.0', { + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], + }), + ('subprocess32', '3.5.4', { + 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('regex', '2020.10.11', { + 'checksums': ['463e770c48da76a8da82b8d4a48a541f314e0df91cbb6d873a341dbe578efafd'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.3.0', { + 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], + }), + ('pastel', '0.2.1', { + 'use_pip': False, + 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + }), + ('clikit', '0.6.2', { + 'use_pip': False, + 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + }), + ('SecretStorage', '2.3.1', { + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), + ('tomlkit', '0.7.0', { + 'use_pip': False, + 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + }), + ('shellingham', '1.3.2', { + 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.16.1', { + 'checksums': ['aa2ae1c2e496f4d6777f869ea5de7166a8ccb9c2e06ebcf6c7ff1b670c98c5ef'], + }), + ('pkginfo', '1.5.0.1', { + 'checksums': ['7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'use_pip': False, + 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.0', { + 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], + }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb index d342d092dd2..2273eb77d3d 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb @@ -261,6 +261,9 @@ exts_list = [ ('alabaster', '0.7.12', { 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), + ('typing', '3.7.4.3', { + 'checksums': ['1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9'], + }), ('sphinxcontrib-applehelp', '1.0.2', { 'modulename': 'sphinxcontrib.applehelp', 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], @@ -288,6 +291,12 @@ exts_list = [ ('Sphinx', '3.2.1', { 'checksums': ['321d6d9b16fa381a5306e5a0b76cd48ffbc588e6340059a729c6fdd66087e0e8'], }), + ('sphinx-bootstrap-theme', '0.7.1', { + 'checksums': ['571e43ccb76d4c6c06576aa24a826b6ebc7adac45a5b54985200128806279d08'], + }), + ('colorama', '0.4.3', { + 'checksums': ['e96da0d330793e2cb9485e9ddfd918d456036c7149416295932478192f4436a1'], + }), ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), @@ -303,6 +312,117 @@ exts_list = [ ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('flit-core', '3.0.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': ['a465052057e2d6d957e6850e9915245adedfc4fd0dd5737d0791bf3132417c2d'], + }), + ('flit', '3.0.0', { + 'checksums': ['b4fe0f84a1ffbf125d003e253ec98c0b6e3e31290b31fba3ad22d28588c20893'], + }), + ('regex', '2020.10.11', { + 'checksums': ['463e770c48da76a8da82b8d4a48a541f314e0df91cbb6d873a341dbe578efafd'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('crashtest', '0.3.1', { + 'use_pip': False, + 'checksums': ['42ca7b6ce88b6c7433e2ce47ea884e91ec93104a4b754998be498a8e6c3d37dd'], + }), + ('pylev', '1.3.0', { + 'checksums': ['063910098161199b81e453025653ec53556c1be7165a9b7c50be2f4d57eae1c3'], + }), + ('pastel', '0.2.1', { + 'use_pip': False, + 'checksums': ['e6581ac04e973cac858828c6202c1e1e81fee1dc7de7683f3e1ffe0bfd8a573d'], + }), + ('clikit', '0.6.2', { + 'use_pip': False, + 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], + }), + ('jeepney', '0.4.3', { + 'use_pip': False, + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), + ('SecretStorage', '3.1.2', { + 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], + }), + ('keyring', '21.4.0', { + 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], + }), + ('keyrings.alt', '4.0.0', { + 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], + }), + ('tomlkit', '0.7.0', { + 'use_pip': False, + 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], + }), + ('shellingham', '1.3.2', { + 'checksums': ['576c1982bea0ba82fb46c36feb951319d7f42214a82634233f58b40d858a751e'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('pkginfo', '1.5.0.1', { + 'checksums': ['7424f2c8511c186cd5424bbf31045b77435b37a8d604990b79d4e70d741148bb'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '0.8.1', { + 'use_pip': False, + 'checksums': ['3d0e22d30117851b45970b6c14aca4ab0b18b1b53c8af57bed13208147e4069f'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.0', { + 'checksums': ['9534d5cc480d4aff720233411a1f765be90885750b07df772380b34c10ecb5c0'], + }), + ('CacheControl', '0.12.6', { + 'checksums': ['be9aa45477a134aee56c8fac518627e1154df063e85f67d4f83ce0ccc23688e8'], + }), + ('ptyprocess', '0.6.0', { + 'use_pip': False, + 'checksums': ['923f299cc5ad920c68f2bc0bc98b75b9f838b93b599941a6b63ddbc2476394c0'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.0.0', { + 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], + }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), + ('fsspec', '0.8.4', { + 'checksums': ['e1e494d4814f6804769f3c7bfd7a722a15113cc0339d14755297f09306b8f21f'], + }), + ('threadpoolctl', '2.1.0', { + 'checksums': ['ddc57c96a38beb63db45d6c159b5ab07b6bced12c45a1f07b2b92f272aebfa6b'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), ] moduleclass = 'lang' From b6265bf22a863489af2dd52a4a75147230893484 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Oct 2020 12:02:55 +0200 Subject: [PATCH 489/698] Remove orphan comment in ABINIT-9.2.1-intel-2020a.eb --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb index b9a6c524f03..3f8347410c4 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.2.1-intel-2020a.eb @@ -1,4 +1,3 @@ -# easyblock = 'ConfigureMake' name = 'ABINIT' From a9ec99315393d8fb064db6050b8fea4071264b51 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 14:47:55 +0000 Subject: [PATCH 490/698] adding easyconfigs: fmt-6.2.1-GCCcore-9.3.0.eb --- .../f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..4dcf689687c --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '6.2.1' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['94fea742ddcccab6607b517f6e608b1e5d63d712ddbc5982e44bafec5279881a'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 94a5c045c69602557d5f82ab83f4e03636be34f1 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 14:48:39 +0000 Subject: [PATCH 491/698] adding easyconfigs: fmt-7.0.3-GCCcore-9.3.0.eb --- .../f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..b39a93d33a5 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '7.0.3' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['decfdf9ad274070fa85f26407b816f5a4d82205ae86bac1990be658d0795ea4d'] + +builddependencies = [ + ('CMake', '3.16.4'), +] + +separate_build_dir = True + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 0af331298d1897b1f056eec092e440ce4ddb924e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 16:52:41 +0200 Subject: [PATCH 492/698] adding easyconfigs: PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 93 +++++++++++++++++++ 1 file changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb new file mode 100644 index 00000000000..2122c835fca --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -0,0 +1,93 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.34')] +dependencies = [ + ('Python', '3.8.2'), + ('Qt5', '5.14.1'), +] + +default_easyblock = 'PythonPackage' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.4.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['4282ab45948674f5ef74278a8e70d1302f65c95b519a0af19409002f5715d641'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.5.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['11bbe26e8e3d5ffec6d2ef2f50596b1670eb2d8b49aee0f859821922d8282841'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.8.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['30e944db9abee9cc757aea16906d4198129558533eb7fadbe48c5da2bd18e0bd'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d9a76b850246d08da9863189ecb98f6c2aa9b4d97a3e85e29330a264aed0f9a1'], + 'easyblock': 'Binary', + 'start_dir': '%(name)s-%(version)s', + 'skipsteps': ['configure', 'build'], + 'install_cmd': local_setup_env + local_pyqt5_sip_install, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['f0ca7915ee206ba5d703168c6ca40b0aad62c67360328fae4af5359cdbcee439'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 59993968e7834942eaa360ef9d29fcc37392b51d Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 15:11:23 +0000 Subject: [PATCH 493/698] Added missing binutils builddeps --- easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb index 4dcf689687c..945ac3c6ac7 100644 --- a/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/fmt/fmt-6.2.1-GCCcore-9.3.0.eb @@ -15,6 +15,7 @@ checksums = ['94fea742ddcccab6607b517f6e608b1e5d63d712ddbc5982e44bafec5279881a'] builddependencies = [ ('CMake', '3.16.4'), + ('binutils', '2.34') ] separate_build_dir = True From d41dcf3d57e5582263da83be62c930e2a5b107df Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 15:12:11 +0000 Subject: [PATCH 494/698] Added missing binutils builddeps --- easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb index b39a93d33a5..aefd2a77072 100644 --- a/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/fmt/fmt-7.0.3-GCCcore-9.3.0.eb @@ -15,6 +15,7 @@ checksums = ['decfdf9ad274070fa85f26407b816f5a4d82205ae86bac1990be658d0795ea4d'] builddependencies = [ ('CMake', '3.16.4'), + ('binutils', '2.34') ] separate_build_dir = True From f02d7f11cd5b5a31e11059d541223b61f25e5846 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 15:39:08 +0000 Subject: [PATCH 495/698] adding easyconfigs: CCfits-2.5-GCCcore-9.3.0.eb --- .../c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..87ef8a6e00a --- /dev/null +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -0,0 +1,20 @@ +easyblock = 'ConfigureMake' + +name = 'CCfits' +version = '2.5' + +homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/CCfits/' +description = """CCfits is an object oriented interface to the cfitsio library. It is designed to make +the capabilities of cfitsio available to programmers working in C++.""" + +toolchain = {'version': '9.3.0', 'name': 'GCCcore'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/%(name)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['938ecd25239e65f519b8d2b50702416edc723de5f0a5387cceea8c4004a44740'] + +dependencies = [ + ('CFITSIO', '3.48'), +] + From 1133bb8701c51213b998846b768e9f0be162d46d Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 16:19:53 +0000 Subject: [PATCH 496/698] adding easyconfigs: Cereal-1.3.0.eb --- .../easyconfigs/c/Cereal/Cereal-1.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb new file mode 100644 index 00000000000..03f8f3b03e8 --- /dev/null +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb @@ -0,0 +1,30 @@ +## +# @Authors:: Maxime Boissonneault, Compute Canada +# @date: October 15, 2020 +## + +easyblock = 'CMakeMake' + +name = 'Cereal' +version = '1.3.0' + +homepage = 'http://uscilab.github.io/cereal/' +description = """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly +turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be +fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or +used standalone.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/USCiLab/cereal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['329ea3e3130b026c03a4acc50e168e7daff4e6e661bc6a7dfec0d77b570851d5'] + +configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' + +sanity_check_paths = { + 'files': ['include/cereal/cereal.hpp'], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From 4b375fb716ec5c62bd2836183feab47ddb6fe5f0 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 16:29:36 +0000 Subject: [PATCH 497/698] added sanity checks --- easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb index 87ef8a6e00a..3629d8680be 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -18,3 +18,9 @@ dependencies = [ ('CFITSIO', '3.48'), ] +sanity_check_paths = { + 'files': ['lib/libCCfits.%s' % SHLIB_EXT], + 'dirs': ['include/CCfits'], +} + + From 564d6a2a9724f54c1c8930d5779e43e9c8ed4207 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 16:41:11 +0000 Subject: [PATCH 498/698] updating https instead of http --- easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb index 03f8f3b03e8..5c109893599 100644 --- a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb @@ -8,7 +8,7 @@ easyblock = 'CMakeMake' name = 'Cereal' version = '1.3.0' -homepage = 'http://uscilab.github.io/cereal/' +homepage = 'https://uscilab.github.io/cereal/' description = """cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or From d795b69f12d0b91c903f2a0e56583952b655075a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 15 Oct 2020 18:58:01 +0200 Subject: [PATCH 499/698] adding easyconfigs: xarray-0.16.1-intel-2020a-Python-3.8.2.eb --- .../xarray-0.16.1-intel-2020a-Python-3.8.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..a312783b64c --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-0.16.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '0.16.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['5e1af056ff834bf62ca57da917159328fab21b1f8c25284f92083016bb2d92a5'] + +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', versionsuffix), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'data' From 3ab561e0512d78b79a0ab059395772a09707886b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 19:10:38 +0200 Subject: [PATCH 500/698] Remove problematic python2 packages --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 39 +++++++------------ 1 file changed, 15 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index fae6a3ac0ef..95c964e8ddb 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -38,15 +38,15 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ - ('pip', '20.2.3', { - 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], - }), ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', 'use_pip': False, 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], }), + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -223,8 +223,9 @@ exts_list = [ ('contextlib2', '0.6.0.post1', { 'checksums': ['01f490098c18b19d2bd5bb5dc445b2054d2fa97f09a4280ba2c5f3c394c8162e'], }), - ('importlib_metadata', '2.0.0', { - 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + ('importlib-metadata', '1.7.0', { + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], }), ('pluggy', '0.13.1', { 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], @@ -236,6 +237,10 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], }), + ('backports.functools-lru-cache', '1.6.1', { + 'source_tmpl': 'backports.functools_lru_cache-%(version)s.tar.gz', + 'checksums': ['8fde5f188da2d593bd5bc0be98d9abc46c95bb8a9dde93429570192ee6cc2d4a'], + }), ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], }), @@ -303,9 +308,6 @@ exts_list = [ ('intervaltree', '3.1.0', { 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], }), - ('entrypoints', '0.3', { - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), ('functools32', '3.2.3-2', { 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), @@ -315,10 +317,6 @@ exts_list = [ ('glob2', '0.6', { 'checksums': ['f5b0a686ff21f820c4d3f0c4edd216704cea59d79d00fa337e244a2f2ff83ed6'], }), - ('importlib-metadata', '1.7.0', { - 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', - 'checksums': ['90bb658cdbbf6d1735b6341ce708fc7024a3e14e99ffdc5783edea9f9b077f83'], - }), ('subprocess32', '3.5.4', { 'checksums': ['eb2937c80497978d181efa1b839ec2d9622cf9600a039a79d0e108d1f9aec79d'], }), @@ -342,14 +340,9 @@ exts_list = [ 'use_pip': False, 'checksums': ['442ee5db9a14120635c5990bcdbfe7c03ada5898291f0c802f77be71569ded59'], }), - ('SecretStorage', '2.3.1', { - 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], - }), - ('keyring', '18.0.1', { - 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], - }), - ('keyrings.alt', '3.2.0', { - 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), ('tomlkit', '0.7.0', { 'use_pip': False, @@ -403,11 +396,9 @@ exts_list = [ 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('poetry-core', '1.0.0', { + 'modulename': 'poetry.core', 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], }), - ('poetry', '1.1.3', { - 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], - }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], From a4d1d0371e84ca9b7331b87b1b1a0149e781116a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 19:30:58 +0200 Subject: [PATCH 501/698] Remove module check for 'futures' --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index 95c964e8ddb..f8b07e20ea6 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -312,6 +312,7 @@ exts_list = [ 'checksums': ['f6253dfbe0538ad2e387bd8fdfd9293c925d63553f5813c4e587745416501e6d'], }), ('futures', '3.3.0', { + 'modulename': False, 'checksums': ['7e033af76a5e35f58e56da7a91e687706faf4e7bdfb2cbc3f2cca6b9bcda9794'], }), ('glob2', '0.6', { From 55daf3ce4d1fbb8a69cd44f65cdc2f5e35b692ee Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 17:52:34 +0000 Subject: [PATCH 502/698] updating https instead of http --- easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb index 3629d8680be..4b7ce20991f 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -3,14 +3,14 @@ easyblock = 'ConfigureMake' name = 'CCfits' version = '2.5' -homepage = 'http://heasarc.gsfc.nasa.gov/fitsio/CCfits/' +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/CCfits/' description = """CCfits is an object oriented interface to the cfitsio library. It is designed to make the capabilities of cfitsio available to programmers working in C++.""" toolchain = {'version': '9.3.0', 'name': 'GCCcore'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://heasarc.gsfc.nasa.gov/fitsio/%(name)s/'] +source_urls = ['https://heasarc.gsfc.nasa.gov/fitsio/%(name)s/'] sources = [SOURCE_TAR_GZ] checksums = ['938ecd25239e65f519b8d2b50702416edc723de5f0a5387cceea8c4004a44740'] From 1c8af228fb4a3ce703994a4a51d002c99bfffaea Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 18:16:04 +0000 Subject: [PATCH 503/698] adding missing binutils builddpes --- easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb index 4b7ce20991f..5725e69e7cc 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -17,6 +17,9 @@ checksums = ['938ecd25239e65f519b8d2b50702416edc723de5f0a5387cceea8c4004a44740'] dependencies = [ ('CFITSIO', '3.48'), ] +builddependencies = [ + ('binutils', '2.34'), +] sanity_check_paths = { 'files': ['lib/libCCfits.%s' % SHLIB_EXT], From 2e41e01012d27eef94f7a3402e7dfbe7819dc1b7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 20:31:20 +0200 Subject: [PATCH 504/698] adding easyconfigs: Spyder-4.1.5-foss-2020a-Python-3.8.2.eb --- .../Spyder-4.1.5-foss-2020a-Python-3.8.2.eb | 229 ++++++++++++++++++ 1 file changed, 229 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..1ad58558b2b --- /dev/null +++ b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,229 @@ +easyblock = 'PythonBundle' + +name = 'Spyder' +version = '4.1.5' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/spyder-ide/spyder' +description = """Spyder is an interactive Python development environment providing MATLAB-like features in a simple + and light-weighted software.""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [ + ('CMake', '3.16.4'), +] +dependencies = [ + ('Python', '3.8.2'), + ('ZeroMQ', '4.3.2'), + ('PyQt5', '5.15.1', versionsuffix), + ('IPython', '7.15.0', versionsuffix), + ('geopandas', '0.8.1', versionsuffix), +] + +use_pip = True + +# strip out (too strict version) requirements for pyqt5 and pyqtwebengine, +# because they are not installed with pip, but are provided via the PyQt5 dependency +local_spyder_preinstallopts = ( + """sed -i "s/'pyqt5.*,//g" setup.py && """ + """sed -i "s/'pyqtwebengine.*,//g" setup.py && """ +) + +exts_default_options = {'source_urls': [PYPI_SOURCE]} +exts_list = [ + ('astroid', '2.4.2', { + 'checksums': ['2f4078c2a41bf377eea06d71c9d2ba4eb8f6b1af2135bec27bbbb7d8f12bb703'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('autopep8', '1.5.4', { + 'checksums': ['d21d3901cb0da6ebd1e83fc9b0dfbde8b46afc2ede4fe32fbda0c7c6118ca094'], + }), + ('backcall', '0.2.0', { + 'use_pip': False, + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('bleach', '3.2.1', { + 'checksums': ['52b5919b81842b1854196eaae5ca29679a2f2e378905c346d3ca8227c2c66080'], + }), + ('cloudpickle', '1.6.0', { + 'checksums': ['9bc994f9e9447593bd0a45371f0e7ac7333710fcf64a4eb9834bf149f4ef2f32'], + }), + ('cookiecutter', '1.7.2', { + 'checksums': ['efb6b2d4780feda8908a873e38f0e61778c23f6a2ea58215723bcceb5b515dac'], + }), + ('decorator', '4.4.2', { + 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('diff-match-patch', '20200713', { + 'checksums': ['da6f5a01aa586df23dfc89f3827e1cafbb5420be9d87769eeb079ddfd9477a18'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('flake8', '3.8.4', { + 'checksums': ['aadae8761ec651813c24be05c6f7b4680857ef6afaae4651a4eccaef97ce6c3b'], + }), + ('helpdev', '0.7.1', { + 'checksums': ['bb62a79acbac141dadf42cadeb92bb7450dd18b9824a62043b6a0b149190db3d'], + }), + ('isort', '5.6.3', { + 'use_pip': False, + 'checksums': ['3820dd92c3214290cda6351f2ae2cedd5170759bc434af600eaad4f7a82a6ade'], + }), + ('jedi', '0.17.1', { + 'checksums': ['807d5d4f96711a2bcfdd5dfa3b1ae6d09aa53832b182090b222b5efb81f52f63'], + }), + ('jeepney', '0.4.3', { + 'use_pip': False, + 'checksums': ['3479b861cc2b6407de5188695fa1a8d57e5072d7059322469b62628869b8e36e'], + }), + ('arrow', '0.17.0', { + 'checksums': ['ff08d10cda1d36c68657d6ad20d74fbea493d980f8b2d45344e00d6ed2bf6ed4'], + }), + ('jinja2-time', '0.2.0', { + 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('keyring', '21.4.0', { + 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], + }), + ('keyrings.alt', '4.0.0', { + 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], + }), + ('lazy-object-proxy', '1.4.3', { + 'checksums': ['f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0'], + }), + ('mccabe', '0.6.1', { + 'checksums': ['dd8d182285a0fe56bace7f45b5e7d1a6ebcbf524e8f3bd87eb0f125271b8831f'], + }), + ('jupyter_client', '6.1.7', { + 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], + }), + ('nbclient', '0.5.1', { + 'checksums': ['01e2d726d16eaf2cde6db74a87e2451453547e8832d142f73f72fddcd4fe0250'], + }), + ('nest_asyncio', '1.4.1', { + 'checksums': ['b86c3193abda5b2eeccf8c79894bc71c680369a178f4b068514ac00720b14e01'], + }), + ('numpydoc', '1.1.0', { + 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], + }), + ('parso', '0.7.0', { + 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('poyo', '0.5.0', { + 'checksums': ['e26956aa780c45f011ca9886f044590e2d8fd8b61db7b1c1cf4e0869f48ed4dd'], + }), + ('pycodestyle', '2.6.0', { + 'checksums': ['c58a7d2815e0e8d7972bf1803331fb0152f867bd89adf8a01dfd55085434192e'], + }), + ('pydocstyle', '5.1.1', { + 'checksums': ['19b86fa8617ed916776a11cd8bc0197e5b9856d5433b777f51a3defe13075325'], + }), + ('pyflakes', '2.2.0', { + 'checksums': ['35b2d75ee967ea93b55750aa9edbbf72813e06a66ba54438df2cfac9e3c27fc8'], + }), + ('pylint', '2.6.0', { + 'checksums': ['bb4a908c9dadbc3aac18860550e870f58e1a02c9f2c204fdf5693d73be061210'], + }), + ('ujson', '4.0.1', { + 'checksums': ['26cf6241b36ff5ce4539ae687b6b02673109c5e3efc96148806a7873eaa229d3'], + }), + ('python-language-server', '0.35.1', { + 'checksums': ['6e0c9a3b2ae98e0eb22e98ed6b3c4e190a6bf9e27af53efd2396da60cd92b221'], + 'modulename': 'pyls', + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('python-jsonrpc-server', '0.4.0', { + 'checksums': ['62c543e541f101ec5b57dc654efc212d2c2e3ea47ff6f54b2e7dcb36ecf20595'], + 'modulename': 'pyls_jsonrpc', + }), + ('python-slugify', '4.0.1', { + 'checksums': ['69a517766e00c1268e5bbfc0d010a0a8508de0b18d30ad5a1ff357f8ae724270'], + 'modulename': 'slugify', + }), + ('pyxdg', '0.26', { + 'checksums': ['fe2928d3f532ed32b39c32a482b54136fe766d19936afc96c8f00645f9da1a06'], + 'modulename': 'xdg', + }), + ('rope', '0.18.0', { + 'checksums': ['786b5c38c530d4846aa68a42604f61b4e69a493390e3ca11b88df0fbfdc3ed04'], + }), + ('QDarkStyle', '2.8.1', { + 'checksums': ['d53b0120bddd9e3efba9801731e22ef86ed798bb5fc6a802f5f7bb32dedf0321'], + }), + ('QtAwesome', '1.0.1', { + 'checksums': ['d612a313e531966d17f5a8fb7604faba961cf7ce3c77a9168c6f60e60140b767'], + }), + ('qtconsole', '4.7.7', { + 'checksums': ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'], + }), + ('QtPy', '1.9.0', { + 'checksums': ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'], + }), + ('SecretStorage', '3.1.2', { + 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], + 'modulename': 'secretstorage', + }), + ('spyder', version, { + 'checksums': ['d467f020b694193873a237ce6744ae36bd5a59f4d2b7ffbeb15dda68b03f5aa1'], + 'preinstallopts': local_spyder_preinstallopts, + }), + ('spyder-kernels', '1.9.4', { + 'checksums': ['ca9d997c475b714b54d2fd67aa140837ec3630e91cbbc2e0cd190f1b0bd9fe9d'], + 'modulename': 'spyder_kernels', + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('traitlets', '5.0.4', { + 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], + }), + ('typed_ast', '1.4.1', { + 'checksums': ['8c8aaad94455178e3187ab22c8b01a3837f8ee50e09cf31f1ba129eb293ec30b'], + }), + ('watchdog', '0.10.3', { + 'checksums': ['4214e1379d128b0588021880ccaf40317ee156d4603ac388b9adcf29165e0c04'], + }), + ('wurlitzer', '2.0.1', { + 'checksums': ['d08f0728a998441aac3d7a0f8cd6dfed2ba2525144878fb49599b719085b7543'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('yapf', '0.30.0', { + 'checksums': ['3000abee4c28daebad55da6c85f3cd07b8062ce48e2e9943c8da1b9667d48427'], + }), +] + +sanity_check_paths = { + 'files': ['bin/spyder3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["spyder3 --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 77df3b4f934b6104ec5741733577fe5a37a23483 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Thu, 15 Oct 2020 18:35:49 +0000 Subject: [PATCH 505/698] removed blank line at the end --- easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb index 5725e69e7cc..2ee97a09780 100644 --- a/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/CCfits/CCfits-2.5-GCCcore-9.3.0.eb @@ -25,5 +25,3 @@ sanity_check_paths = { 'files': ['lib/libCCfits.%s' % SHLIB_EXT], 'dirs': ['include/CCfits'], } - - From b28490c00d52a6846c16120138b6ad27c38f74ac Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 21:14:00 +0200 Subject: [PATCH 506/698] add missing ncurses dep for Clang 5.0.x, 6.0.1, 7.0.x --- .../easyconfigs/c/Clang/Clang-5.0.0-GCC-6.4.0-2.28.eb | 7 ++++--- .../easyconfigs/c/Clang/Clang-5.0.1-GCC-6.4.0-2.28.eb | 5 +++-- .../easyconfigs/c/Clang/Clang-6.0.1-GCC-6.4.0-2.28.eb | 5 +++-- .../easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb | 5 +++-- .../easyconfigs/c/Clang/Clang-7.0.0-GCC-6.4.0-2.28.eb | 5 +++-- .../easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb | 3 ++- 6 files changed, 18 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-5.0.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/Clang/Clang-5.0.0-GCC-6.4.0-2.28.eb index bb6d732bca9..e3169ee61a8 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-5.0.0-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-5.0.0-GCC-6.4.0-2.28.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '5.0.0' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -39,6 +39,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.0'), ] builddependencies = [ @@ -48,7 +49,7 @@ builddependencies = [ ] assertions = True - usepolly = True +skip_all_tests = True moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/c/Clang/Clang-5.0.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/Clang/Clang-5.0.1-GCC-6.4.0-2.28.eb index 3f787018c62..fd7af8cca99 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-5.0.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-5.0.1-GCC-6.4.0-2.28.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '5.0.1' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -39,6 +39,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.0'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-6.4.0-2.28.eb index d733dc18ec2..356bf71d652 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-6.4.0-2.28.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '6.0.1' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -39,6 +39,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.0'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb index de357910d8a..ac40df50ff9 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-6.0.1-GCC-7.3.0-2.30.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '6.0.1' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -39,6 +39,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.1'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-7.0.0-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/c/Clang/Clang-7.0.0-GCC-6.4.0-2.28.eb index e9938ab4871..4173ef81846 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-7.0.0-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-7.0.0-GCC-6.4.0-2.28.eb @@ -11,7 +11,7 @@ name = 'Clang' version = '7.0.0' -homepage = 'http://clang.llvm.org/' +homepage = 'https://clang.llvm.org/' description = """C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC.""" @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -39,6 +39,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.0'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb index 5cbcc2e2ed1..a6435e60871 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-7.0.1-GCC-7.3.0-2.30.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} # Do not set optarch to True: it will cause the build to fail toolchainopts = {'optarch': False} -source_urls = ["http://llvm.org/releases/%(version)s"] +source_urls = ["https://llvm.org/releases/%(version)s"] sources = [ 'llvm-%(version)s.src.tar.xz', 'cfe-%(version)s.src.tar.xz', @@ -46,6 +46,7 @@ checksums = [ dependencies = [ ('GMP', '6.1.2'), + ('ncurses', '6.1'), ] builddependencies = [ From 4016bfdde6aafda19d54d73a46272f6949f9f744 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 21:26:41 +0200 Subject: [PATCH 507/698] add crossmeta extension to Bioconductor 3.11 bundle --- ...le-Bioconductor-3.11-foss-2020a-R-4.0.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb index 1b8235b72fa..a8620914e89 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb @@ -838,6 +838,36 @@ exts_list = [ ('MethylSeekR', '1.28.0', { 'checksums': ['47852110485865f5582d7a59bb62dfe268f1a65f71ead93ea31b69776bc993df'], }), + ('affxparser', '1.60.0', { + 'checksums': ['d8a3f876e5d60a9b34b6d5754a5f5ac78bbd32e6676b9cde22b50d0578c09034'], + }), + ('ccdata', '1.14.0', { + 'checksums': ['29cef251d129c84d79d95a1ea30fdbc277b1ca9cf1ec6c4802360783f3cf1f9a'], + }), + ('xgboost', '1.2.0.1', { + 'checksums': ['44472e673e4f346c05257ec78a260e0148285a79819d0fd2f3ec370ec5de179a'], + }), + ('lsa', '0.73.2', { + 'checksums': ['cb0017bbda9b0eb1d05b451e0f557d02f789f65b2f8bf005606b63a3708e63a8'], + }), + ('ccmap', '1.14.0', { + 'checksums': ['40b5d5de9be2a77ce1ae386fa75ef2a7d88df1e87bc97566d75c2c49c79457e2'], + }), + ('oligo', '1.52.1', { + 'checksums': ['8d4f07d7218a0fc6f0f2000320e5eefe2c7a99dc3732a93e7de17f7ec7c8fbbe'], + }), + ('SMVar', '1.3.3', { + 'checksums': ['17625e89eb8be7a6dbb77e6bd9daca1ea1acff69026049f213e30edf2325999f'], + }), + ('metaMA', '3.1.2', { + 'checksums': ['01851d9632cdf1988d6a43ba44500e51477b9b25d5df1e1da488cd800df85ed6'], + }), + ('sva', '3.36.0', { + 'checksums': ['24caa3a13cef2933a3c98d055af4ca0859fa08ec66a90ad28bd6a83041a54175'], + }), + ('crossmeta', '1.14.0', { + 'checksums': ['0ced79094cd3d2aea3f9745efe26de967d5225b01706ded7b528f633ba6226c5'], + }), ] modextrapaths = {'R_LIBS': ''} From a8341906dafce7eb26c67a198fee79e9bf726864 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 22:16:09 +0200 Subject: [PATCH 508/698] adding easyconfigs: GitPython-2.1.15.eb --- .../g/GitPython/GitPython-2.1.15.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb new file mode 100644 index 00000000000..bc1ad3c9fbc --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-2.1.15.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '2.1.15' + +homepage = 'https://github.com/gitpython-developers/GitPython' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = SYSTEM + +# can't be sure that pip is installed in the OS +use_pip = False + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +# version are pick to be compatible with both Python 2 and 3 +exts_list = [ + ('setuptools', '44.1.1', { + 'source_tmpl': 'setuptools-%(version)s.zip', + 'checksums': ['c67aa55db532a0dadc4d2e20ba9961cbd3ccc84d544e9029699822542b5a476b'], + }), + ('smmap', '3.0.4', { + 'checksums': ['9c98bbd1f9786d22f14b3d4126894d56befb835ec90cef151af566c7e19b5d24'], + }), + ('smmap2', '3.0.1', { + 'checksums': ['44cc8bdaf96442dbb9a8e2e14377d074b3d0eea292eee3c95c8c449b6c92c557'], + # just a wrapper for smmap, so skip import check + 'modulename': False, + }), + ('gitdb2', '2.0.6', { + 'modulename': 'gitdb', + 'checksums': ['1b6df1433567a51a4a9c1a5a0de977aa351a405cc56d7d35f3388bad1f630350'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['838c38d882a97b2fd146dbd4eb9baaf857cb65ebaa64e4c06fca48aaa491e1c6'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%s/site-packages' % '.'.join(SYS_PYTHON_VERSION.split('.')[:2])], +} + +moduleclass = 'lib' From da349985aecff8339dfc24b684c1538b7972ad5c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 22:40:54 +0200 Subject: [PATCH 509/698] Add python 3.8.4 changes that i missed previously --- .../p/Python/Python-3.8.4-GCCcore-10.2.0.eb | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb index 2273eb77d3d..de23ee4367e 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb @@ -46,14 +46,14 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ - ('pip', '20.2.3', { - 'use_pip': False, - 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], - }), ('setuptools', '50.3.0', { 'source_tmpl': '%(name)s-%(version)s.zip', 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], }), + ('pip', '20.2.3', { + 'use_pip': False, + 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], + }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -227,6 +227,9 @@ exts_list = [ ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], }), + ('iniconfig', '1.0.1', { + 'checksums': ['e5f92f89355a67de0595932a6c6c02ab4afddc6fcdc0bfc5becd0d60884d3f69'], + }), ('pytest', '6.1.1', { 'checksums': ['8f593023c1a0f916110285b6efd7f99db07d59546e3d8c36fc60e2ab05d3be92'], }), @@ -261,9 +264,6 @@ exts_list = [ ('alabaster', '0.7.12', { 'checksums': ['a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02'], }), - ('typing', '3.7.4.3', { - 'checksums': ['1187fb9c82fd670d10aa07bbb6cfcfe4bdda42d6fab8d5134f04e8c4d0b71cc9'], - }), ('sphinxcontrib-applehelp', '1.0.2', { 'modulename': 'sphinxcontrib.applehelp', 'checksums': ['a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58'], @@ -351,9 +351,11 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('keyring', '21.4.0', { + 'modulename': False, # Broken if keyring files are present in HOME 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '4.0.0', { + 'modulename': False, # Broken if keyring files are present in HOME 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { @@ -408,6 +410,7 @@ exts_list = [ 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], }), ('poetry-core', '1.0.0', { + 'modulename': 'poetry.core', 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], }), ('poetry', '1.1.3', { From 7f484636796a03798db6796a502aef370d8efb2c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 22:46:49 +0200 Subject: [PATCH 510/698] stick to academic version (fix sources + drop versionsuffix), add checksum, use SYSTEM toolchain --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb index fcec1426753..8aecd33ba10 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb @@ -1,6 +1,5 @@ name = 'FLUENT' version = '18.2' -versionsuffix = 'com' homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed @@ -8,8 +7,9 @@ to model flow, turbulence, heat transfer, and reactions for industrial applicati air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM -sources = ['FLUIDS_%(version_major)s%(version_minor)s_LINX64.tar'] +sources = ['FLUIDSTRUCTURES_%(version_major)s%(version_minor)s_LINX64.tar'] +checksums = ['5ffee69710504649f3458ea6ea44d5a3947085a4da76fa2b69f80bf6929cff4d'] moduleclass = 'cae' From ebab805e10d10269ac6299929ca4d46cef73d2e3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Oct 2020 23:12:08 +0200 Subject: [PATCH 511/698] use https in homepage for FLUENT 18.2 --- easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb index 8aecd33ba10..d09ebf29205 100644 --- a/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb +++ b/easybuild/easyconfigs/f/FLUENT/FLUENT-18.2.eb @@ -1,7 +1,7 @@ name = 'FLUENT' version = '18.2' -homepage = 'http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' +homepage = 'https://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent' description = """ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, From b81e9a542977de35b0e3e9e5c919104637b81a58 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 15 Oct 2020 23:26:34 +0200 Subject: [PATCH 512/698] Style fix --- easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb index de23ee4367e..12378dc0a5b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb @@ -351,11 +351,11 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('keyring', '21.4.0', { - 'modulename': False, # Broken if keyring files are present in HOME + 'modulename': False, # Broken if keyring files are present in HOME 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '4.0.0', { - 'modulename': False, # Broken if keyring files are present in HOME + 'modulename': False, # Broken if keyring files are present in HOME 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { From c77c4afef35af0c81d3b0c78cf092fe28614c77d Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Oct 2020 12:36:17 +0800 Subject: [PATCH 513/698] switch to https --- easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb index f6e6f9bea2b..5289bbe2a36 100644 --- a/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.0-foss-2017b.eb @@ -1,7 +1,7 @@ name = 'Siesta' version = '4.0' -homepage = 'http://departments.icmab.es/leem/siesta' +homepage = 'https://departments.icmab.es/leem/siesta' description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" From 95069d3d73a4588aa18fb1c8e79b00ad9f47b951 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 08:40:11 +0200 Subject: [PATCH 514/698] make PyCUDA 2017.1.1 depend on Boost.Python 1.65.1 --- ....Python-1.65.1-foss-2017b-Python-2.7.14.eb | 25 +++++++++++++++++++ ...1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 2 +- 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb new file mode 100644 index 00000000000..48c4535fffb --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb @@ -0,0 +1,25 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.65.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} + +source_urls = ['http://download.sourceforge.net/boost/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] + +dependencies = [ + ('Python', '2.7.14'), + ('Boost', version), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb index 288607f0525..f4a348646ac 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -17,7 +17,7 @@ checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] dependencies = [ ('Python', '2.7.14'), ('CUDA', '9.0.176', '', True), - ('Boost', '1.65.1', '-Python-%(pyver)s'), + ('Boost.Python', '1.65.1', '-Python-%(pyver)s'), ] prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " From d242ec93512cbbe3a211154626a2111b1f4c16da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 08:41:54 +0200 Subject: [PATCH 515/698] gaussian: Update comments to make it more clear where to get the sources and which source to use. --- easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb | 8 +++++++- easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb | 8 +++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb index e036a8343c3..561efd6b8d4 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb @@ -8,6 +8,9 @@ version = '09.e.01' versionsuffix = '-AVX' homepage = 'http://www.gaussian.com/' + +# For the sake of users I advise changing the last line in the description +# and versionsuffix to match the actual installed version. description = """ Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer @@ -20,7 +23,10 @@ This is the official gaussian AVX build. toolchain = {'name': 'dummy', 'version': 'dummy'} -# Gaussian is licensed software. Need to download by hand. +# Gaussian is licensed software. +# You need to pick the tar file of your choice from the DVD, +# put it in your sources tree (should be a tree that ordinary users can't read) +# and change the name in "sources" sources = ['09.e.01-AVX-A64-114X.tgz'] checksums = ['af1e1cdf7d2799690a642b27ee0779b7cca9695b9a86a48739f3d9fc8c54a98d'] diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb index b8f408218a1..e59554e54e4 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb @@ -8,6 +8,9 @@ version = '16.A.03' versionsuffix = '-AVX2' homepage = 'http://www.gaussian.com/' + +# For the sake of users I advise changing the last line in the description +# and versionsuffix to match the actual installed version. description = """ Gaussian provides state-of-the-art capabilities for electronic structure modeling. Gaussian 09 is licensed for a wide variety of computer @@ -20,7 +23,10 @@ This is the official gaussian AVX2 build. toolchain = {'name': 'dummy', 'version': 'dummy'} -# Gaussian is licensed software. Need to download by hand. +# Gaussian is licensed software. +# You need to pick the tar file of your choice from the DVD, +# put it in your sources tree (should be a tree that ordinary users can't read) +# and change the name in "sources" sources = ['16.A.03-AVX2-E6B-132X.tbz'] checksums = ['c83bbcb6ce136d257c8810cb447dfb0880bedf887efe6a4b828635938603384a'] From 440e7cc939863589788b9ffe7ece5eb2e27ebb95 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 09:01:09 +0200 Subject: [PATCH 516/698] Gaussian: Renamed gaussian to Gaussian, see (PR #7553) Picked up some extra env vars from #7553. --- .../Gaussian-09.e.01-AVX.eb} | 13 +++++++++---- .../Gaussian-16.A.03-AVX2.eb} | 13 +++++++++---- 2 files changed, 18 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/g/{gaussian/gaussian-09.e.01-AVX.eb => Gaussian/Gaussian-09.e.01-AVX.eb} (85%) rename easybuild/easyconfigs/g/{gaussian/gaussian-16.A.03-AVX2.eb => Gaussian/Gaussian-16.A.03-AVX2.eb} (85%) diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb similarity index 85% rename from easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb rename to easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb index 561efd6b8d4..00690c32236 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb @@ -3,11 +3,11 @@ easyblock = 'Tarball' # IMPORTANT!! # Needs to be installed with --umask=007 -name = 'gaussian' +name = 'Gaussian' version = '09.e.01' versionsuffix = '-AVX' -homepage = 'http://www.gaussian.com/' +homepage = 'https://www.gaussian.com/' # For the sake of users I advise changing the last line in the description # and versionsuffix to match the actual installed version. @@ -21,7 +21,7 @@ other than your computing resources and patience. This is the official gaussian AVX build. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Gaussian is licensed software. # You need to pick the tar file of your choice from the DVD, @@ -46,6 +46,9 @@ sanity_check_paths = { modextravars = { 'g%(version_major)sroot': '%(installdir)s', 'G%(version_major)sBASIS': '%(installdir)s/g%(version_major)s/basis', + 'GAUSS_BSDDIR': '%(installdir)s/g%(version_major)s/bsd', + '_DSM_BARRIER': 'SHM', + 'PGI_TERM': 'trace,abort', } modextrapaths = { @@ -54,4 +57,6 @@ modextrapaths = { 'LD_LIBRARY_PATH': 'g%(version_major)s', } -moduleclass = 'bio' +modaliases = {'sl': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb similarity index 85% rename from easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb rename to easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb index e59554e54e4..503d22ce05f 100644 --- a/easybuild/easyconfigs/g/gaussian/gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb @@ -3,11 +3,11 @@ easyblock = 'Tarball' # IMPORTANT!! # Needs to be installed with --umask=007 -name = 'gaussian' +name = 'Gaussian' version = '16.A.03' versionsuffix = '-AVX2' -homepage = 'http://www.gaussian.com/' +homepage = 'https://www.gaussian.com/' # For the sake of users I advise changing the last line in the description # and versionsuffix to match the actual installed version. @@ -21,7 +21,7 @@ other than your computing resources and patience. This is the official gaussian AVX2 build. """ -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM # Gaussian is licensed software. # You need to pick the tar file of your choice from the DVD, @@ -46,6 +46,9 @@ sanity_check_paths = { modextravars = { 'g%(version_major)sroot': '%(installdir)s', 'G%(version_major)sBASIS': '%(installdir)s/g%(version_major)s/basis', + 'GAUSS_BSDDIR': '%(installdir)s/g%(version_major)s/bsd', + '_DSM_BARRIER': 'SHM', + 'PGI_TERM': 'trace,abort', } modextrapaths = { @@ -54,4 +57,6 @@ modextrapaths = { 'LD_LIBRARY_PATH': 'g%(version_major)s', } -moduleclass = 'bio' +modaliases = {'sl': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} + +moduleclass = 'chem' From fc95fef262b6525d9cccb5037d5386f73f0041ec Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:01:13 +0200 Subject: [PATCH 517/698] create missing __init__ in mpl_toolkits + add custom sanity check paths in ESMValTool easyconfig --- .../ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index fca15aae9d7..171fed1e528 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -204,6 +204,15 @@ exts_list = [ }), ] +postinstallcmds = [ + 'touch %(installdir)s/lib/python%(pyshortver)s/site-packages/mpl_toolkits/__init__.py', +] + +sanity_check_paths = { + 'files': ['ESMValTool-%(version)s.tar.gz'], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages', 'ncdf4'], +} + modextrapaths = { 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'R_LIBS': '', From 9e39e0f8de87f7980f796fc480f8e2143357aff4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:07:00 +0200 Subject: [PATCH 518/698] use %(cudaver)s template value in PyCUDA 2017.1.1 easyconfig --- .../PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb index f4a348646ac..c73c553e65f 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -2,8 +2,7 @@ easyblock = 'PythonPackage' name = 'PyCUDA' version = '2017.1.1' -cudaver = '9.0.176' -versionsuffix = '-CUDA-{0}-Python-%(pyver)s'.format(cudaver) +versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' homepage = 'http://mathema.tician.de/software/pycuda' description = """PyCUDA lets you access Nvidias CUDA parallel computation API from Python.""" From 18922bd72f5deef206cd7dbcd0ca8c1253ba2245 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:25:59 +0200 Subject: [PATCH 519/698] use PythonBundle for PyCUDA 2017.1.1 + add missing dependencies --- ...1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb | 38 +++++++++++++------ 1 file changed, 26 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb index c73c553e65f..4d6b28f646a 100644 --- a/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb +++ b/easybuild/easyconfigs/p/PyCUDA/PyCUDA-2017.1.1-foss-2017b-CUDA-9.0.176-Python-2.7.14.eb @@ -1,32 +1,46 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'PyCUDA' version = '2017.1.1' versionsuffix = '-CUDA-%(cudaver)s-Python-%(pyver)s' -homepage = 'http://mathema.tician.de/software/pycuda' +homepage = 'https://mathema.tician.de/software/pycuda' description = """PyCUDA lets you access Nvidias CUDA parallel computation API from Python.""" toolchain = {'name': 'foss', 'version': '2017b'} -source_urls = [PYPI_LOWER_SOURCE] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'] - dependencies = [ ('Python', '2.7.14'), ('CUDA', '9.0.176', '', True), ('Boost.Python', '1.65.1', '-Python-%(pyver)s'), + ('Mako', '1.0.7', '-Python-%(pyver)s'), + ('pytest', '3.8.2', '-Python-%(pyver)s'), ] -prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " -prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost --boost-python-libname=boost_python && " +local_prebuildopts = "./configure.py --cuda-root=$EBROOTCUDA --boost-inc-dir=$EBROOTBOOST/include/boost/ " +local_prebuildopts += "--boost-lib-dir=$EBROOTBOOST/lib/ --no-use-shipped-boost " +local_prebuildopts += "--boost-python-libname=boost_python && " -options = {'modulename': '%(namelower)s'} +use_pip = True +sanity_pip_check = True -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], +exts_default_options = { + 'source_urls': [PYPI_LOWER_SOURCE], + 'source_tmpl': SOURCELOWER_TAR_GZ, } +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2020.1', { + 'checksums': ['c132d17855584ad61c6e00f3ff11146499755944afc400cce9eae0ecf03d04a6'], + }), + (name, version, { + 'prebuildopts': local_prebuildopts, + 'use_pip': False, + 'checksums': ['6b5a9384e38c603ee429f8a6bee424532db7b3505027ce22f7e18ad19564b563'], + }), +] + moduleclass = 'lang' From d49faaaf167a2926643ab3ad82026c3aca1116e6 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 09:26:27 +0200 Subject: [PATCH 520/698] Address some review comments on python3 --- ....2.0.eb => Python-3.8.6-GCCcore-10.2.0.eb} | 21 ++++---- .../u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb | 52 +++++++++++++++++++ 2 files changed, 64 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/p/Python/{Python-3.8.4-GCCcore-10.2.0.eb => Python-3.8.6-GCCcore-10.2.0.eb} (98%) create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb similarity index 98% rename from easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 12378dc0a5b..356b5e89b9b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -1,5 +1,5 @@ name = 'Python' -version = '3.8.4' +version = '3.8.6' homepage = 'https://python.org/' description = """Python is a programming language that lets you work more quickly and integrate your systems @@ -10,7 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] -checksums = ['32c4d9817ef11793da4d0d95b3191c4db81d2e45544614e8449255ca9ae3cc18'] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] + +dependencies = [ + ('UnZip', '6.0'), +] dependencies = [ ('binutils', '2.35'), @@ -34,7 +38,6 @@ osdependencies = [OS_PKG_OPENSSL_DEV] # required so we can update pip to version included in extensions, using pip installopts = " && ln -s %(installdir)s/bin/pip3 %(installdir)s/bin/pip" - exts_default_options = { 'download_dep_fail': True, 'sanity_pip_check': True, @@ -46,14 +49,14 @@ exts_default_options = { # order is important! # package versions updated 13 October 2020 exts_list = [ - ('setuptools', '50.3.0', { - 'source_tmpl': '%(name)s-%(version)s.zip', - 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], - }), ('pip', '20.2.3', { 'use_pip': False, 'checksums': ['30c70b6179711a7c4cf76da89e8a0f5282279dfb0278bec7b94134be92543b6d'], }), + ('setuptools', '50.3.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['39060a59d91cf5cf403fa3bacbb52df4205a8c3585e0b9ba4b30e0e19d4c4b18'], + }), ('wheel', '0.35.1', { 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], }), @@ -351,11 +354,11 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('keyring', '21.4.0', { - 'modulename': False, # Broken if keyring files are present in HOME + 'modulename': False, 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '4.0.0', { - 'modulename': False, # Broken if keyring files are present in HOME + 'modulename': False, 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..43ecaaf0413 --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 9d31b97a2e54f624c9b7d4d142d01925547d334b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 09:42:53 +0200 Subject: [PATCH 521/698] Gaussian: Change sources to user %(version)s%(versionsuffix)s Enhance comment on what to do with the "source"-tarfile --- easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb | 5 +++-- easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb | 5 +++-- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb index 00690c32236..4043bd50d07 100644 --- a/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb @@ -25,9 +25,10 @@ toolchain = SYSTEM # Gaussian is licensed software. # You need to pick the tar file of your choice from the DVD, -# put it in your sources tree (should be a tree that ordinary users can't read) +# put it in your sources tree with a proper name. +# (should be a tree that ordinary users can't read due to license restrictions) # and change the name in "sources" -sources = ['09.e.01-AVX-A64-114X.tgz'] +sources = ['%(version)s%(versionsuffix)s-A64-114X.tgz'] checksums = ['af1e1cdf7d2799690a642b27ee0779b7cca9695b9a86a48739f3d9fc8c54a98d'] start_dir = '..' diff --git a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb index 503d22ce05f..9cccb6280eb 100644 --- a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb @@ -25,9 +25,10 @@ toolchain = SYSTEM # Gaussian is licensed software. # You need to pick the tar file of your choice from the DVD, -# put it in your sources tree (should be a tree that ordinary users can't read) +# put it in your sources tree with a proper name. +# (should be a tree that ordinary users can't read due to license restrictions) # and change the name in "sources" -sources = ['16.A.03-AVX2-E6B-132X.tbz'] +sources = ['%(version)s%(versionsuffix)s-E6B-132X.tgz'] checksums = ['c83bbcb6ce136d257c8810cb447dfb0880bedf887efe6a4b828635938603384a'] start_dir = '..' From 8d4cfa084e2ae3a96f3cd4ee76715710765ea232 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:51:49 +0200 Subject: [PATCH 522/698] use https in Boost 1.65.1 easyconfig --- .../Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb index 48c4535fffb..39fd25ad4de 100644 --- a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.65.1-foss-2017b-Python-2.7.14.eb @@ -4,14 +4,14 @@ name = 'Boost.Python' version = '1.65.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://boostorg.github.io/python' +homepage = 'https://boostorg.github.io/python' description = """Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/boost/'] +source_urls = ['https://download.sourceforge.net/boost/'] sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] checksums = ['a13de2c8fbad635e6ba9c8f8714a0e6b4264b60a29b964b940a22554705b6b60'] From 9e7f7016df9396b83c8ac9a555a7f9dd66ad0fcc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 09:52:00 +0200 Subject: [PATCH 523/698] Gaussian: Fix typo in sources --- easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb index 9cccb6280eb..258bf7b36ce 100644 --- a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb @@ -28,7 +28,7 @@ toolchain = SYSTEM # put it in your sources tree with a proper name. # (should be a tree that ordinary users can't read due to license restrictions) # and change the name in "sources" -sources = ['%(version)s%(versionsuffix)s-E6B-132X.tgz'] +sources = ['%(version)s%(versionsuffix)s-E6B-132X.tbz'] checksums = ['c83bbcb6ce136d257c8810cb447dfb0880bedf887efe6a4b828635938603384a'] start_dir = '..' From 907d20143d27795b458f03e40eef8b6679bdcea3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:52:28 +0200 Subject: [PATCH 524/698] fix long line in Boost 1.65.1 easyconfig --- .../b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb index 864dd89bfe5..b7d6db75269 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb @@ -23,7 +23,8 @@ dependencies = [ # also build boost_mpi boost_mpi = True -# Compile Boost with -std=c++11, see https://gist.github.com/dennycd/5890475 and https://groups.google.com/forum/#!topic/fenics-support/yrseUpq3PSA +# Compile Boost with -std=c++11, see https://gist.github.com/dennycd/5890475 +# and https://groups.google.com/forum/#!topic/fenics-support/yrseUpq3PSA # -stdlib is left out, because that is an option for M*X (MacOS) only # Strangely enough, it does cause the option -std=c++11 to be not recognized anymore.. buildopts = 'cxxflags="$CXXFLAGS -std=c++11" linkflags="$LDFLAGS -std=c++11" ' From 3d67386b6a12dfe40556def4fa02718e9288d7ae Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 09:55:41 +0200 Subject: [PATCH 525/698] use https in easyconfigs for R 3.4.3 and ESMValTool 1.1.0 --- .../ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb | 10 +++++----- .../R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb index 171fed1e528..d8838e62951 100644 --- a/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/e/ESMValTool/ESMValTool-1.1.0-intel-2017b-Python-2.7.14.eb @@ -122,8 +122,8 @@ exts_list = [ 'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'], }), ('PyKE', '1.1.1', { - 'source_tmpl': 'pyke-1.1.1.zip', - 'source_urls': ['http://download.sourceforge.net/pyke'], + 'source_tmpl': 'pyke-%(version)s.zip', + 'source_urls': ['https://download.sourceforge.net/pyke'], 'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'], }), ('cf_units', '1.2.0', { @@ -196,9 +196,9 @@ exts_list = [ ('ncdf4', '1.16', { 'source_tmpl': '%(name)s_%(version)s.tar.gz', 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/ncdf4', - 'http://cran.r-project.org/src/contrib/', - 'http://cran.freestatistics.org/src/contrib', + 'https://cran.r-project.org/src/contrib/Archive/ncdf4', + 'https://cran.r-project.org/src/contrib/', + 'https://cran.freestatistics.org/src/contrib', ], 'checksums': ['edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253'], }), diff --git a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb index 9b473a61b46..72a1d8f4d5b 100644 --- a/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb +++ b/easybuild/easyconfigs/r/R/R-3.4.3-intel-2017b-X11-20171023-HDF5-1.8.19.eb @@ -4,13 +4,13 @@ local_x11ver = '20171023' local_hdf5ver = '1.8.19' versionsuffix = '-X11-%s-HDF5-%s' % (local_x11ver, local_hdf5ver) -homepage = 'http://www.r-project.org/' +homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" toolchain = {'name': 'intel', 'version': '2017b'} sources = [SOURCE_TAR_GZ] -source_urls = ['http://cran.us.r-project.org/src/base/R-%(version_major)s'] +source_urls = ['https://cran.us.r-project.org/src/base/R-%(version_major)s'] checksums = ['7a3cb831de5b4151e1f890113ed207527b7d4b16df9ec6b35e0964170007f426'] builddependencies = [ @@ -60,9 +60,9 @@ easybuild_version = '3.5.0' exts_default_options = { 'source_urls': [ - 'http://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive - 'http://cran.r-project.org/src/contrib/', # current version of packages - 'http://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], 'source_tmpl': '%(name)s_%(version)s.tar.gz', } From d8f929f64924d1441675953af3646ba98e7d15ce Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 10:09:48 +0200 Subject: [PATCH 526/698] adding easyconfigs: COMSOL-5.4.0.225.eb --- .../easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb diff --git a/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb b/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb new file mode 100644 index 00000000000..5b79330b836 --- /dev/null +++ b/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb @@ -0,0 +1,23 @@ +name = 'COMSOL' +version = '5.4.0.225' + +homepage = 'https://www.comsol.com' +description = """ +COMSOL Multiphysics is a general-purpose software platform, based on +advanced numerical methods, for modeling and simulating physics-based +problems. +""" + +toolchain = {'name': 'dummy', 'version': ''} + +# source tarball has to be created manually from dvd +# mount -o ro path-to-iso /mnt +# cd /mnt +# tar zcf /COMSOL-5.4.0.225.tar.gz . +# umount /mnt +sources = [SOURCE_TAR_GZ] +checksums = [None] + +# license is required, can be specified via $LMCOMSOL_LICENSE_FILE + +moduleclass = 'phys' From 740670d27b3a99d06ce0533ac4e0e56b8a0279da Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Fri, 16 Oct 2020 10:13:25 +0200 Subject: [PATCH 527/698] adding easyconfigs: fastq-join-1.3.1-intel-2020a.eb, fastq-join-1.3.1-intel-2020a.eb, GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb, GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb --- .../fastq-join-1.3.1-intel-2020a.eb | 32 ++++++++++++++ ...BprocesS-2.1.1-intel-2020a-Python-3.8.2.eb | 43 +++++++++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb create mode 100644 easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb b/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb new file mode 100644 index 00000000000..a627a58e6ca --- /dev/null +++ b/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'fastq-join' +version = '1.3.1' + +homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' +description = """ NCIPLOT is a program for revealing non covalent interactions + based on the reduced density gradient. """ + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://github.com/brwnj/fastq-join/archive/'] +sources = ['v%(version)s.tar.gz'] + +# Remove hardcoded values +prebuildopts = "sed -i 's/CC=g++//g' Makefile && " +prebuildopts += "sed -i 's/CFLAGS=-O3 -I.//g' Makefile && " + +# Fix failing test (sqrt(-1) is expected to be NaN but is actually -NaN) +prebuildopts += "sed -i 's/n\", dev)/n\", abs(dev))/g' fastq-join.cpp && " + +runtest = 'check' + +files_to_copy = [(['fastq-join'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/fastq-join'], + 'dirs': [], +} +sanity_check_commands = ['fastq-join -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..70df7af55ae --- /dev/null +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'GBprocesS' +version = '2.1.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://gbprocess.readthedocs.io/' +description = """GBprocesS allows for the extraction of genomic inserts from NGS +data for GBS experiments. Preprocessing is performed in different stages that +are part of a linear pipeline where the steps are performed in order. GBprocesS +provides a flexible way to adjust the functionality to your needs, as the +operations required and the execution order vary depending on the GBS protocol +used.""" + +toolchain = {'name': 'intel', 'version': '2020a'} + +source_urls = ['https://gitlab.com/dschaumont/GBprocesS/-/archive/%(version)s/'] +sources = ['GBprocesS-%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.8.2'), + ('cutadapt', '2.10', '-Python-%(pyver)s'), + ('Biopython', '1.78', versionsuffix), + ('fastq-join', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# Tests expect the package to already be installed, but EB runs them beforehand +pretestopts = ( + "sed -i 's/" + "__version__ = get_distribution(__name__).version/" + "__version__ = \"%(version)s\"/g' gbprocess/__init__.py && " + "sed -i \"s|use_scm_version={'write_to': 'gbprocess/version.py'}|version='%(version)s'|g\" setup.py && " +) + +runtest = 'python -m unittest discover -v -s ./test -p test_*.py' + +options = {'modulename': 'gbprocess'} + +moduleclass = 'bio' From 0146eb15f42d7074664d57eaa47fc2c6f2a51f54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 10:27:10 +0200 Subject: [PATCH 528/698] Use SYSTEM toolchain --- easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb b/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb index 5b79330b836..009dd996efe 100644 --- a/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb +++ b/easybuild/easyconfigs/c/COMSOL/COMSOL-5.4.0.225.eb @@ -8,7 +8,7 @@ advanced numerical methods, for modeling and simulating physics-based problems. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # source tarball has to be created manually from dvd # mount -o ro path-to-iso /mnt From ede89d0ea6d0d10480eaf5d975f56dec1a0e9e77 Mon Sep 17 00:00:00 2001 From: vsc43634 Date: Fri, 16 Oct 2020 10:31:26 +0200 Subject: [PATCH 529/698] GBprocesS: add checksums --- .../easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb | 1 + .../g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb b/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb index a627a58e6ca..aba8ecb20d6 100644 --- a/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb +++ b/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'intel', 'version': '2020a'} source_urls = ['https://github.com/brwnj/fastq-join/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['1748511a7785ad9944850e81f35c980011f5c6346dec1fb67cc99b3110170690'] # Remove hardcoded values prebuildopts = "sed -i 's/CC=g++//g' Makefile && " diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb index 70df7af55ae..ee7334236af 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb @@ -16,6 +16,7 @@ toolchain = {'name': 'intel', 'version': '2020a'} source_urls = ['https://gitlab.com/dschaumont/GBprocesS/-/archive/%(version)s/'] sources = ['GBprocesS-%(version)s.tar.gz'] +checksums = ['968e9431160d4c552e85e6478d79e22f3c1d946130917b3cee0a6c602d51e5e1'] dependencies = [ ('Python', '3.8.2'), From df2001cba04b21bf4b6d81b8424c675cf46512ba Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 10:41:40 +0200 Subject: [PATCH 530/698] Gaussian: Comment out the modaliases, but leave a comment to its potential uesfulness --- easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb | 3 ++- easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb index 4043bd50d07..17d847d73ab 100644 --- a/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-09.e.01-AVX.eb @@ -58,6 +58,7 @@ modextrapaths = { 'LD_LIBRARY_PATH': 'g%(version_major)s', } -modaliases = {'sl': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} +# This might be useful at some sites. +# modaliases = {'g_searchlog': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb index 258bf7b36ce..b107da773c0 100644 --- a/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb +++ b/easybuild/easyconfigs/g/Gaussian/Gaussian-16.A.03-AVX2.eb @@ -58,6 +58,7 @@ modextrapaths = { 'LD_LIBRARY_PATH': 'g%(version_major)s', } -modaliases = {'sl': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} +# This might be useful at some sites. +# modaliases = {'g_searchlog': '%(installdir)s/g%(version_major)s/tests/searchlog.csh'} moduleclass = 'chem' From 25b186d8b41c2a8bd084b467a50deed6209075e7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 10:49:29 +0200 Subject: [PATCH 531/698] use https in homepage of Boost 1.65.1 --- .../b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb index b7d6db75269..6bb7884072c 100644 --- a/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb +++ b/easybuild/easyconfigs/b/Boost/Boost-1.65.1-foss-2017b-Python-2.7.14.eb @@ -2,7 +2,7 @@ name = 'Boost' version = '1.65.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.boost.org/' +homepage = 'https://www.boost.org/' description = "Boost provides free peer-reviewed portable C++ source libraries." toolchain = {'name': 'foss', 'version': '2017b'} From 1a8adef83c2a892aaa4f02434d2ede4a32923c92 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 11:08:56 +0200 Subject: [PATCH 532/698] Fix various things. --- .../p/Python/Python-2.7.18-GCCcore-10.2.0.eb | 17 ++++++++++++++++- .../p/Python/Python-3.8.6-GCCcore-10.2.0.eb | 18 +++++++++--------- 2 files changed, 25 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb index f8b07e20ea6..9328a9011b0 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-10.2.0.eb @@ -36,7 +36,7 @@ exts_default_options = { } # order is important! -# package versions updated 13 October 2020 +# package versions updated 13 October 2020, to the most recent versions still supporting Python 2.x exts_list = [ ('setuptools', '44.1.1', { 'source_tmpl': '%(name)s-%(version)s.zip', @@ -345,6 +345,18 @@ exts_list = [ 'use_pip': False, 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], }), + ('SecretStorage', '2.3.1', { + 'modulename': False, # Doesn't work properly under Python2, but is required for keyring + 'checksums': ['3af65c87765323e6f64c83575b05393f9e003431959c9395d1791d51497f29b6'], + }), + ('keyring', '18.0.1', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['67d6cc0132bd77922725fae9f18366bb314fd8f95ff4d323a4df41890a96a838'], + }), + ('keyrings.alt', '3.2.0', { + 'modulename': False, # Doesn't work properly if HOME directory contains keys + 'checksums': ['1c9981c351dabe902172ccf75bccff78185548f15ad51d5297e6366c0f4c3b51'], + }), ('tomlkit', '0.7.0', { 'use_pip': False, 'checksums': ['ac57f29693fab3e309ea789252fcce3061e19110085aa31af5446ca749325618'], @@ -400,6 +412,9 @@ exts_list = [ 'modulename': 'poetry.core', 'checksums': ['6a664ff389b9f45382536f8fa1611a0cb4d2de7c5a5c885db1f0c600cd11fbd5'], }), + ('poetry', '1.1.3', { + 'checksums': ['49eae89e2c44b0323214d0bbcefc21ebe3a19baa44db98eefabd4db9e82c7253'], + }), ('simplegeneric', '0.8.1', { 'source_tmpl': 'simplegeneric-%(version)s.zip', 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb index 356b5e89b9b..4371dc3f09b 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.8.6-GCCcore-10.2.0.eb @@ -8,11 +8,11 @@ description = """Python is a programming language that lets you work more quickl toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://www.%(namelower)s.org/ftp/%(namelower)s/%(version)s/'] +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] sources = [SOURCE_TGZ] checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] -dependencies = [ +builddependencies = [ ('UnZip', '6.0'), ] @@ -166,6 +166,9 @@ exts_list = [ ('filelock', '3.0.12', { 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), ('virtualenv', '20.0.34', { 'checksums': ['4bf0e2bf99d33b123a895a5a244f0d7adb2a92171c6bbb31c3e2db235624abf1'], }), @@ -214,9 +217,6 @@ exts_list = [ ('zipp', '3.3.0', { 'checksums': ['64ad89efee774d1897a58607895d80789c59778ea02185dd846ac38394a8642b'], }), - ('importlib_metadata', '2.0.0', { - 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], - }), ('pluggy', '0.13.1', { 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], }), @@ -303,8 +303,8 @@ exts_list = [ ('click', '7.1.2', { 'checksums': ['d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a'], }), - ('psutil', '5.7.0', { - 'checksums': ['685ec16ca14d079455892f25bd124df26ff9137664af445563c1bd36629b5e0e'], + ('psutil', '5.7.2', { + 'checksums': ['90990af1c3c67195c44c9a889184f84f5b2320dce3ee3acbd054e3ba0b4a7beb'], }), ('future', '0.18.2', { 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], @@ -354,11 +354,11 @@ exts_list = [ 'checksums': ['15da8a989b65498e29be338b3b279965f1b8f09b9668bd8010da183024c8bff6'], }), ('keyring', '21.4.0', { - 'modulename': False, + 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['9aeadd006a852b78f4b4ef7c7556c2774d2432bbef8ee538a3e9089ac8b11466'], }), ('keyrings.alt', '4.0.0', { - 'modulename': False, + 'modulename': False, # Doesn't work properly if HOME directory contains keys 'checksums': ['f70ef01a8f2b968b83643db370a1e85bc0e4bc8b358f9661504279afb019d21d'], }), ('tomlkit', '0.7.0', { From 1136042b41d123f0bddd7860cc4543912f2991a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 11:19:36 +0200 Subject: [PATCH 533/698] use combined patch for AmberTools 17 based on patched used for Amber 16 --- .../a/AmberTools/AmberTools-17-foss-2018a.eb | 8 +- .../a/AmberTools/AmberTools-17_fixes.patch | 1028 +++++++++++++++++ 2 files changed, 1032 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb index b50569eb2d2..611c41647de 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb @@ -13,10 +13,10 @@ toolchainopts = {'usempi': True} # download requires registration, see http://ambermd.org/AmberTools17-get.html sources = ['AmberTools%(version)s.tar.bz2'] -patches = ['Amber-16_fix-hardcoding.patch'] +patches = ['AmberTools-17_fixes.patch'] checksums = [ '4fbb2cf57d27422949909cc6f7e434c9855333366196a1d539264617c8bc5dec', # AmberTools17.tar.bz2 - '5e25d0671a173d3347d9e4ddec2faec4caed048918a7c339767d7fb312008c52', # Amber-16_fix-hardcoding.patch + '14ff6778e3ed6d9a5c00b627332998ce9e189295bf11afca9b2ee65842331e18', # AmberTools-17_fixes.patch ] builddependencies = [ @@ -31,8 +31,8 @@ dependencies = [ # fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others, # all of which are indirect dependencies via netCDF -netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" -preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % netcdf_libs +local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" +preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % local_netcdf_libs configopts = "-nosanderapi" moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes.patch new file mode 100644 index 00000000000..eaab60e05d0 --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes.patch @@ -0,0 +1,1028 @@ +combination of patches originally created for Amber 16 + +original patches by Åke Sandgren and Davide Vanzo (Vanderbilt University) +combined patch composed by Kenneth Hoste (HPC-UGent) + +* Do not use static for cpptraj, builds fail (was: Amber-16-AT-17-fix-cpptraj-dont-use-static.patch) +* Fix incorrect OMP directive in RISM (was: Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch) +* Fix incorrect intel mpi compiler version detection (was: Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch) +* checkrismunsupported.sh needs to run TESTsander with DO_PARALLEL, otherwise it will get "Killed" instead of a proper exit (was: Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch) +* Fix missing openmp flag at link (was: Amber-16-AT-17-fix_missing_openmp_at_link.patch) +* Fix incorrect mkl include path (was: Amber-16-AT-17-fix_mkl_include_path.patch) +* Fix link of external FFTW3 for sander (was: Amber-16-AT-17-fix_sander_link_with_external_fftw.patch) +* Make nab always use CUSTOMBUILDFLAGS so openmp flags get added when needed (was: Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch) +* Use FFTW_FFT/MKL_FFTW_FFT instead of PUBFFT for pmemd (was: Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch) +* Force using FFTW from external or mkl (was: Amber-16-AT-17-use_fftw_from_mkl_or_external.patch) +* Force the compiler used by nvcc to use the C++11 standard to avoid: error: identifier "__float128" is undefined (was: Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch) +* Allow use of all CUDA 9 versions (was: Amber-16-AT-17_allow_cuda9.patch) +* Make cpptraj use FFTW3 as defined by easyconfig (was: Amber-16-AT-17_cpptraj_use_mkl_fft.patch) +* Fix hardcoding of netcdf, mkl and compiler (was: Amber-16-AT-17_fix-hardcoding.patch) +* Fix incorrect use of fixed sized buffers (was: Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch) +* Fix FFTW3 link flags for rism (was: Amber-16-AT-17_fix_rism_fftw_lib.patch) +* Ignore checks for X11, use easybuild settings instead (was: Amber-16-AT-17_ignore_X11_checks.patch) +* Make cpptraj link with the BLAS/LAPACK/Zlib/Bzip2 from EasyBuild (was: Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch) +* Use FFTW_FFT with FFTW3 instead of PUBFFT for pmemd; this fixes linking with FFTW3 as opposed to using MKL (was: Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch) + +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 12:22:17.981248856 +0200 +@@ -3339,7 +3339,7 @@ + if [ -z "$zlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nozlib" ; fi + if [ -z "$bzlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nobzlib" ; fi + if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi +-if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi ++#if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi + if [ ! -z "$pnetcdf_dir" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS --with-pnetcdf=$pnetcdf_dir" ; fi + if [ -z "$sanderapi_lib" ] ; then + CPPTRAJOPTS="$CPPTRAJOPTS -nosanderlib" + +diff -ru amber16.orig/AmberTools/src/rism/rism3d_c.F90 amber16/AmberTools/src/rism/rism3d_c.F90 +--- amber16.orig/AmberTools/src/rism/rism3d_c.F90 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/rism/rism3d_c.F90 2017-10-10 15:39:22.259467974 +0200 +@@ -4061,7 +4061,7 @@ + numElectronsAtGridCenter = totalSolventElectrons - electronRDFSum + + ! #pragma omp parallel for schedule(dynamic, 10) shared (dx, conc, result, stepx, stepy, stepz, center_grid) +-!$omp parallel do private(local_equal), shared(this, UNITS, electronMap, numSmearGridPoints, numElectronsAtGridCenter) ++!$omp parallel do shared(this, electronMap, numSmearGridPoints, numElectronsAtGridCenter) + do igzCenter = 0, this%grid%globalDimsR(3) - 1 + rzCenter = igzCenter * this%grid%voxelVectorsR(3, :) + do igyCenter = 0, this%grid%globalDimsR(2) - 1 +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 10:34:26.841606227 +0200 +@@ -304,7 +304,8 @@ + | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` + else + cc_version=`$cc $1 2>&1 | grep -E "$cc |[vV]ersion " \ +- | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` ++ | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//' \ ++ | grep -v '^Intel(R)'` + fi + if [ -z "$cc_version" ] ; then + echo "Error: $cc is not well formed or produces unusual version details!" +@@ -354,7 +355,8 @@ + -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` + else + fc_version=`$fc $1 2>&1 | grep -E "$fc |$cc |[vV]ersion " | sed -e "s@$fc @@" \ +- -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` ++ -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//' \ ++ | grep -v '^Intel(R)'` + fi + if [ -z "$fc_version" ] ; then + echo "Error: $fc is not well formed or produces unusual version details!" +diff -ru amber16.orig/test/rism3d/checkrismunsupported.sh amber16/test/rism3d/checkrismunsupported.sh +--- amber16.orig/test/rism3d/checkrismunsupported.sh 2017-04-07 21:08:28.000000000 +0200 ++++ amber16/test/rism3d/checkrismunsupported.sh 2018-02-19 15:17:17.667872717 +0100 +@@ -14,7 +14,7 @@ + echo "$1 is not an executable or does not exist." + exit 1 + fi +-HAS_RISM=`$TESTsander -O -xvv foo 2> /dev/null | grep flag` ++HAS_RISM=`$DO_PARALLEL $TESTsander -O -xvv foo 2> /dev/null | grep flag` + /bin/rm -f foo mdout mdin + if [ -n "$HAS_RISM" ] ; then + echo "$TESTsander compiled without RISM support." +diff -ru amber16.orig/AmberTools/src/byacc/Makefile amber16/AmberTools/src/byacc/Makefile +--- amber16.orig/AmberTools/src/byacc/Makefile 2017-04-07 21:08:11.000000000 +0200 ++++ amber16/AmberTools/src/byacc/Makefile 2017-10-13 22:17:23.837195086 +0200 +@@ -31,7 +31,7 @@ + all: $(PROGRAM) + + $(PROGRAM): $(OBJS) $(LIBS) +- @$(CC) $(LDFLAGS) -o $(PROGRAM) $(OBJS) $(LIBS) ++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROGRAM) $(OBJS) $(LIBS) + + clean: + @rm -f $(OBJS) +diff -ru amber16.orig/AmberTools/src/ucpp-1.3/Makefile amber16/AmberTools/src/ucpp-1.3/Makefile +--- amber16.orig/AmberTools/src/ucpp-1.3/Makefile 2017-04-07 21:08:15.000000000 +0200 ++++ amber16/AmberTools/src/ucpp-1.3/Makefile 2017-10-13 21:54:44.418148511 +0200 +@@ -42,7 +42,7 @@ + rm -f *.o ucpp core + + ucpp$(SFX): $(COBJ) +- $(CC) $(LDFLAGS) -o ucpp$(SFX) $(COBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o ucpp$(SFX) $(COBJ) $(LIBS) + + assert.o: tune.h ucppi.h cpp.h nhash.h mem.h + cpp.o: tune.h ucppi.h cpp.h nhash.h mem.h +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 10:42:48.004066817 +0200 +@@ -2957,7 +2957,7 @@ + if [ -n "$MKL_HOME" ]; then + echo " MKL_HOME set to" "$MKL_HOME" + echo $(mkdir $amberprefix/include) +- echo $(cp $MKL_HOME/include/fftw/fftw3.f $amberprefix/include) ++ echo $(cp $MKL_HOME/mkl/include/fftw/fftw3.f $amberprefix/include) + fi + if [ "$intelmpi" = "yes" ]; then + pmemd_fpp_flags="$pmemd_fppflags -DFFTW_FFT -DMKL_FFTW_FFT " +diff -ru amber16.orig/AmberTools/src/sander/Makefile amber16/AmberTools/src/sander/Makefile +--- amber16.orig/AmberTools/src/sander/Makefile 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/sander/Makefile 2017-05-17 11:04:29.961465834 +0200 +@@ -317,7 +317,7 @@ + -lFpbsa ../lib/nxtsec.o $(EMILLIB) \ + $(SEBOMDLIB) \ + ../lib/sys.a $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -331,7 +331,7 @@ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + +@@ -345,7 +345,7 @@ + $(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o $(EMILLIB) ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(PUPILLIBS) $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + +@@ -358,7 +358,7 @@ + $(XRAY_OBJS) -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -370,7 +370,7 @@ + $(PARTPIMDOBJ) $(LSCIVROBJ) $(XRAY_OBJS) \ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) $(SEBOMDLIB) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -385,7 +385,7 @@ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +diff -ru amber16.orig/AmberTools/src/amberlite/Makefile amber16/AmberTools/src/amberlite/Makefile +--- amber16.orig/AmberTools/src/amberlite/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/amberlite/Makefile 2017-10-12 12:42:23.319122932 +0200 +@@ -16,13 +16,13 @@ + cd ../nab && $(MAKE) $@ + + $(BINDIR)/ffgbsa$(SFX): ffgbsa.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/ffgbsa$(SFX) ffgbsa.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/ffgbsa$(SFX) ffgbsa.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/minab$(SFX): minab.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/minab$(SFX) minab.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/minab$(SFX) minab.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/mdnab$(SFX): mdnab.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mdnab$(SFX) mdnab.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mdnab$(SFX) mdnab.nab $(CUSTOMBUILDFLAGS) + + clean: + /bin/rm -f *.c +diff -ru amber16.orig/AmberTools/src/etc/Makefile amber16/AmberTools/src/etc/Makefile +--- amber16.orig/AmberTools/src/etc/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/etc/Makefile 2017-10-11 14:49:01.168646077 +0200 +@@ -68,14 +68,14 @@ + $(CC) $(CFLAGS) $(AMBERCFLAGS) -o elsize$(SFX) elsize.o $(LM) + + molsurf$(SFX): molsurf.nab +- $(BINDIR)/nab$(SFX) -o molsurf$(SFX) molsurf.nab ++ $(BINDIR)/nab$(SFX) -o molsurf$(SFX) molsurf.nab $(CUSTOMBUILDFLAGS) + + resp$(SFX): lapack.o resp.o + $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + lapack.o resp.o -o resp$(SFX) + + tinker_to_amber$(SFX): tinker_to_amber.o cspline.o +- $(FC) -o tinker_to_amber$(SFX) tinker_to_amber.o cspline.o ++ $(FC) -o tinker_to_amber$(SFX) tinker_to_amber.o cspline.o $(CUSTOMBUILDFLAGS) + + new_crd_to_dyn$(SFX): new_crd_to_dyn.o nxtsec + $(FC) $(LDFLAGS) -o new_crd_to_dyn$(SFX) new_crd_to_dyn.o ../lib/nxtsec.o +diff -ru amber16.orig/AmberTools/src/mm_pbsa/Makefile amber16/AmberTools/src/mm_pbsa/Makefile +--- amber16.orig/AmberTools/src/mm_pbsa/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/mm_pbsa/Makefile 2017-10-12 10:08:57.265288431 +0200 +@@ -21,7 +21,7 @@ + + #Note dependency on nab from AMBERTools here. + $(BINDIR)/mm_pbsa_nabnmode$(SFX): mm_pbsa_nabnmode.nab +- $(BINDIR)/nab$(SFX) $(NABFLAGS) -o $(BINDIR)/mm_pbsa_nabnmode$(SFX) mm_pbsa_nabnmode.nab ++ $(BINDIR)/nab$(SFX) $(NABFLAGS) -o $(BINDIR)/mm_pbsa_nabnmode$(SFX) mm_pbsa_nabnmode.nab $(CUSTOMBUILDFLAGS) + + ../lib/amopen.o: ../lib/amopen.F + cd ../lib; $(MAKE) amopen.o +diff -ru amber16.orig/AmberTools/src/mmpbsa_py/Makefile amber16/AmberTools/src/mmpbsa_py/Makefile +--- amber16.orig/AmberTools/src/mmpbsa_py/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/mmpbsa_py/Makefile 2017-10-12 06:44:59.043135426 +0200 +@@ -9,10 +9,10 @@ + $(PYTHON) setup.py install -f $(PYTHON_INSTALL) --install-scripts=$(BINDIR) + + $(BINDIR)/mmpbsa_py_nabnmode$(SFX): mmpbsa_entropy.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_nabnmode$(SFX) mmpbsa_entropy.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_nabnmode$(SFX) mmpbsa_entropy.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/mmpbsa_py_energy$(SFX): mmpbsa_energy.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_energy$(SFX) mmpbsa_energy.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_energy$(SFX) mmpbsa_energy.nab $(CUSTOMBUILDFLAGS) + + serial: install + +diff -ru amber16.orig/AmberTools/src/nss/Makefile amber16/AmberTools/src/nss/Makefile +--- amber16.orig/AmberTools/src/nss/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/nss/Makefile 2017-10-11 08:24:51.121320716 +0200 +@@ -54,28 +54,28 @@ + -ranlib $(LIBDIR)/libnab.a + + matextract$(SFX): matextract.o +- $(NAB) -o matextract$(SFX) matextract.o ++ $(NAB) -o matextract$(SFX) matextract.o $(CUSTOMBUILDFLAGS) + + matgen$(SFX): matgen.o +- $(NAB) -o matgen$(SFX) matgen.o ++ $(NAB) -o matgen$(SFX) matgen.o $(CUSTOMBUILDFLAGS) + + matmerge$(SFX): matmerge.o +- $(NAB) -o matmerge$(SFX) matmerge.o ++ $(NAB) -o matmerge$(SFX) matmerge.o $(CUSTOMBUILDFLAGS) + + matmul$(SFX): matmul.o +- $(NAB) -o matmul$(SFX) matmul.o ++ $(NAB) -o matmul$(SFX) matmul.o $(CUSTOMBUILDFLAGS) + + transform$(SFX): transform.o +- $(NAB) -o transform$(SFX) transform.o ++ $(NAB) -o transform$(SFX) transform.o $(CUSTOMBUILDFLAGS) + + tss_init$(SFX): tss_init.o +- $(NAB) -o tss_init$(SFX) tss_init.o ++ $(NAB) -o tss_init$(SFX) tss_init.o $(CUSTOMBUILDFLAGS) + + tss_main$(SFX): tss_main.o +- $(NAB) -o tss_main$(SFX) tss_main.o ++ $(NAB) -o tss_main$(SFX) tss_main.o $(CUSTOMBUILDFLAGS) + + tss_next$(SFX): tss_next.o +- $(NAB) -o tss_next$(SFX) tss_next.o ++ $(NAB) -o tss_next$(SFX) tss_next.o $(CUSTOMBUILDFLAGS) + + clean: + /bin/rm -f \ +diff -ru amber16.orig/AmberTools/src/rism/Makefile amber16/AmberTools/src/rism/Makefile +--- amber16.orig/AmberTools/src/rism/Makefile 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/rism/Makefile 2017-10-11 20:00:32.189972509 +0200 +@@ -92,9 +92,9 @@ + # ------ Single-Point information ------------------------------------------ + SPSRC=rism3d.snglpnt.nab + rism3d.snglpnt$(SFX): $(SPSRC) +- $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) ++ $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) + rism3d.snglpnt.MPI$(SFX): $(SPSRC) +- $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) ++ $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) $(CUSTOMBUILDFLAGS) + # -------------------------------------------------------------------------- + + yes: install +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-10-14 19:07:22.137281514 +0200 +@@ -1384,9 +1384,9 @@ + # PMEMD Specifics + pmemd_fpp_flags='-DPUBFFT' + # following lines commented out, since pmemd is not GPL: +-# if [ "$has_fftw3" = 'yes' ]; then +-# pmemd_fpp_flags='-DFFTW_FFT' +-# fi ++ if [ "$has_fftw3" = 'yes' ]; then ++ pmemd_fpp_flags='-DFFTW_FFT' ++ fi + pmemd_foptflags="$foptflags" + if [ "$pmemd_openmp" = 'yes' ]; then + pmemd_foptflags= "$pmemd_foptflags -fopenmp -D_OPENMP_" +@@ -2958,8 +2958,6 @@ + echo " MKL_HOME set to" "$MKL_HOME" + echo $(mkdir $amberprefix/include) + echo $(cp $MKL_HOME/mkl/include/fftw/fftw3.f $amberprefix/include) +- fi +- if [ "$intelmpi" = "yes" ]; then + pmemd_fpp_flags="$pmemd_fppflags -DFFTW_FFT -DMKL_FFTW_FFT " + pmemd_coptflags="$pmemd_coptflags -DFFTW_FFT " # it would be best if we had a cflags var + fi +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 11:01:38.539389560 +0200 +@@ -2978,63 +2978,83 @@ + fi + + if [ "$has_fftw3" = 'yes' ]; then +- echo +- echo "Configuring fftw-3.3 (may be time-consuming)..." +- echo +- enable_mpi="" +- enable_debug="" +- enable_sse="--enable-sse=no --enable-sse2=no --enable-avx=no" +- mpicc="" +- if [ "$mpi" = "yes" ]; then +- enable_mpi="--enable-mpi=yes" +- fi +- if [ "$intelmpi" = "yes" ]; then +- mpicc="MPICC=mpiicc" +- fi +- if [ "$debug" = "yes" ]; then +- enable_debug="--enable-debug=yes --enable-debug-malloc=yes --enable-debug-alignment=yes" +- fi +- if [ "$sse" = "yes" ]; then +- enable_sse="--enable-sse2=yes" # --enable-avx=yes" +- fi +- if [ "$mic" = 'yes' ]; then +- echo " --configuring for mic (native mode)..." +- echo +- cd fftw-3.3 && \ +- ./configure --prefix=$amberprefix --libdir=$amberprefix/lib \ +- --enable-static --enable-shared --host=x86_64-k1om-linux \ +- --build=x86_64-unknown-linux \ +- $enable_mpi $mpicc $enable_debug \ +- CC="$cc -mmic" CFLAGS="$cflags $coptflags " \ +- F77="$fc -mmic" FFLAGS="$fflags $foptflags " \ +- FLIBS="$flibs_arch" \ +- > ../fftw3_config.log 2>&1 +- ncerror=$? +- else +- cd fftw-3.3 && \ +- ./configure --prefix=$amberprefix --libdir=$amberprefix/lib \ +- --enable-static --enable-shared \ +- $enable_mpi $mpicc $enable_debug $enable_sse\ +- CC="$cc" CFLAGS="$cflags $coptflags" \ +- F77="$fc" FFLAGS="$fflags $foptflags" \ +- FLIBS="$flibs_arch" \ +- > ../fftw3_config.log 2>&1 +- ncerror=$? +- fi +- if [ $ncerror -gt 0 ]; then +- echo "Error: FFTW configure returned $ncerror" +- echo " FFTW configure failed! Check the fftw3_config.log file" +- echo " in the $AMBERHOME/AmberTools/src directory." +- exit 1 ++ if [ -n "$EBROOTFFTW" ]; then ++ echo ++ echo "Using external FFTW3" ++ echo ++ flibs_fftw3="-lfftw3" ++ if [ "$mpi" = 'yes' ]; then ++ flibs_fftw3="-lfftw3_mpi $flibs_fftw3" ++ fi ++ flibs_fftw3="-L$FFT_LIB_DIR $flibs_fftw3" ++ fftw3="" ++ fppflags="$fppflags -I$FFT_INC_DIR" ++ elif [ -n "$MKL_HOME" ]; then ++ echo ++ echo "Using FFTW3 from MKL" ++ echo ++ flibs_fftw3="-lfftw3xf_intel $flibs_mkl" ++ fftw3="" ++ fppflags="$fppflags -I$FFT_INC_DIR" + else +- echo " fftw-3.3 configure succeeded." +- fi +- cd .. +- flibs_fftw3="-lfftw3" +- fftw3="\$(LIBDIR)/libfftw3.a" +- if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then +- flibs_fftw3="-lfftw3_mpi $flibs_fftw3" +- fftw3="\$(LIBDIR)/libfftw3_mpi.a \$(LIBDIR)/libfftw3.a" ++ echo ++ echo "Configuring fftw-3.3 (may be time-consuming)..." ++ echo ++ enable_mpi="" ++ enable_debug="" ++ enable_sse="--enable-sse=no --enable-sse2=no --enable-avx=no" ++ mpicc="" ++ if [ "$mpi" = "yes" ]; then ++ enable_mpi="--enable-mpi=yes" ++ fi ++ if [ "$intelmpi" = "yes" ]; then ++ mpicc="MPICC=mpiicc" ++ fi ++ if [ "$debug" = "yes" ]; then ++ enable_debug="--enable-debug=yes --enable-debug-malloc=yes --enable-debug-alignment=yes" ++ fi ++ if [ "$sse" = "yes" ]; then ++ enable_sse="--enable-sse2=yes" # --enable-avx=yes" ++ fi ++ if [ "$mic" = 'yes' ]; then ++ echo " --configuring for mic (native mode)..." ++ echo ++ cd fftw-3.3 && \ ++ ./configure --prefix=$amberprefix --libdir=$amberprefix/lib \ ++ --enable-static --enable-shared --host=x86_64-k1om-linux \ ++ --build=x86_64-unknown-linux \ ++ $enable_mpi $mpicc $enable_debug \ ++ CC="$cc -mmic" CFLAGS="$cflags $coptflags " \ ++ F77="$fc -mmic" FFLAGS="$fflags $foptflags " \ ++ FLIBS="$flibs_arch" \ ++ > ../fftw3_config.log 2>&1 ++ ncerror=$? ++ else ++ cd fftw-3.3 && \ ++ ./configure --prefix=$amberprefix --libdir=$amberprefix/lib \ ++ --enable-static --enable-shared \ ++ $enable_mpi $mpicc $enable_debug $enable_sse\ ++ CC="$cc" CFLAGS="$cflags $coptflags" \ ++ F77="$fc" FFLAGS="$fflags $foptflags" \ ++ FLIBS="$flibs_arch" \ ++ > ../fftw3_config.log 2>&1 ++ ncerror=$? ++ fi ++ if [ $ncerror -gt 0 ]; then ++ echo "Error: FFTW configure returned $ncerror" ++ echo " FFTW configure failed! Check the fftw3_config.log file" ++ echo " in the $AMBERHOME/AmberTools/src directory." ++ exit 1 ++ else ++ echo " fftw-3.3 configure succeeded." ++ fi ++ cd .. ++ flibs_fftw3="-lfftw3" ++ fftw3="\$(LIBDIR)/libfftw3.a" ++ if [ "$mpi" = 'yes' -a "$intelmpi" = 'no' ]; then ++ flibs_fftw3="-lfftw3_mpi $flibs_fftw3" ++ fftw3="\$(LIBDIR)/libfftw3_mpi.a \$(LIBDIR)/libfftw3.a" ++ fi + fi + elif [ "$mdgx" = 'yes' ]; then + echo +diff -ru amber16.orig/AmberTools/src/rism/Makefile amber16/AmberTools/src/rism/Makefile +--- amber16.orig/AmberTools/src/rism/Makefile 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/rism/Makefile 2017-05-17 10:56:15.935011987 +0200 +@@ -5,7 +5,7 @@ + export AMBERHOME=$(AMBER_PREFIX) + + # rism1d Fortran source files are free format +-LOCALFLAGS = $(FREEFORMAT_FLAG) ++LOCALFLAGS = $(FREEFORMAT_FLAG) -I$$FFT_INC_DIR + + # ------- rism1d information: ---------------------------------------------- + +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/configure2 2019-02-28 11:31:13.125415364 -0600 +@@ -1731,9 +1731,9 @@ + pmemd_cu_libs="./cuda/cuda.a -L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcurand -lcufft -lcudart $fc_cxx_link_flag" + pbsa_cu_libs="-L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcublas -lcusparse -lcudart -lcuda $fc_cxx_link_flag" + if [ "$optimise" = 'yes' ]; then +- nvcc="$nvcc -use_fast_math -O3 " ++ nvcc="$nvcc -use_fast_math -O3 -Xcompiler '-std=c++11'" + else +- nvcc="$nvcc -use_fast_math -O0 " ++ nvcc="$nvcc -use_fast_math -O0 -Xcompiler '-std=c++11'" + fi + + if [ "$mpi" = 'yes' ]; then +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-07-27 10:27:34.745642223 +0200 ++++ amber16/AmberTools/src/configure2 2018-07-27 10:30:05.442542975 +0200 +@@ -1203,7 +1203,8 @@ + #SM2.0 = All GF variants = C2050, 2075, M2090, GTX480, GTX580 etc. + sm20flags='-gencode arch=compute_20,code=sm_20' + cudaversion=`$nvcc --version | grep 'release' | cut -d' ' -f5 | cut -d',' -f1` +- if [ "$cudaversion" = "9.0" ]; then ++ cudamajversion=`echo $cudaversion | cut -d. -f1` ++ if [ $cudamajversion -ge 9 ]; then + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM3.0, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0" + nvccflags="$sm30flags $sm50flags $sm52flags $sm53flags $sm60flags $sm61flags $sm70flags -Wno-deprecated-declarations" +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-04-03 20:55:27.031610543 +0200 ++++ amber16/AmberTools/src/configure2 2018-04-03 20:55:19.359682056 +0200 +@@ -3338,7 +3358,7 @@ + if [ "$optimise" = 'no' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -noopt" ; fi + if [ -z "$zlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nozlib" ; fi + if [ -z "$bzlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nobzlib" ; fi +-if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi ++#if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi + #if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi + if [ ! -z "$pnetcdf_dir" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS --with-pnetcdf=$pnetcdf_dir" ; fi + if [ -z "$sanderapi_lib" ] ; then +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 09:05:08.644115630 +0200 +@@ -439,12 +439,12 @@ + write(6,*) 'testing a Fortran program' + end program testf + EOF +- $fc $fflags $netcdfinc -o testp$suffix testp.f90 $netcdfflagf > /dev/null 2> compile.err ++ $fc $fflags $netcdffinc -o testp$suffix testp.f90 $netcdfflagf > /dev/null 2> compile.err + if [ ! -e "testp$suffix" ] ; then + status=1 + if [ "$1" = "verbose" ] ; then + echo "Error: Could not compile with NetCDF Fortran interface." +- echo " $fc $fflags $netcdfinc -o testp$suffix testp.f90 $netcdfflagf" ++ echo " $fc $fflags $netcdffinc -o testp$suffix testp.f90 $netcdfflagf" + echo " Compile error follows:" + cat compile.err + echo "" +@@ -545,6 +545,7 @@ + mpi='no' + mtkpp='' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + pnetcdf_dir='' +@@ -630,6 +631,7 @@ + --skip-python) skippython='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + --with-pnetcdf) shift; pnetcdf_dir="$1" ;; + --python-install) shift; python_install="$1";; + -netcdfstatic) netcdfstatic='yes' ;; +@@ -900,7 +902,7 @@ + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build or when a static build is + # automatically set, eg, windows: +-staticflag='-static' ++staticflag='' + omp_flag= + mpi_flag= + fp_flags= +@@ -1418,7 +1420,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1737,7 +1739,7 @@ + fi + + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2069,7 +2071,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2206,7 +2208,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2279,17 +2281,17 @@ + blas=skip + flibs="-larpack " + flibsf="-larpack " +- mkll="$MKL_HOME/lib/32" ++ mkll="$MKL_HOME/mkl/lib/32" + mkl_processor="32" + mkl_procstring="ia32" + mklinterfacelayer='libmkl_intel.a' + if [ "$x86_64" = 'yes' ]; then +- if [ -d "$MKL_HOME/lib/em64t" ]; then +- mkll="$MKL_HOME/lib/em64t" ++ if [ -d "$MKL_HOME/mkl/lib/em64t" ]; then ++ mkll="$MKL_HOME/mkl/lib/em64t" + mkl_processor="em64t" + mkl_procstring="em64t" + else +- mkll="$MKL_HOME/lib/intel64" ++ mkll="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2715,11 +2717,17 @@ + else + # A NetCDF directory was specified. Check that library exists and compiles + printf "\tUsing external NetCDF in '$netcdf_dir'\n" ++ # Support separate NetCDF-Fortran installation with --with-netcdf-fort ++ if [ ! -e "$netcdf_fort_dir" ]; then ++ netcdf_fort_dir="$netcdf_dir" ++ fi ++ printf "\tUsing external NetCDF-Fortran in '$netcdf_fort_dir'\n" + netcdfinc="-I"$netcdf_dir"/include" ++ netcdffinc="-I"$netcdf_fort_dir"/include" + if [ "${netcdf_dir}" != '/usr' -a "$netcdf_dir" != '/usr/' ]; then + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" + fi +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ "$netcdfstatic" = 'no' ] ; then + if [ "${netcdf_dir}" != '/usr' -a "${netcdf_dir}" != '/usr/' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" +@@ -2735,7 +2743,7 @@ + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + echo "Error: '$netcdfflagf' not found." + exit 1 +@@ -2755,6 +2763,7 @@ + netcdfflagf='' + netcdfflagc='' + netcdfinc='' ++ netcdffinc='' + fi + + #------------------------------------------------------------------------------ +@@ -3726,7 +3735,7 @@ + NETCDF=$netcdf + NETCDFLIB=$netcdfflagc + NETCDFLIBF=$netcdfflagf +-NETCDFINC=$netcdfinc ++NETCDFINC=$netcdfinc $netcdffinc + PNETCDFLIB=$pnetcdflib + PNETCDFINC=$pnetcdfinc + PNETCDFDEF=$pnetcdfdef +diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c +--- amber16.orig/AmberTools/src/nab/nab.c 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/nab/nab.c 2019-02-28 19:12:13.618946740 -0600 +@@ -22,7 +22,7 @@ + + static void n2c( int, int, char *, int, int, int, char *[], char [], char * ); + static void cc( int, int, int, int, char [], int, char *[], char [] ); +-static int split( char [], char *[], char * ); ++static int split( char [], char ***, char * ); + static int execute( char **, int, int, int ); + + int main( int argc, char *argv[] ) +@@ -128,8 +128,8 @@ + char cpp_ofname[ 256 ]; + + char cmd[ 1024 ]; +- char *fields[ 256 ]; +- int nfields; ++ char **fields; ++ int nfields, i; + int cpp_ofd, n2c_ofd; + int status; + char *amberhome; +@@ -169,7 +169,7 @@ + amberhome, cppstring, amberhome, + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + #ifndef USE_MKSTEMP + if( (cpp_ofd = +@@ -205,7 +205,7 @@ + nodebug ? "-nodebug" : "", + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "nab2c cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + status = execute( fields, cpp_ofd, n2c_ofd, 2 ); + unlink( cpp_ofname ); +@@ -213,6 +213,10 @@ + unlink( n2c_ofname ); + fprintf( stderr, "nab2c failed!\n" ); exit(1); + } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); + } + } + unlink( n2c_ofname ); +@@ -233,20 +237,28 @@ + { + int ac; + char *dotp, *amberhome; +- char cmd[ 1024 ], word[ 1024 ]; +- char *fields[256]; ++#define WORDSZ 1024 ++ char *cmd, word[ WORDSZ ]; ++ char **fields; ++ int cmd_sz; + int status; +- int nfields; ++ int nfields, i; + + amberhome = (char *) getenv("AMBERHOME"); + if( amberhome == NULL ){ + fprintf( stderr, "AMBERHOME is not set!\n" ); + exit(1); + } ++ cmd_sz = WORDSZ; ++ cmd = malloc(cmd_sz); + sprintf( cmd, "%s -I%s/include", CC, amberhome ); + if( aopt ){ + #ifdef AVSDIR + sprintf( word, " -I%s/include", AVSDIR ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + #else + fprintf( stderr, "-avs not supported.\n" ); +@@ -257,9 +269,17 @@ + dotp = strrchr( argv[ ac ], '.' ); + strcpy( &dotp[ 1 ], "c" ); + sprintf( word, " %s", argv[ ac ] ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + }else if( argv[ ac ] ){ + sprintf( word, " %s", argv[ ac ] ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + } + } +@@ -268,71 +288,100 @@ + if( aopt ){ + sprintf( word, " -L%s/lib -lflow_c -lgeom -lutil", + AVSDIR ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + } + #endif + sprintf( word, " -L%s/lib -lnab -lcifparse", amberhome ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); +- sprintf( word, " %s ", FLIBS ); +- strcat( cmd, word ); ++ /* FLIBS can be very big and there is no need to copy it into word first. */ ++ /* Make sure there is space enough for the " -lm" too */ ++ if (strlen(cmd) + strlen(FLIBS) + 6 > cmd_sz) { ++ cmd_sz += strlen(FLIBS) + 6; ++ cmd = realloc(cmd, cmd_sz); ++ } ++ strcat( cmd, " " ); ++ strcat( cmd, FLIBS ); + strcat( cmd, " -lm" ); + } + if( cgdopt ) fprintf( stderr, "cc cmd: %s\n", cmd ); +- nfields = split(cmd,fields," "); ++ nfields = split(cmd, &fields, " "); + status = execute(fields, 0, 1, 2); + if (status != 0) { + fprintf(stderr,"cc failed!\n"); exit (1); + } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); ++ free(cmd); + } + +-static int split( char str[], char *fields[], char *fsep ) ++static int split( char str[], char ***fields, char *fsep ) + { +- int nf, flen; ++ int nf, flen, maxnf; + char *sp, *fp, *efp, *nfp; + + if( !str ) + return( 0 ); + ++ maxnf = 10; ++ *fields = (char **) malloc(sizeof(char *) * maxnf); + /* Use fsep of white space is special */ + if( strspn( fsep, " \t\n" ) ){ + for( nf = 0, sp = str; ; ){ + fp = sp + strspn( sp, fsep ); + if( !*fp ) + return( nf ); ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (efp = strpbrk( fp, fsep )) ){ + if( !( flen = efp - fp ) ) + return( nf ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, fp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; ++ (*fields)[ nf ] = nfp; + sp = efp; +- fields[++nf] = NULL; ++ (*fields)[++nf] = NULL; + }else{ + flen = strlen( fp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, fp ); +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + return( nf ); + } + } + }else{ + for( nf = 0, sp = str; ; ){ ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (fp = strchr( sp, *fsep )) ){ + flen = fp - sp; + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, sp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + sp = fp + 1; + }else{ + flen = strlen( sp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, sp ); +- fields[ nf ] = nfp; +- fields[++nf] = NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf] = NULL; + return( nf ); + } + } +diff -ru amber16.orig/AmberTools/src/rism/Makefile amber16/AmberTools/src/rism/Makefile +--- amber16.orig/AmberTools/src/rism/Makefile 2018-04-03 21:52:52.811347758 +0200 ++++ amber16/AmberTools/src/rism/Makefile 2018-04-03 21:51:47.999962945 +0200 +@@ -92,7 +92,7 @@ + # ------ Single-Point information ------------------------------------------ + SPSRC=rism3d.snglpnt.nab + rism3d.snglpnt$(SFX): $(SPSRC) +- $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) ++ $(BINDIR)/nab $(SPSRC) $(FLIBS_FFTW3) -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) + rism3d.snglpnt.MPI$(SFX): $(SPSRC) + $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) $(CUSTOMBUILDFLAGS) + # -------------------------------------------------------------------------- +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-04-03 20:55:27.031610543 +0200 ++++ amber16/AmberTools/src/configure2 2018-04-03 21:38:41.383450159 +0200 +@@ -920,83 +920,6 @@ + if [ "$noX11" = "true" ]; then + make_xleap="skip_xleap" + xhome='' +-else +- if [ -d /usr/X11R6/lib ]; then +- xhome='/usr/X11R6' +- elif [ -d /usr/X11/lib ]; then # location for MacOSX 10.11 +- xhome='/usr/X11' +- elif [ -d /usr/lib/x86_64-linux-gnu ]; then +- xhome='/usr' +- elif [ -f /usr/lib/i386-linux-gnu/libX11.a ]; then +- xhome='/usr' +- elif [ -f /usr/lib/libX11.a -o -f /usr/lib/libX11.so \ +- -o -f /usr/lib/libX11.dll.a \ +- -o -f /usr/lib64/libX11.a -o -f /usr/lib64/libX11.so ]; then +- xhome='/usr' +- elif [ -f /opt/local/lib/libX11.a -o -f /opt/local/lib/libX11.dylib ]; then +- xhome='/opt/local' +- else +- echo "Could not find the X11 libraries; you may need to edit config.h" +- echo " to set the XHOME and XLIBS variables." +- fi +- +- if [ "$xhome" != "/usr" ]; then +- # Do not add -L/usr/lib to linker. This is always in the standard path +- # and could cause issues trying to build MPI when /usr has an MPI +- # installed that you *don't* want to use. +- xlibs="-L$xhome/lib" +- if [ "$x86_64" = 'yes' ]; then +- xlibs="-L$xhome/lib64 $xlibs" +- fi +- fi +- if [ -d /usr/lib/x86_64-linux-gnu ]; then +- xlibs="-L/usr/lib/x86_64-linux-gnu $xlibs" +- fi +-fi +-#-------------------------------------------------------------------------- +-# Check if the X11 library files for XLEaP are present: +-#-------------------------------------------------------------------------- +-if [ "$noX11" = "false" ]; then +- if [ -r "$xhome/lib/libXt.a" -o -r "$xhome/lib/libXt.dll.a" \ +- -o -r "$xhome/lib/libXt.dylib" \ +- -o -r /usr/lib/x86_64-linux-gnu/libXt.a \ +- -o -r /usr/lib/x86_64-linux-gnu/libXt.so \ +- -o -r /usr/lib/i386-linux-gnu/libXt.a \ +- -o -r /usr/lib/i386-linux-gnu/libXt.so \ +- -o -r /usr/lib/libXt.so \ +- -o -r /usr/lib64/libXt.so \ +- -o -r /usr/X11/lib/libXt.dylib \ +- -o "$x86_64" = 'yes' -a -r "$xhome/lib64/libXt.a" ] +- then +- empty_statement= +- else +- echo "Error: The X11 libraries are not in the usual location !" +- echo " To search for them try the command: locate libXt" +- echo " On new Fedora OS's install the libXt-devel libXext-devel" +- echo " libX11-devel libICE-devel libSM-devel packages." +- echo " On old Fedora OS's install the xorg-x11-devel package." +- echo " On RedHat OS's install the XFree86-devel package." +- echo " On Ubuntu OS's install the xorg-dev and xserver-xorg packages." +- echo +- echo " ...more info for various linuxes at ambermd.org/ubuntu.html" +- echo +- echo " To build Amber without XLEaP, re-run configure with '-noX11:" +- echo " `mod_command_args '' '-noX11'`" +- exit 1 +- fi +- +- if [ -d /usr/include/X11/extensions -o $is_mac = "yes" ] +- then +- empty_statement= +- elif [ "$is_mac" = "no" ]; then +- echo "Error: The X11 extensions headers are not in the usual location!" +- echo " To search for them try the command: locate X11/extensions" +- echo " On new Fedora OSes install libXext-devel" +- echo " On RedHat OSes install libXext-devel" +- echo " To build Amber without XLEaP, re-run configure with '-noX11:" +- echo " `mod_command_args '' '-noX11'`" +- exit 1 +- fi + fi + + #------------------------------------------------------------------------------ +diff -ru amber16.orig/AmberTools/src/cpptraj/configure amber16/AmberTools/src/cpptraj/configure +--- amber16.orig/AmberTools/src/cpptraj/configure 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/cpptraj/configure 2018-12-16 09:13:28.413318032 +0100 +@@ -523,10 +523,10 @@ + XDRFILE=$XDRFILE_TARGET + NETCDFLIB="-lnetcdf" + PNETCDFLIB="" +-BZLIB="-lbz2" +-ZLIB="-lz" +-BLAS="-lblas" +-LAPACK="-llapack" ++BZLIB="-L$EBROOTBZIP2/lib -lbz2" ++ZLIB="-L$EBROOTZLIB/lib -lz" ++BLAS="$LIBBLAS" ++LAPACK="$LIBLAPACK" + ARPACK="-larpack" + FFT_LIB="pub_fft.o" + FFT_LIBDIR="" +@@ -960,13 +960,13 @@ + if [[ $STATIC -eq 2 ]] ; then + # Static linking for specified libraries + if [[ ! -z $BLAS_HOME && ! -z $BLAS ]] ; then +- BLAS="$BLAS_HOME/lib/libblas.a" ++ BLAS="$LIBBLAS" + fi + if [[ ! -z $ARPACK_HOME && ! -z $ARPACK ]] ; then + ARPACK="$ARPACK_HOME/lib/libarpack.a" + fi + if [[ ! -z $LAPACK_HOME && ! -z $LAPACK ]] ; then +- LAPACK="$LAPACK_HOME/lib/liblapack.a" ++ LAPACK="$LIBLAPACK" + fi + if [[ ! -z $NETCDF_HOME && ! -z $NETCDFLIB ]] ; then + NETCDFLIB="$NETCDF_HOME/lib/libnetcdf.a" +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2018-10-06 19:30:27.186868451 +0200 +@@ -3765,7 +3765,7 @@ + PMEMD_FOPTFLAGS=$pmemd_foptflags \$(AMBERBUILDFLAGS) + PMEMD_CC=$cc + PMEMD_COPTFLAGS=$pmemd_coptflags $mpi_flag \$(AMBERBUILDFLAGS) +-PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib ++PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib $flibs_fftw3 + PMEMD_LD=$ld \$(AMBERBUILDFLAGS) + LDOUT=$ldout + PMEMD_GNU_BUG303=$pmemd_gnu_bug303 From 9dcc397f3fddf734632a10dcddf383265ae4da3d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 11:36:59 +0200 Subject: [PATCH 534/698] use https in homepage of BCFtools --- easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb index b4d197f457d..18a01673e00 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.3.1-foss-2016b.eb @@ -8,7 +8,7 @@ easyblock = 'MakeCp' name = 'BCFtools' version = '1.3.1' -homepage = 'http://www.htslib.org/' +homepage = 'https://www.htslib.org/' description = """BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF""" From f58e0821c3a4d40937a81acb8d5705b57de86f9b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 11:45:49 +0200 Subject: [PATCH 535/698] add missing versionsuffix for AmberTools 17 --- ...7-foss-2018a.eb => AmberTools-17-foss-2018a-Python-2.7.14.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/a/AmberTools/{AmberTools-17-foss-2018a.eb => AmberTools-17-foss-2018a-Python-2.7.14.eb} (97%) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb similarity index 97% rename from easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb rename to easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb index 611c41647de..53e5d650e74 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb @@ -2,6 +2,7 @@ easyblock = 'EB_Amber' name = 'AmberTools' version = '17' +versionsuffix = '-Python-%(pyver)s' homepage = 'http://ambermd.org/' description = """AmberTools consists of several independently developed packages that work well by themselves, From 11ca15bcb4d39f6f1111a48f1a3f4fb6dc576fc0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 11:48:12 +0200 Subject: [PATCH 536/698] Genome_Profiler: Fix incorrect regex in cmds_map Also use fix_perl_shebang command instead of sed --- .../Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb index 0591e40261b..0c643e8802e 100644 --- a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -26,7 +26,7 @@ dependencies = [ # skip uncompress because this is plain .pl file skipsteps = ['source'] -cmds_map = [("GeP*.pl", "cp %(source)s GeP.pl")] +cmds_map = [("GeP.*\.pl", "cp %(source)s GeP.pl")] files_to_copy = [(['GeP.pl'], 'bin')] @@ -35,8 +35,9 @@ sanity_check_paths = { 'dirs': [], } +fix_perl_shebang_for = ['bin/GeP.pl'] + postinstallcmds = [ - "sed -i -e 's|/usr/bin/perl|/usr/bin/env\ perl|' %(installdir)s/bin/GeP.pl", # fix shebang line "chmod +x %(installdir)s/bin/GeP.pl", ] From 85351d7986a6b628b25e7c4759a816b18b5ea112 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 12:18:34 +0200 Subject: [PATCH 537/698] Remove \\n\\r from modloadmsg --- .../Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb index 0c643e8802e..fd97fa26520 100644 --- a/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb +++ b/easybuild/easyconfigs/g/Genome_Profiler/Genome_Profiler-2.1-foss-2016b-Perl-5.24.0.eb @@ -41,6 +41,6 @@ postinstallcmds = [ "chmod +x %(installdir)s/bin/GeP.pl", ] -modloadmsg = "To launch execute script GeP.pl\n\r" +modloadmsg = "To launch execute script GeP.pl" moduleclass = 'bio' From 334da3d327b81400c44dd280775a00df666d6d11 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 12:19:38 +0200 Subject: [PATCH 538/698] remove easyconfig for cuDNN 5.1.5, installation files are not longer available --- .../c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb deleted file mode 100644 index f3b966f8e73..00000000000 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-5.1.5-CUDA-8.0.44.eb +++ /dev/null @@ -1,46 +0,0 @@ -## -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# -# Author: Stephane Thiell -## -easyblock = 'Tarball' - -name = 'cuDNN' -version = '5.1.5' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA -cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) -versionsuffix = '-CUDA-%s' % cuda_version - -homepage = 'https://developer.nvidia.com/cudnn' - -description = """ - The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated - library of primitives for deep neural networks. -""" - -toolchain = {'name': 'dummy', 'version': ''} - -# Nvidia developer registration required. -# Download link: https://developer.nvidia.com/rdp/cudnn-download -# Download as cudnn-8.0-linux-x64-v5.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz -# Note, NVIDIA may release another cudnn-8.0-linux-x64-v5.tgz with different %(version)s libraries -# so use the checksum to verify and modify as needed. -sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] -checksums = ['a87cb2df2e5e7cc0a05e266734e679ee1a2fadad6f06af82a76ed81a23b102c8'] - -dependencies = [('CUDA', cuda_version)] - -postinstallcmds = [ - # toss duplicates and create symlinks instead - 'cd %%(installdir)s/lib64 && rm -vf libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version[0:1], SHLIB_EXT), - 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s' % (SHLIB_EXT, version, SHLIB_EXT), - 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:1]), - 'cd %%(installdir)s/lib64 && ln -vs libcudnn.%s.%s libcudnn.%s.%s' % (SHLIB_EXT, version, SHLIB_EXT, version[0:3]), -] - -sanity_check_paths = { - 'files': ['include/cudnn.h', 'lib64/libcudnn_static.a', 'lib64/libcudnn.%s.%%(version)s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'numlib' From 53db122ab4a7fe7d9f0b0ba49b8535333df49375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 12:23:49 +0200 Subject: [PATCH 539/698] fix names of local variables in old cuDNN easyconfigs --- .../easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb | 10 +++++----- .../easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb | 10 +++++----- .../easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb | 10 +++++----- .../easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb | 10 +++++----- 4 files changed, 20 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb index c2a3f5a7a18..1b8c2a567f2 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb @@ -7,9 +7,9 @@ easyblock = 'Tarball' name = 'cuDNN' version = '6.0.21' # the version of the libcudnn.so provided -cuda_version = '7.5.18' # the latest matching CUDA -cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) -versionsuffix = '-CUDA-%s' % cuda_version +local_cuda_version = '7.5.18' # the latest matching CUDA +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' @@ -25,10 +25,10 @@ toolchain = {'name': 'dummy', 'version': ''} # Download as cudnn-7.5-linux-x64-v6.tgz, rename to cudnn-7.5-linux-x64-v%(version)s.tgz # Note, NVIDIA may release another cudnn-7.5-linux-x64-v6.tgz with different %(version)s libraries # so use the checksum to verify and modify as needed. -sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['568d4b070c5f91ab8a15b287b73dd072b99c7267a43edad13f70337cd186c82c'] -dependencies = [('CUDA', cuda_version)] +dependencies = [('CUDA', local_cuda_version)] postinstallcmds = [ # toss duplicates and create symlinks instead diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb index c9b5c1049ae..837a5fb73c5 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb @@ -7,9 +7,9 @@ easyblock = 'Tarball' name = 'cuDNN' version = '6.0.21' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA -cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) -versionsuffix = '-CUDA-%s' % cuda_version +local_cuda_version = '8.0.44' # the latest matching CUDA +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' @@ -25,10 +25,10 @@ toolchain = {'name': 'dummy', 'version': ''} # Download as cudnn-8.0-linux-x64-v6.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz # Note, NVIDIA may release another cudnn-8.0-linux-x64-v6.tgz with different %(version)s libraries # so use the checksum to verify and modify as needed. -sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c'] -dependencies = [('CUDA', cuda_version)] +dependencies = [('CUDA', local_cuda_version)] postinstallcmds = [ # toss duplicates and create symlinks instead diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb index d56e0073310..db30cada562 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb @@ -7,9 +7,9 @@ easyblock = 'Tarball' name = 'cuDNN' version = '7.0.5' # the version of the libcudnn.so provided -cuda_version = '8.0.44' # the latest matching CUDA -cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) -versionsuffix = '-CUDA-%s' % cuda_version +local_cuda_version = '8.0.44' # the latest matching CUDA +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' @@ -25,10 +25,10 @@ toolchain = {'name': 'dummy', 'version': ''} # Download as cudnn-8.0-linux-x64-v7.tgz, rename to cudnn-8.0-linux-x64-v%(version)s.tgz # Note, NVIDIA may release another cudnn-8.0-linux-x64-v7.tgz with different %(version)s libraries # so use the checksum to verify and modify as needed. -sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['9e0b31735918fe33a79c4b3e612143d33f48f61c095a3b993023cdab46f6d66e'] -dependencies = [('CUDA', cuda_version)] +dependencies = [('CUDA', local_cuda_version)] postinstallcmds = [ # toss duplicates and create symlinks instead diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb index 7bb5e9b2f45..b774d51eb2d 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb @@ -7,9 +7,9 @@ easyblock = 'Tarball' name = 'cuDNN' version = '7.0.5' # the version of the libcudnn.so provided -cuda_version = '9.0.176' # the latest matching CUDA -cuda_version_major_minor = '.'.join(cuda_version.split('.')[:2]) -versionsuffix = '-CUDA-%s' % cuda_version +local_cuda_version = '9.0.176' # the latest matching CUDA +local_cuda_version_major_minor = '.'.join(local_cuda_version.split('.')[:2]) +versionsuffix = '-CUDA-%s' % local_cuda_version homepage = 'https://developer.nvidia.com/cudnn' @@ -25,10 +25,10 @@ toolchain = {'name': 'dummy', 'version': ''} # Download as cudnn-9.0-linux-x64-v7.tgz, rename to cudnn-9.0-linux-x64-v%(version)s.tgz # Note, NVIDIA may release another cudnn-9.0-linux-x64-v7.tgz with different %(version)s libraries # so use the checksum to verify and modify as needed. -sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % cuda_version_major_minor] +sources = ['%%(namelower)s-%s-linux-x64-v%%(version)s.tgz' % local_cuda_version_major_minor] checksums = ['1a3e076447d5b9860c73d9bebe7087ffcb7b0c8814fd1e506096435a2ad9ab0e'] -dependencies = [('CUDA', cuda_version)] +dependencies = [('CUDA', local_cuda_version)] postinstallcmds = [ # toss duplicates and create symlinks instead From cd664cb234390b57f8c10516f478044cf21dacde Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 12:24:58 +0200 Subject: [PATCH 540/698] use https in homepage of AmberTools 17 --- .../a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb index 53e5d650e74..94c29a7a8db 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb @@ -4,7 +4,7 @@ name = 'AmberTools' version = '17' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://ambermd.org/' +homepage = 'https://ambermd.org/' description = """AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.""" From d660fd982947beb1e7a5c16c29afe1993b2fcc6a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 12:40:37 +0200 Subject: [PATCH 541/698] use SYSTEM toolchain in old cuDNN easyconfigs --- easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb | 2 +- easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb | 2 +- easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb | 2 +- easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb index 1b8c2a567f2..bcb702f1bdb 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-7.5.18.eb @@ -18,7 +18,7 @@ description = """ library of primitives for deep neural networks. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb index 837a5fb73c5..a2f3a425b88 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-6.0.21-CUDA-8.0.44.eb @@ -18,7 +18,7 @@ description = """ library of primitives for deep neural networks. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb index db30cada562..bfbc66a3dec 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-8.0.44.eb @@ -18,7 +18,7 @@ description = """ library of primitives for deep neural networks. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb index b774d51eb2d..f012a48b217 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-7.0.5-CUDA-9.0.176.eb @@ -18,7 +18,7 @@ description = """ library of primitives for deep neural networks. """ -toolchain = {'name': 'dummy', 'version': ''} +toolchain = SYSTEM # Nvidia developer registration required. # Download link: https://developer.nvidia.com/rdp/cudnn-download From 5e9e1d410d01719f7f608d05b72cf63231867d6b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 12:41:49 +0200 Subject: [PATCH 542/698] Add local_ prefix to pythonpath and add checksums. --- .../pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb index f0082c99d44..7fb26d9dbad 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb @@ -14,11 +14,15 @@ toolchain = {'name': 'intel', 'version': '2017a'} source_urls = ['http://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] - patches = [ 'pbs_python-%(version)s_CC.patch', 'pbs_python-%(version)s_remove-printf.patch', ] +checksums = [ + '2f7e1416b801cc6498395aa824772fd6092572ad98eec74550ddc222ae4b30f7', # pbs_python-4.6.0.tar.gz + '3d4e0b2aa6f69a80ea2e84f8dd42e101f0cea48d880187f5c1734f0da0abccc0', # pbs_python-4.6.0_CC.patch + 'e2f368d28763a0ffa1a59ffa76ce70d93535e7aa82daa3281c284e1d235f2352', # pbs_python-4.6.0_remove-printf.patch +] dependencies = [('Python', '2.7.13')] @@ -29,12 +33,12 @@ configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' preinstallopts = prebuildopts -pythonpath = 'lib/python%(pyshortver)s/site-packages' -modextrapaths = {'PYTHONPATH': pythonpath} +local_pythonpath = 'lib/python%(pyshortver)s/site-packages' +modextrapaths = {'PYTHONPATH': local_pythonpath} sanity_check_paths = { 'files': [], - 'dirs': ["%s/pbs" % pythonpath] + 'dirs': ["%s/pbs" % local_pythonpath] } moduleclass = 'tools' From ee8fb2cf1ceddf9db0f3916ea9f06690a47af9da Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Oct 2020 13:02:59 +0200 Subject: [PATCH 543/698] source tarballs were fixed upstream --- .../n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb index e779b65b09d..ccc2fde1811 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -9,11 +9,9 @@ description = """NAMD is a parallel molecular dynamics code designed for high-pe toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} -sources = [{ - 'filename': 'NAMD_%(version)s_Source.tar.gz', - 'extract_cmd': "tar xfv %s", # source file is actually not gzipped -}] -checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/832164/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a'] dependencies = [ ('Tcl', '8.6.5'), From 861729b06c1dd63d5cb4c0868ea0945fd58c2251 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:04:08 +0200 Subject: [PATCH 544/698] Remove outdated comment and add sanity_check_paths --- easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb index a948fdf2cd0..2e6ca21d868 100644 --- a/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libav/libav-11.10-GCCcore-6.4.0.eb @@ -16,7 +16,6 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -# https://libav.org/releases/libav-11.9.tar.gz source_urls = ['https://libav.org/releases/'] sources = [SOURCELOWER_TAR_XZ] checksums = ['5437d8861c3c34f0d258105a370ee61e4e2cc72898b1f577c50304d24d79f4e0'] @@ -30,4 +29,9 @@ dependencies = [ ('zlib', '1.2.11'), ] +sanity_check_paths = { + 'files': ['bin/avconv', 'bin/avprobe', 'lib/libavcodec.a'], + 'dirs': ['lib/pkgconfig'], +} + moduleclass = 'vis' From b2afb0f3ea942bc3dc27208ae8f3400400a7b7e3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:15:50 +0200 Subject: [PATCH 545/698] SDL, SDL_image: Fix style according to comments from Kenneth. --- .../easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb | 13 ++++--------- .../s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb | 8 ++------ 2 files changed, 6 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb index df61b21a554..84b116673e9 100644 --- a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb @@ -6,18 +6,14 @@ name = 'SDL' version = '1.2.15' homepage = 'http://www.libsdl.org/' - -description = """ - SDL: Simple DirectMedia Layer, a cross-platform multimedia library -""" +description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -# http://www.libsdl.org/release/SDL-1.2.15.tar.gz source_urls = ['http://www.libsdl.org/release/'] sources = [SOURCE_TAR_GZ] -patches = ['SDL-1.2.15-91ad7b43317a.patch'] # from: https://bugzilla.libsdl.org/show_bug.cgi?id=1769 +patches = ['SDL-%(version)s-91ad7b43317a.patch'] checksums = [ 'd6d316a793e5e348155f0dd93b979798933fb98aa1edebcc108829d6474aad00', # SDL-1.2.15.tar.gz '48e6afdad171e896e81d7d7aa610a54f0f51175423c5093efe083c70b5219151', # SDL-1.2.15-91ad7b43317a.patch @@ -32,8 +28,8 @@ dependencies = [ ('X11', '20180131'), ] -preconfigopts = """ - ./autogen.sh # else we get error: conflicting types for ‘_XData32’... even with patch above +# else we get error: conflicting types for ‘_XData32’... even with patch above +preconfigopts = "./autogen.sh && " """ sanity_check_paths = { @@ -42,4 +38,3 @@ sanity_check_paths = { } moduleclass = 'lib' -# EOF diff --git a/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb index b206c5194f8..34ffbe913d6 100644 --- a/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL_image/SDL_image-1.2.12-GCCcore-6.4.0.eb @@ -6,14 +6,10 @@ name = 'SDL_image' version = '1.2.12' homepage = 'https://www.libsdl.org/projects/SDL_image/release-1.2.html' - -description = """ - SDL_image is an image file loading library. -""" +description = "SDL_image is an image file loading library." toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# https://www.libsdl.org/projects/SDL_image/release/SDL_image-1.2.12.tar.gz source_urls = ['https://www.libsdl.org/projects/%(name)s/release'] sources = [SOURCE_TAR_GZ] checksums = ['0b90722984561004de84847744d566809dbb9daf732a9e503b91a1b5a84e5699'] @@ -30,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/SDL/SDL_image.h', 'lib/libSDL_image.so', + 'files': ['include/SDL/SDL_image.h', 'lib/libSDL_image.%s' % SHLIB_EXT, 'lib/pkgconfig/SDL_image.pc'], 'dirs': [] } From 8032d60e79709b034af8f5250199bde3cb16b580 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:18:01 +0200 Subject: [PATCH 546/698] SDL: use https --- easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb index 84b116673e9..b49318d23bb 100644 --- a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb @@ -5,13 +5,13 @@ easyblock = 'ConfigureMake' name = 'SDL' version = '1.2.15' -homepage = 'http://www.libsdl.org/' +homepage = 'https://www.libsdl.org/' description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['http://www.libsdl.org/release/'] +source_urls = ['https://www.libsdl.org/release/'] sources = [SOURCE_TAR_GZ] patches = ['SDL-%(version)s-91ad7b43317a.patch'] checksums = [ From dbe56a8fa9c0b413ab5207d9cf4752471d087037 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:19:30 +0200 Subject: [PATCH 547/698] SDL: Remove forgotten """ --- easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb index b49318d23bb..4cf34e04661 100644 --- a/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL/SDL-1.2.15-GCCcore-6.4.0.eb @@ -30,7 +30,6 @@ dependencies = [ # else we get error: conflicting types for ‘_XData32’... even with patch above preconfigopts = "./autogen.sh && " -""" sanity_check_paths = { 'dirs': ['bin', 'include/SDL', 'lib/pkgconfig', 'share/man/man3'], From 1900643deb0510728a8eec1ead28e5fc4238f302 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Oct 2020 13:25:22 +0200 Subject: [PATCH 548/698] fix homepage URL of NAMD-2.12-foss-2016b-CUDA-8.0.61.eb --- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb index ccc2fde1811..9cf921ff8e5 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2016b-CUDA-8.0.61.eb @@ -2,7 +2,7 @@ name = 'NAMD' version = '2.12' versionsuffix = '-CUDA-8.0.61' -homepage = 'http://www.ks.uiuc.edu/Research/namd/' +homepage = 'https://www.ks.uiuc.edu/Research/namd/' description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" From 8a8fcd131d8ebd11cb50fd453c1c84df7079075b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:26:06 +0200 Subject: [PATCH 549/698] Use https for source_urls --- .../p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb index 7fb26d9dbad..d7216695265 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb @@ -12,7 +12,7 @@ description = """The pbs_python package is a wrapper class for the Torque C libr toolchain = {'name': 'intel', 'version': '2017a'} -source_urls = ['http://ftp.sara.nl/pub/outgoing/'] +source_urls = ['https://ftp.sara.nl/pub/outgoing/'] sources = [SOURCE_TAR_GZ] patches = [ 'pbs_python-%(version)s_CC.patch', From c4dc21dc9b3e0d6470747c7a573844d490659c05 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:30:58 +0200 Subject: [PATCH 550/698] SDL2,SDL2_image: Fix style according to comments from Kenneth. And use https for homepage and source_urls --- easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb | 6 ++---- .../s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb | 8 ++------ 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb index f48f27a6cff..3c34499d253 100644 --- a/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL2/SDL2-2.0.8-GCCcore-6.4.0.eb @@ -15,14 +15,12 @@ easyblock = 'ConfigureMake' name = 'SDL2' version = '2.0.8' -homepage = 'http://www.libsdl.org/' - +homepage = 'https://www.libsdl.org/' description = "SDL: Simple DirectMedia Layer, a cross-platform multimedia library" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# http://www.libsdl.org/release/SDL2-2.0.8.tar.gz -source_urls = ['http://www.libsdl.org/release/'] +source_urls = ['https://www.libsdl.org/release/'] sources = [SOURCE_TAR_GZ] checksums = ['edc77c57308661d576e843344d8638e025a7818bff73f8fbfab09c3c5fd092ec'] diff --git a/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb index 0adc78ec7f6..476497eec2c 100644 --- a/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/s/SDL2_image/SDL2_image-2.0.3-GCCcore-6.4.0.eb @@ -6,14 +6,10 @@ name = 'SDL2_image' version = '2.0.3' homepage = 'https://www.libsdl.org/projects/SDL_image/' - -description = """ - SDL_image is an image file loading library. -""" +description = "SDL_image is an image file loading library." toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -# https://www.libsdl.org/projects/SDL_image/release/SDL2_image-2.0.3.tar.gz source_urls = ['https://www.libsdl.org/projects/SDL_image/release'] sources = [SOURCE_TAR_GZ] checksums = ['3510c25da735ffcd8ce3b65073150ff4f7f9493b866e85b83738083b556d2368'] @@ -30,7 +26,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['include/SDL2/SDL_image.h', 'lib/libSDL2_image.so', + 'files': ['include/SDL2/SDL_image.h', 'lib/libSDL2_image.%s' % SHLIB_EXT, 'lib/pkgconfig/SDL2_image.pc'], 'dirs': [] } From 4e47e94b6c14465d1f4e482f56f2570da37c9f32 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:43:23 +0200 Subject: [PATCH 551/698] PCRE: Use SOURCEFORGE_SOURCE for source_urls. --- easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb index 98d5303a0a2..3b8ca49c662 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.42-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'PCRE' version = '8.42' -homepage = 'http://www.pcre.org/' +homepage = 'https://www.pcre.org/' description = """ The PCRE library is a set of functions that implement regular expression @@ -13,7 +13,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} toolchainopts = {'pic': True} -source_urls = ['ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/'] +source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['69acbc2fbdefb955d42a4c606dfde800c2885711d2979e356c0636efde9ec3b5'] From 363107d82e64445a8b5f8a5c8ee744fcaab88933 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 13:50:04 +0200 Subject: [PATCH 552/698] cURL: Use https for source_urls --- easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb index 606c3eb444b..9a884573abe 100644 --- a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'cURL' version = '7.59.0' -homepage = 'http://curl.haxx.se' +homepage = 'https://curl.haxx.se' description = """ libcurl is a free and easy-to-use client-side URL transfer library, @@ -17,7 +17,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://curl.haxx.se/download/'] +source_urls = ['https://curl.haxx.se/download/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] From 24c15ddbe712b9a816e64b9ebe921d81b315b31a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 14:04:09 +0200 Subject: [PATCH 553/698] HTSlib: Move this PR's HTSlib from GCCcore to GCC since it's performance sensitive. Copied from the existing 1.9 --- .../h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb | 36 ++++++++++++++++ .../h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb | 43 ------------------- 2 files changed, 36 insertions(+), 43 deletions(-) create mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb delete mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb new file mode 100644 index 00000000000..6d895312d0f --- /dev/null +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb @@ -0,0 +1,36 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +easyblock = 'ConfigureMake' + +name = 'HTSlib' +version = '1.8' + +homepage = "http://www.htslib.org/" +description = """A C library for reading/writing high-throughput sequencing data. + This package includes the utilities bgzip and tabix""" + +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} + +source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1'] + +# cURL added for S3 support +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.6'), + ('XZ', '5.2.3'), + ('cURL', '7.58.0'), +] + +sanity_check_paths = { + 'files': ['bin/bgzip', 'bin/tabix', 'lib/libhts.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb deleted file mode 100644 index 8a4b5b4494f..00000000000 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 1.4 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'HTSlib' -version = '1.8' - -homepage = "http://www.htslib.org/" - -description = """ - A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('cURL', '7.59.0'), - ('XZ', '5.2.3'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' From 27ba5ac50721be2abd8a482e23263f6a8ba4e7e2 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 16 Oct 2020 12:09:41 +0000 Subject: [PATCH 554/698] adding easyconfigs: TINKER-8.8.1-foss-2020a.eb --- .../t/TINKER/TINKER-8.8.1-foss-2020a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb new file mode 100644 index 00000000000..b5c58542d0e --- /dev/null +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb @@ -0,0 +1,22 @@ +name = 'TINKER' +version = '8.8.1' + +homepage = 'https://dasher.wustl.edu/tinker' +description = """The TINKER molecular modeling software is a complete and general package for molecular mechanics + and dynamics, with some special features for biopolymers.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] +sources = [SOURCELOWER_TAR_GZ] + +# patches = [] + +checksums = ['8477afb51a0dcbba421948645eb77df3d071de984440b2e2d14063f9477e6d2e'] + +runtest = True + + +# sanity_check_commands is not possible since all the programs require multiple other inputs + +moduleclass = 'chem' From 4197e61d80ea3d9c5e2db7ab81bd77c74e9b6532 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 14:12:11 +0200 Subject: [PATCH 555/698] fix checksum in NAMD 2.12 easyconfigs + add source URL --- .../easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb | 10 ++++------ .../easyconfigs/n/NAMD/NAMD-2.12-foss-2017b-mpi.eb | 10 ++++------ .../easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb | 10 ++++------ .../easyconfigs/n/NAMD/NAMD-2.12-intel-2017b-mpi.eb | 10 ++++------ 4 files changed, 16 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb index 740dab2e769..f7173434f80 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017a-mpi.eb @@ -2,18 +2,16 @@ name = 'NAMD' version = '2.12' versionsuffix = '-mpi' -homepage = 'http://www.ks.uiuc.edu/Research/namd/' +homepage = 'https://www.ks.uiuc.edu/Research/namd/' description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" toolchain = {'name': 'foss', 'version': '2017a'} toolchainopts = {'usempi': True, 'pic': True} -sources = [{ - 'filename': 'NAMD_%(version)s_Source.tar.gz', - 'extract_cmd': "tar xfv %s", # source file is actually not gzipped -}] -checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/832164/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a'] dependencies = [ ('Tcl', '8.5.19'), diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017b-mpi.eb index f57bfe3b7a2..4ebd879e084 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-foss-2017b-mpi.eb @@ -2,18 +2,16 @@ name = 'NAMD' version = '2.12' versionsuffix = '-mpi' -homepage = 'http://www.ks.uiuc.edu/Research/namd/' +homepage = 'https://www.ks.uiuc.edu/Research/namd/' description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'usempi': True, 'pic': True} -sources = [{ - 'filename': 'NAMD_%(version)s_Source.tar.gz', - 'extract_cmd': "tar xfv %s", # source file is actually not gzipped -}] -checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/832164/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a'] dependencies = [ ('Tcl', '8.6.7'), diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb index 74f323256c9..2475457b10e 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017a-mpi.eb @@ -2,18 +2,16 @@ name = 'NAMD' version = '2.12' versionsuffix = '-mpi' -homepage = 'http://www.ks.uiuc.edu/Research/namd/' +homepage = 'https://www.ks.uiuc.edu/Research/namd/' description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True, 'usempi': True} -sources = [{ - 'filename': 'NAMD_%(version)s_Source.tar.gz', - 'extract_cmd': "tar xfv %s", # source file is actually not gzipped -}] -checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/832164/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a'] dependencies = [ ('Tcl', '8.6.6'), diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017b-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017b-mpi.eb index 184c643a7af..5cd20ee0c21 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017b-mpi.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.12-intel-2017b-mpi.eb @@ -2,18 +2,16 @@ name = 'NAMD' version = '2.12' versionsuffix = '-mpi' -homepage = 'http://www.ks.uiuc.edu/Research/namd/' +homepage = 'https://www.ks.uiuc.edu/Research/namd/' description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.""" toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True, 'usempi': True} -sources = [{ - 'filename': 'NAMD_%(version)s_Source.tar.gz', - 'extract_cmd': "tar xfv %s", # source file is actually not gzipped -}] -checksums = ['3be34f04c64a1e4225c04560c676ca8ff9bb57aa8830e42a46bf9ac6b16eb403'] +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/832164/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +checksums = ['436d11e4ff78136c7463d448d2eee92509a39b4c03cab8d07176bb20ddcb675a'] dependencies = [ ('Tcl', '8.6.7'), From 1f8c9bb252bccb739d67414d170adc1183f92bb3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 14:14:38 +0200 Subject: [PATCH 556/698] Drop cURL from this PR, it already exists in develop --- .../c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb deleted file mode 100644 index 9a884573abe..00000000000 --- a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cURL' -version = '7.59.0' - -homepage = 'https://curl.haxx.se' - -description = """ - libcurl is a free and easy-to-use client-side URL transfer library, - supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, - LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. - libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP - form based upload, proxies, cookies, user+password authentication (Basic, - Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling - and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['https://curl.haxx.se/download/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.0e') - ('zlib', '1.2.11'), -] - -configopts = '--with-zlib=$EBROOTZLIB' -# configopts += '--with-ssl=$EBROOTOPENSSL' - -modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} - -sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'tools' From ac50e13978ac37b6057d3e9937198fb9c7c907bb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 14:23:06 +0200 Subject: [PATCH 557/698] Drop cURL from this PR, it already exists in develop --- .../c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb | 49 ------------------- 1 file changed, 49 deletions(-) delete mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb deleted file mode 100644 index 606c3eb444b..00000000000 --- a/easybuild/easyconfigs/c/cURL/cURL-7.59.0-GCCcore-6.4.0.eb +++ /dev/null @@ -1,49 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'cURL' -version = '7.59.0' - -homepage = 'http://curl.haxx.se' - -description = """ - libcurl is a free and easy-to-use client-side URL transfer library, - supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, - LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. - libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP - form based upload, proxies, cookies, user+password authentication (Basic, - Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling - and more. -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['http://curl.haxx.se/download/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['099d9c32dc7b8958ca592597c9fabccdf4c08cfb7c114ff1afbbc4c6f13c9e9e'] - -osdependencies = [ - ('openssl-devel', 'libssl-dev', 'libopenssl-devel'), -] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - # OS dependency should be preferred if the os version is more recent then this version, - # it's nice to have an up to date openssl for security reasons - # ('OpenSSL', '1.1.0e') - ('zlib', '1.2.11'), -] - -configopts = '--with-zlib=$EBROOTZLIB' -# configopts += '--with-ssl=$EBROOTOPENSSL' - -modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} - -sanity_check_paths = { - 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], - 'dirs': ['lib/pkgconfig'], -} - -moduleclass = 'tools' From 94df5dfccd32cf28ffbab85054de08ab90e2aa8b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 14:24:35 +0200 Subject: [PATCH 558/698] Drop HTSlib-1.8-GCCcore from this PR. HTSlib-1.8-GCC is in another PR and should be used instead. --- .../h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb deleted file mode 100644 index 8a4b5b4494f..00000000000 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCCcore-6.4.0.eb +++ /dev/null @@ -1,43 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Pablo Escobar Lopez -# Swiss Institute of Bioinformatics -# Biozentrum - University of Basel -# 1.4 modified by: -# Adam Huffman -# The Francis Crick Institute - -easyblock = 'ConfigureMake' - -name = 'HTSlib' -version = '1.8' - -homepage = "http://www.htslib.org/" - -description = """ - A C library for reading/writing high-throughput sequencing data. - This package includes the utilities bgzip and tabix -""" - -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} - -source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s/'] -sources = [SOURCELOWER_TAR_BZ2] -checksums = ['c0ef1eec954a98cc708e9f99f6037db85db45670b52b6ab37abcc89b6c057ca1'] - -builddependencies = [ - ('binutils', '2.28'), -] - -dependencies = [ - ('bzip2', '1.0.6'), - ('cURL', '7.59.0'), - ('XZ', '5.2.3'), - ('zlib', '1.2.11'), -] - -sanity_check_paths = { - 'files': ["bin/bgzip", "bin/tabix", "lib/libhts.%s" % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'bio' From 892a8047201b471be7b1828e61572657ab8ec656 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 14:42:26 +0200 Subject: [PATCH 559/698] use https in homepage for HTSlib 1.8 --- easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb index 6d895312d0f..25eaa5e70c0 100644 --- a/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb +++ b/easybuild/easyconfigs/h/HTSlib/HTSlib-1.8-GCC-6.4.0-2.28.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'HTSlib' version = '1.8' -homepage = "http://www.htslib.org/" +homepage = "https://www.htslib.org/" description = """A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix""" From cb6484ebb0e890aad1e4d7dd86d7801f96914648 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 14:46:45 +0200 Subject: [PATCH 560/698] Change BCFtools in this PR from GCCcore to GCC. --- ....4.0.eb => BCFtools-1.8-GCC-6.4.0-2.28.eb} | 21 ++++--------------- 1 file changed, 4 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/b/BCFtools/{BCFtools-1.8-GCCcore-6.4.0.eb => BCFtools-1.8-GCC-6.4.0-2.28.eb} (67%) diff --git a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCC-6.4.0-2.28.eb similarity index 67% rename from easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb rename to easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCC-6.4.0-2.28.eb index 31222b15021..d30ed7f576b 100644 --- a/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/b/BCFtools/BCFtools-1.8-GCC-6.4.0-2.28.eb @@ -3,44 +3,31 @@ easyblock = 'ConfigureMake' name = 'BCFtools' version = '1.8' -homepage = 'http://www.htslib.org/' - +homepage = 'https://www.htslib.org/' description = """ Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants """ -toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchain = {'name': 'GCC', 'version': '6.4.0-2.28'} toolchainopts = {'pic': True} source_urls = ['https://github.com/samtools/%(namelower)s/releases/download/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] checksums = ['4acbfd691f137742e0be63d09f516434f0faf617a5c60f466140e0677915fced'] -builddependencies = [ - ('binutils', '2.28'), -] - dependencies = [ ('GSL', '2.4'), ('HTSlib', '1.8'), ('zlib', '1.2.11'), ] -configopts = """\ - --enable-gsl\ - --with-htslib=$EBROOTHTSLIB\ -""" - -postinstallcmds = [ - 'mkdir -p %(installdir)s/lib/plugins', - 'cp -a plugins/*.so %(installdir)s/lib/plugins/.', -] +configopts = "--with-htslib=$EBROOTHTSLIB --enable-libgsl" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bcftools', 'plot-vcfstats', 'vcfutils.pl']], - 'dirs': ['lib/plugins'], + 'dirs': ['libexec/bcftools'], } moduleclass = 'bio' From 4eeb28378a270bb43b190402337913be9f38b39d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 15:06:56 +0200 Subject: [PATCH 561/698] minor formatting changes --- easybuild/easyconfigs/m/MATLAB/README.md | 26 ++++++++++++++---------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB/README.md b/easybuild/easyconfigs/m/MATLAB/README.md index 6f033643659..c9eda0180d2 100644 --- a/easybuild/easyconfigs/m/MATLAB/README.md +++ b/easybuild/easyconfigs/m/MATLAB/README.md @@ -1,21 +1,25 @@ This example uses Matlab 2018a and MATLAB-2018a.eb Steps to install Matlab: -1. Install the appropriate Java install which requires manual configuration. See Java documentation for install. -1. Matlab needs a "File Installation Key". There are a few options available: - 1. Your Matlab license should have a "File Installation Key" in under "Advanced Options" in the "Install and Activate" tab of your "License Center". This will only install the products associated with this license. - 1. If you need to install all of the toolboxes to support multiple licenses Mathworks can enable a "All Product File Installation Key". This will install all of the client products but will not install server products like MDCS. A second manual installation on top of the first will be required. - 1. If you have a server product key, like MDCS, the "File Installation Key" may not install client products like Matlab Compilers. A second manual installation on top of the first will be required. -1. Edit the EasyBuild script. - 1. Update the version of Java to match the version installed in step 1. - 1. Add the following three lines +* Install the appropriate Java install which requires manual download. See Java documentation for install. +* Matlab needs a "File Installation Key". There are a few options available: + * Your Matlab license should have a "`File Installation Key`" in under "`Advanced Options`" in the "`Install and Activate`" tab of your "`License Center`". + This will only install the products associated with this license. + * If you need to install all of the toolboxes to support multiple licenses Mathworks can enable a "`All Product File Installation Key`". + This will install all of the client products but will not install server products like MDCS. + A second manual installation on top of the first will be required. + * If you have a server product key, like MDCS, the "`File Installation Key`" may not install client products like Matlab Compilers. + A second manual installation on top of the first will be required. +* Edit the easyconfig file (`MATLAB-2018a.eb`). + * Update the version of Java to match the version installed in step 1. + * Add the following three lines ``` # This string could be really long key = 'XXXXX-XXXXX-XXXXX-XXXXX-XXXXX-XXXXX' license_server = '' license_server_port = '' ``` -1. Download both ISO files from Mathworks. -1. Create the tar file needed for install. +* Download both ISO files from Mathworks. +* Create the tar file needed for install. ``` $ mkdir R2018a $ mount -o loop,ro R2018a_glnxa64_dvd1.iso /mnt/ @@ -26,7 +30,7 @@ Steps to install Matlab: $ umount /mnt $ tar -zcvf /my/easybuild/download/path/matlab-2018a.tar.gz R2018a ``` -1. Install with EasyBuild +* Install with EasyBuild ``` $ eb MATLAB-2018a.eb -r ``` From 74639d21955a69b9c2979c73ec17d9b6404c0561 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 15:12:04 +0200 Subject: [PATCH 562/698] HyPhy: Use cURL version that exists for the relevant toolchain version. --- easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb index 3298eaa084a..12f827e2abe 100644 --- a/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb +++ b/easybuild/easyconfigs/h/HyPhy/HyPhy-2.3.13-foss-2016b.eb @@ -21,11 +21,9 @@ checksums = ['29b72574302c98d38a92d5316b9283caa80a54c3e74c5e278c5bc9ae3d3df499'] builddependencies = [('CMake', '3.4.3')] -configopts = '-DINSTALL_PREFIX=%(installdir)s' +dependencies = [('cURL', '7.49.1')] -dependencies = [ - ('cURL', '7.40.0', '', True), -] +configopts = '-DINSTALL_PREFIX=%(installdir)s ' sanity_check_paths = { 'files': ['bin/HYPHYMP', 'bin/HYPHYMPI'], From c81fc314ce6e5642a08c12dd426dd49b449b7c17 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 16 Oct 2020 15:14:51 +0200 Subject: [PATCH 563/698] adding easyconfigs: Meson-0.55.3-GCCcore-10.2.0.eb, Ninja-1.10.1-GCCcore-10.2.0.eb --- .../m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb | 35 +++++++++++++++++++ .../n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb | 29 +++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..deecc4136fa --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.55.3-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.55.3' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6bed2a25a128bbabe97cf40f63165ebe800e4fcb46db8ab7ef5c2b5789f092a5'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Ninja', '1.10.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..82f318c76b7 --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.10.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a6b6f7ac360d4aabd54e299cc1d8fa7b234cd81b9401693da21221c62569a23e'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +moduleclass = 'tools' From d1cfca7555b29adf7d27d691d2d6a876c744da45 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Fri, 16 Oct 2020 15:29:30 +0200 Subject: [PATCH 564/698] Removed download_dep_fail from python bundles --- .../p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb | 1 - .../easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb | 1 - .../s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb index c66513372b3..5aeecedd1f5 100644 --- a/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb @@ -15,7 +15,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb index efee4607300..e2df5bc0af4 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb @@ -25,7 +25,6 @@ dependencies = [ use_pip = True -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb index 66d3145008d..1405be88c1e 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb @@ -26,7 +26,6 @@ dependencies = [ use_pip = True -download_dep_fail = True sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} From 2f5a0898952f74b5d6af7787b1c768869ab73f23 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Fri, 16 Oct 2020 15:43:33 +0200 Subject: [PATCH 565/698] Update easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit removed unnecessary commented line Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb b/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb index b5c58542d0e..30d6f3491ae 100644 --- a/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb +++ b/easybuild/easyconfigs/t/TINKER/TINKER-8.8.1-foss-2020a.eb @@ -10,8 +10,6 @@ toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://dasher.wustl.edu/tinker/downloads/'] sources = [SOURCELOWER_TAR_GZ] -# patches = [] - checksums = ['8477afb51a0dcbba421948645eb77df3d071de984440b2e2d14063f9477e6d2e'] runtest = True From 0ebc973c06cab00ae95ecf366d25810dc4c978b7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Oct 2020 15:47:59 +0200 Subject: [PATCH 566/698] fix installation paths and sanity checks in pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb --- .../pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb index d7216695265..65e77b7ed86 100644 --- a/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb +++ b/easybuild/easyconfigs/p/pbs_python/pbs_python-4.6.0-intel-2017a-Python-2.7.13.eb @@ -28,17 +28,19 @@ dependencies = [('Python', '2.7.13')] osdependencies = ['torque-devel'] -# this is needed for setup.py script -configopts = "--datarootdir=%(installdir)s --docdir=%(installdir)s" +# use CFLAGS from EB and torque headers from host system prebuildopts = 'export CFLAGS="$CFLAGS -I/usr/include/torque/" && ' preinstallopts = prebuildopts local_pythonpath = 'lib/python%(pyshortver)s/site-packages' -modextrapaths = {'PYTHONPATH': local_pythonpath} sanity_check_paths = { 'files': [], - 'dirs': ["%s/pbs" % local_pythonpath] + 'dirs': ['%s/pbs' % local_pythonpath, 'share/doc'] } +sanity_check_commands = ["python -c 'import PBSQuery'"] + +modextrapaths = {'PYTHONPATH': [local_pythonpath, '%s/pbs' % local_pythonpath]} + moduleclass = 'tools' From 7009cc78671b6a4fab0414a0fd12b5dbd22b89f6 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Fri, 16 Oct 2020 15:55:27 +0200 Subject: [PATCH 567/698] Remove JSC-specific things --- .../easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 16 ++++------------ 1 file changed, 4 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 3a7c95879e8..1c01e4f4ff4 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -9,17 +9,18 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] +checksums = ['dbc2ed6135009edf28d4e1c2c4f63984'] dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.34', '', ('GCCcore', local_gccver)), ('CUDA', '11.0', '', SYSTEM), # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails - ('numactl', '2.0.13', '', SYSTEM) + ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) ] -default_cuda_version = "11.0" -compute_capability = "70" +default_cuda_version = None # Use strings like "11.0" or use the command line: --try-amend=default_cuda_version="10.2" +cuda_compute_capabilities = None # Only single values supported (like "7.0" or "8.0"); use also via CLI # Options to add/remove things to/from environment module module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) @@ -30,14 +31,5 @@ module_add_nccl = False # Add NVHPC's NCCL library module_add_nvshmem = False # Add NVHPC's NVSHMEM library module_add_cuda = False # Add NVHPC's bundled CUDA -# We use a HMNS, so let's enforce a unique compiler -modluafooter = ''' -family("compiler") -add_property("arch","gpu") -''' - -# Always do a recursive unload on compilers -recursive_module_unload = True - # this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) moduleclass = 'compiler' From a22f90649bec1d567ae55db7ba91dc6da1730d1d Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Fri, 16 Oct 2020 16:04:20 +0200 Subject: [PATCH 568/698] Add documentation to file --- .../n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 1c01e4f4ff4..941120cb7bf 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -20,16 +20,28 @@ dependencies = [ ] default_cuda_version = None # Use strings like "11.0" or use the command line: --try-amend=default_cuda_version="10.2" -cuda_compute_capabilities = None # Only single values supported (like "7.0" or "8.0"); use also via CLI - -# Options to add/remove things to/from environment module -module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) -module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI -module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) -module_add_profilers = False # Add NVHPC's NVIDIA Profilers -module_add_nccl = False # Add NVHPC's NCCL library -module_add_nvshmem = False # Add NVHPC's NVSHMEM library -module_add_cuda = False # Add NVHPC's bundled CUDA # this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) moduleclass = 'compiler' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# Install NVHPC for an associated CUDA version: +# default_cuda_version = "11.0" +# Can also be specified via --try-amend=default_cuda_version="10.2" +# If not given, is tried to be taken from the CUDA module, if the CUDA module is a dependency +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA From 74971c643c8e1ef401a059aab67a77662ef117c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 16:16:36 +0200 Subject: [PATCH 569/698] update patch for Nek5000 to make it donwload Hypre from hypre-space/hypre rather than LLNL/hypre --- .../easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb | 2 +- .../easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb index 721d55040e3..b04680abfce 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0-intel-2018a.eb @@ -18,7 +18,7 @@ patches = [ checksums = [ '4d8d4793ce3c926c54e09a5a5968fa959fe0ba46bd2e6b8043e099528ee35a60', # v17.0.tar.gz - '62ef4277156ddad2520b9107df8329039a0e4d427a7717c58aa948f3e8c385f3', # Nek5000-17.0_hypre_blas.patch + 'b3820a9e141a1c3087aaabbb140ecf11756b552a175619f9e12d913afd850794', # Nek5000-17.0_hypre_blas.patch 'af9e3771483d9a1732135ca1fd25f902706bf6e8f9c8552bc4bdf24d9a1c0244', # Nek5000-17.0_sundials.patch ] diff --git a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch index 6b8700c8738..b601fc81267 100644 --- a/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch +++ b/easybuild/easyconfigs/n/Nek5000/Nek5000-17.0_hypre_blas.patch @@ -3,7 +3,13 @@ diff -ru Nek5000-17.0.org/tools/amg_hypre/hypre/install Nek5000-17.0/tools/amg_hypre/hypre/install --- Nek5000-17.0.org/tools/amg_hypre/hypre/install 2017-12-17 10:08:30.000000000 +0100 +++ Nek5000-17.0/tools/amg_hypre/hypre/install 2018-05-30 15:51:20.546161373 +0200 -@@ -9,5 +9,5 @@ +@@ -4,10 +4,10 @@ + exit 0 + fi + if [ ! -f v2.11.2.tar.gz ]; then +- wget -O v2.11.2.tar.gz https://github.com/LLNL/hypre/archive/v2.11.2.tar.gz ++ wget -O v2.11.2.tar.gz https://github.com/hypre-space/hypre/archive/v2.11.2.tar.gz + fi tar -zxf *.tar.gz cd hypre*/src From c87c1af6e0965bd442a681a101c1237c456181a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 16:19:46 +0200 Subject: [PATCH 570/698] don't link with -liomp5 when using foss toolchain --- .../AmberTools-17-foss-2018a-Python-2.7.14.eb | 2 +- .../AmberTools/AmberTools-17_fixes-foss.patch | 860 ++++++++++++++++++ 2 files changed, 861 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes-foss.patch diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb index 94c29a7a8db..2b7e507c4e4 100644 --- a/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17-foss-2018a-Python-2.7.14.eb @@ -32,7 +32,7 @@ dependencies = [ # fix linking to netCDF library: also requires linking to HDF5 & cURL libs, which in turns require others, # all of which are indirect dependencies via netCDF -local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -liomp5 -lcurl -lssl -lcrypto -lz -lm -lpthread" +local_netcdf_libs = "-lnetcdf -lhdf5 -lsz -ldl -lcurl -lssl -lcrypto -lz -lm -lpthread" preconfigopts = "sed -i'' 's/-lnetcdf/%s/g' AmberTools/src/cpptraj/configure && " % local_netcdf_libs configopts = "-nosanderapi" diff --git a/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes-foss.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes-foss.patch new file mode 100644 index 00000000000..eecc293beef --- /dev/null +++ b/easybuild/easyconfigs/a/AmberTools/AmberTools-17_fixes-foss.patch @@ -0,0 +1,860 @@ +combination of patches originally created for Amber 16 + +original patches by Åke Sandgren and Davide Vanzo (Vanderbilt University) +combined patch composed by Kenneth Hoste (HPC-UGent) + +* Do not use static for cpptraj, builds fail (was: Amber-16-AT-17-fix-cpptraj-dont-use-static.patch) +* Fix incorrect OMP directive in RISM (was: Amber-16-AT-17-fix_incorrect_omp_directive_rism.patch) +* Fix incorrect intel mpi compiler version detection (was: Amber-16-AT-17-fix_intel_mpi_compiler_version_detection.patch) +* checkrismunsupported.sh needs to run TESTsander with DO_PARALLEL, otherwise it will get "Killed" instead of a proper exit (was: Amber-16-AT-17-fix_missing_do_parallel_in_checkrismunsupported.patch) +* Fix missing openmp flag at link (was: Amber-16-AT-17-fix_missing_openmp_at_link.patch) +* Fix link of external FFTW3 for sander (was: Amber-16-AT-17-fix_sander_link_with_external_fftw.patch) +* Make nab always use CUSTOMBUILDFLAGS so openmp flags get added when needed (was: Amber-16-AT-17-use_CUSTOMBUILDFLAGS_for_nab.patch) +* Use FFTW_FFT/MKL_FFTW_FFT instead of PUBFFT for pmemd (was: Amber-16-AT-17-use_FFTW_FFT_instead_of_PUBFFT.patch) +* Force the compiler used by nvcc to use the C++11 standard to avoid: error: identifier "__float128" is undefined (was: Amber-16-AT-17_Fix_intelcuda_undefined_float128.patch) +* Allow use of all CUDA 9 versions (was: Amber-16-AT-17_allow_cuda9.patch) +* Make cpptraj use FFTW3 as defined by easyconfig (was: Amber-16-AT-17_cpptraj_use_mkl_fft.patch) +* Fix hardcoding of netcdf, mkl and compiler (was: Amber-16-AT-17_fix-hardcoding.patch) +* Fix incorrect use of fixed sized buffers (was: Amber-16-AT-17_fix_fixed_size_cmd_in_nab.patch) +* Fix FFTW3 link flags for rism (was: Amber-16-AT-17_fix_rism_fftw_lib.patch) +* Ignore checks for X11, use easybuild settings instead (was: Amber-16-AT-17_ignore_X11_checks.patch) +* Make cpptraj link with the BLAS/LAPACK/Zlib/Bzip2 from EasyBuild (was: Amber-16-AT-17_make_cpptraj_link_with_EBs_blas_lapack_zlib_bzip2.patch) +* Use FFTW_FFT with FFTW3 instead of PUBFFT for pmemd; this fixes linking with FFTW3 as opposed to using MKL (was: Amber-16-AT-17_use_FFTW_FFT_instead_of_PUBFFT_part2.patch) + +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 12:22:17.981248856 +0200 +@@ -3339,7 +3339,7 @@ + if [ -z "$zlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nozlib" ; fi + if [ -z "$bzlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nobzlib" ; fi + if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi +-if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi ++#if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi + if [ ! -z "$pnetcdf_dir" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS --with-pnetcdf=$pnetcdf_dir" ; fi + if [ -z "$sanderapi_lib" ] ; then + CPPTRAJOPTS="$CPPTRAJOPTS -nosanderlib" + +diff -ru amber16.orig/AmberTools/src/rism/rism3d_c.F90 amber16/AmberTools/src/rism/rism3d_c.F90 +--- amber16.orig/AmberTools/src/rism/rism3d_c.F90 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/rism/rism3d_c.F90 2017-10-10 15:39:22.259467974 +0200 +@@ -4061,7 +4061,7 @@ + numElectronsAtGridCenter = totalSolventElectrons - electronRDFSum + + ! #pragma omp parallel for schedule(dynamic, 10) shared (dx, conc, result, stepx, stepy, stepz, center_grid) +-!$omp parallel do private(local_equal), shared(this, UNITS, electronMap, numSmearGridPoints, numElectronsAtGridCenter) ++!$omp parallel do shared(this, electronMap, numSmearGridPoints, numElectronsAtGridCenter) + do igzCenter = 0, this%grid%globalDimsR(3) - 1 + rzCenter = igzCenter * this%grid%voxelVectorsR(3, :) + do igyCenter = 0, this%grid%globalDimsR(2) - 1 +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 10:34:26.841606227 +0200 +@@ -304,7 +304,8 @@ + | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` + else + cc_version=`$cc $1 2>&1 | grep -E "$cc |[vV]ersion " \ +- | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` ++ | sed -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//' \ ++ | grep -v '^Intel(R)'` + fi + if [ -z "$cc_version" ] ; then + echo "Error: $cc is not well formed or produces unusual version details!" +@@ -354,7 +355,8 @@ + -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` + else + fc_version=`$fc $1 2>&1 | grep -E "$fc |$cc |[vV]ersion " | sed -e "s@$fc @@" \ +- -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//'` ++ -e 's/Open64//' -e 's/^[a-zA-Z :]* //' -e 's/ .*//' \ ++ | grep -v '^Intel(R)'` + fi + if [ -z "$fc_version" ] ; then + echo "Error: $fc is not well formed or produces unusual version details!" +diff -ru amber16.orig/test/rism3d/checkrismunsupported.sh amber16/test/rism3d/checkrismunsupported.sh +--- amber16.orig/test/rism3d/checkrismunsupported.sh 2017-04-07 21:08:28.000000000 +0200 ++++ amber16/test/rism3d/checkrismunsupported.sh 2018-02-19 15:17:17.667872717 +0100 +@@ -14,7 +14,7 @@ + echo "$1 is not an executable or does not exist." + exit 1 + fi +-HAS_RISM=`$TESTsander -O -xvv foo 2> /dev/null | grep flag` ++HAS_RISM=`$DO_PARALLEL $TESTsander -O -xvv foo 2> /dev/null | grep flag` + /bin/rm -f foo mdout mdin + if [ -n "$HAS_RISM" ] ; then + echo "$TESTsander compiled without RISM support." +diff -ru amber16.orig/AmberTools/src/byacc/Makefile amber16/AmberTools/src/byacc/Makefile +--- amber16.orig/AmberTools/src/byacc/Makefile 2017-04-07 21:08:11.000000000 +0200 ++++ amber16/AmberTools/src/byacc/Makefile 2017-10-13 22:17:23.837195086 +0200 +@@ -31,7 +31,7 @@ + all: $(PROGRAM) + + $(PROGRAM): $(OBJS) $(LIBS) +- @$(CC) $(LDFLAGS) -o $(PROGRAM) $(OBJS) $(LIBS) ++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROGRAM) $(OBJS) $(LIBS) + + clean: + @rm -f $(OBJS) +diff -ru amber16.orig/AmberTools/src/ucpp-1.3/Makefile amber16/AmberTools/src/ucpp-1.3/Makefile +--- amber16.orig/AmberTools/src/ucpp-1.3/Makefile 2017-04-07 21:08:15.000000000 +0200 ++++ amber16/AmberTools/src/ucpp-1.3/Makefile 2017-10-13 21:54:44.418148511 +0200 +@@ -42,7 +42,7 @@ + rm -f *.o ucpp core + + ucpp$(SFX): $(COBJ) +- $(CC) $(LDFLAGS) -o ucpp$(SFX) $(COBJ) $(LIBS) ++ $(CC) $(LDFLAGS) $(CFLAGS) -o ucpp$(SFX) $(COBJ) $(LIBS) + + assert.o: tune.h ucppi.h cpp.h nhash.h mem.h + cpp.o: tune.h ucppi.h cpp.h nhash.h mem.h +diff -ru amber16.orig/AmberTools/src/sander/Makefile amber16/AmberTools/src/sander/Makefile +--- amber16.orig/AmberTools/src/sander/Makefile 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/sander/Makefile 2017-05-17 11:04:29.961465834 +0200 +@@ -317,7 +317,7 @@ + -lFpbsa ../lib/nxtsec.o $(EMILLIB) \ + $(SEBOMDLIB) \ + ../lib/sys.a $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -331,7 +331,7 @@ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + +@@ -345,7 +345,7 @@ + $(LSCIVROBJ) -L$(LIBDIR) -lsqm -lFpbsa \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o $(EMILLIB) ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(PUPILLIBS) $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + +@@ -358,7 +358,7 @@ + $(XRAY_OBJS) -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -370,7 +370,7 @@ + $(PARTPIMDOBJ) $(LSCIVROBJ) $(XRAY_OBJS) \ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) $(SEBOMDLIB) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +@@ -385,7 +385,7 @@ + -L$(LIBDIR) -lsqm -lFpbsa $(EMILLIB) \ + $(SEBOMDLIB) $(XRAY_OBJS) \ + ../lib/nxtsec.o ../lib/sys.a $(NFE_OBJECTS) $(NETCDFLIBF) \ +- $(FLIBS_RISMSANDER) $(FFTW3) $(FLIBSF) \ ++ $(FLIBS_RISMSANDER) $(FLIBS_FFTW3) $(FLIBSF) \ + $(LDFLAGS) $(AMBERLDFLAGS) $(LIOLIBS) $(PLUMED_LOAD) + + #--------------------------------------------------------------------------- +diff -ru amber16.orig/AmberTools/src/amberlite/Makefile amber16/AmberTools/src/amberlite/Makefile +--- amber16.orig/AmberTools/src/amberlite/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/amberlite/Makefile 2017-10-12 12:42:23.319122932 +0200 +@@ -16,13 +16,13 @@ + cd ../nab && $(MAKE) $@ + + $(BINDIR)/ffgbsa$(SFX): ffgbsa.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/ffgbsa$(SFX) ffgbsa.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/ffgbsa$(SFX) ffgbsa.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/minab$(SFX): minab.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/minab$(SFX) minab.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/minab$(SFX) minab.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/mdnab$(SFX): mdnab.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mdnab$(SFX) mdnab.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mdnab$(SFX) mdnab.nab $(CUSTOMBUILDFLAGS) + + clean: + /bin/rm -f *.c +diff -ru amber16.orig/AmberTools/src/etc/Makefile amber16/AmberTools/src/etc/Makefile +--- amber16.orig/AmberTools/src/etc/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/etc/Makefile 2017-10-11 14:49:01.168646077 +0200 +@@ -68,14 +68,14 @@ + $(CC) $(CFLAGS) $(AMBERCFLAGS) -o elsize$(SFX) elsize.o $(LM) + + molsurf$(SFX): molsurf.nab +- $(BINDIR)/nab$(SFX) -o molsurf$(SFX) molsurf.nab ++ $(BINDIR)/nab$(SFX) -o molsurf$(SFX) molsurf.nab $(CUSTOMBUILDFLAGS) + + resp$(SFX): lapack.o resp.o + $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) $(LDFLAGS) $(AMBERLDFLAGS) \ + lapack.o resp.o -o resp$(SFX) + + tinker_to_amber$(SFX): tinker_to_amber.o cspline.o +- $(FC) -o tinker_to_amber$(SFX) tinker_to_amber.o cspline.o ++ $(FC) -o tinker_to_amber$(SFX) tinker_to_amber.o cspline.o $(CUSTOMBUILDFLAGS) + + new_crd_to_dyn$(SFX): new_crd_to_dyn.o nxtsec + $(FC) $(LDFLAGS) -o new_crd_to_dyn$(SFX) new_crd_to_dyn.o ../lib/nxtsec.o +diff -ru amber16.orig/AmberTools/src/mm_pbsa/Makefile amber16/AmberTools/src/mm_pbsa/Makefile +--- amber16.orig/AmberTools/src/mm_pbsa/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/mm_pbsa/Makefile 2017-10-12 10:08:57.265288431 +0200 +@@ -21,7 +21,7 @@ + + #Note dependency on nab from AMBERTools here. + $(BINDIR)/mm_pbsa_nabnmode$(SFX): mm_pbsa_nabnmode.nab +- $(BINDIR)/nab$(SFX) $(NABFLAGS) -o $(BINDIR)/mm_pbsa_nabnmode$(SFX) mm_pbsa_nabnmode.nab ++ $(BINDIR)/nab$(SFX) $(NABFLAGS) -o $(BINDIR)/mm_pbsa_nabnmode$(SFX) mm_pbsa_nabnmode.nab $(CUSTOMBUILDFLAGS) + + ../lib/amopen.o: ../lib/amopen.F + cd ../lib; $(MAKE) amopen.o +diff -ru amber16.orig/AmberTools/src/mmpbsa_py/Makefile amber16/AmberTools/src/mmpbsa_py/Makefile +--- amber16.orig/AmberTools/src/mmpbsa_py/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/mmpbsa_py/Makefile 2017-10-12 06:44:59.043135426 +0200 +@@ -9,10 +9,10 @@ + $(PYTHON) setup.py install -f $(PYTHON_INSTALL) --install-scripts=$(BINDIR) + + $(BINDIR)/mmpbsa_py_nabnmode$(SFX): mmpbsa_entropy.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_nabnmode$(SFX) mmpbsa_entropy.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_nabnmode$(SFX) mmpbsa_entropy.nab $(CUSTOMBUILDFLAGS) + + $(BINDIR)/mmpbsa_py_energy$(SFX): mmpbsa_energy.nab +- $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_energy$(SFX) mmpbsa_energy.nab ++ $(BINDIR)/nab$(SFX) -o $(BINDIR)/mmpbsa_py_energy$(SFX) mmpbsa_energy.nab $(CUSTOMBUILDFLAGS) + + serial: install + +diff -ru amber16.orig/AmberTools/src/nss/Makefile amber16/AmberTools/src/nss/Makefile +--- amber16.orig/AmberTools/src/nss/Makefile 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/nss/Makefile 2017-10-11 08:24:51.121320716 +0200 +@@ -54,28 +54,28 @@ + -ranlib $(LIBDIR)/libnab.a + + matextract$(SFX): matextract.o +- $(NAB) -o matextract$(SFX) matextract.o ++ $(NAB) -o matextract$(SFX) matextract.o $(CUSTOMBUILDFLAGS) + + matgen$(SFX): matgen.o +- $(NAB) -o matgen$(SFX) matgen.o ++ $(NAB) -o matgen$(SFX) matgen.o $(CUSTOMBUILDFLAGS) + + matmerge$(SFX): matmerge.o +- $(NAB) -o matmerge$(SFX) matmerge.o ++ $(NAB) -o matmerge$(SFX) matmerge.o $(CUSTOMBUILDFLAGS) + + matmul$(SFX): matmul.o +- $(NAB) -o matmul$(SFX) matmul.o ++ $(NAB) -o matmul$(SFX) matmul.o $(CUSTOMBUILDFLAGS) + + transform$(SFX): transform.o +- $(NAB) -o transform$(SFX) transform.o ++ $(NAB) -o transform$(SFX) transform.o $(CUSTOMBUILDFLAGS) + + tss_init$(SFX): tss_init.o +- $(NAB) -o tss_init$(SFX) tss_init.o ++ $(NAB) -o tss_init$(SFX) tss_init.o $(CUSTOMBUILDFLAGS) + + tss_main$(SFX): tss_main.o +- $(NAB) -o tss_main$(SFX) tss_main.o ++ $(NAB) -o tss_main$(SFX) tss_main.o $(CUSTOMBUILDFLAGS) + + tss_next$(SFX): tss_next.o +- $(NAB) -o tss_next$(SFX) tss_next.o ++ $(NAB) -o tss_next$(SFX) tss_next.o $(CUSTOMBUILDFLAGS) + + clean: + /bin/rm -f \ +diff -ru amber16.orig/AmberTools/src/rism/Makefile amber16/AmberTools/src/rism/Makefile +--- amber16.orig/AmberTools/src/rism/Makefile 2017-04-13 15:00:54.000000000 +0200 ++++ amber16/AmberTools/src/rism/Makefile 2017-10-11 20:00:32.189972509 +0200 +@@ -92,9 +92,9 @@ + # ------ Single-Point information ------------------------------------------ + SPSRC=rism3d.snglpnt.nab + rism3d.snglpnt$(SFX): $(SPSRC) +- $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) ++ $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) + rism3d.snglpnt.MPI$(SFX): $(SPSRC) +- $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) ++ $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) $(CUSTOMBUILDFLAGS) + # -------------------------------------------------------------------------- + + yes: install +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-10-14 19:07:22.137281514 +0200 +@@ -1384,9 +1384,9 @@ + # PMEMD Specifics + pmemd_fpp_flags='-DPUBFFT' + # following lines commented out, since pmemd is not GPL: +-# if [ "$has_fftw3" = 'yes' ]; then +-# pmemd_fpp_flags='-DFFTW_FFT' +-# fi ++ if [ "$has_fftw3" = 'yes' ]; then ++ pmemd_fpp_flags='-DFFTW_FFT' ++ fi + pmemd_foptflags="$foptflags" + if [ "$pmemd_openmp" = 'yes' ]; then + pmemd_foptflags= "$pmemd_foptflags -fopenmp -D_OPENMP_" +@@ -2958,8 +2958,6 @@ + echo " MKL_HOME set to" "$MKL_HOME" + echo $(mkdir $amberprefix/include) + echo $(cp $MKL_HOME/mkl/include/fftw/fftw3.f $amberprefix/include) +- fi +- if [ "$intelmpi" = "yes" ]; then + pmemd_fpp_flags="$pmemd_fppflags -DFFTW_FFT -DMKL_FFTW_FFT " + pmemd_coptflags="$pmemd_coptflags -DFFTW_FFT " # it would be best if we had a cflags var + fi + +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/configure2 2019-02-28 11:31:13.125415364 -0600 +@@ -1731,9 +1731,9 @@ + pmemd_cu_libs="./cuda/cuda.a -L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcurand -lcufft -lcudart $fc_cxx_link_flag" + pbsa_cu_libs="-L\$(CUDA_HOME)/lib64 -L\$(CUDA_HOME)/lib -lcublas -lcusparse -lcudart -lcuda $fc_cxx_link_flag" + if [ "$optimise" = 'yes' ]; then +- nvcc="$nvcc -use_fast_math -O3 " ++ nvcc="$nvcc -use_fast_math -O3 -Xcompiler '-std=c++11'" + else +- nvcc="$nvcc -use_fast_math -O0 " ++ nvcc="$nvcc -use_fast_math -O0 -Xcompiler '-std=c++11'" + fi + + if [ "$mpi" = 'yes' ]; then +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-07-27 10:27:34.745642223 +0200 ++++ amber16/AmberTools/src/configure2 2018-07-27 10:30:05.442542975 +0200 +@@ -1203,7 +1203,8 @@ + #SM2.0 = All GF variants = C2050, 2075, M2090, GTX480, GTX580 etc. + sm20flags='-gencode arch=compute_20,code=sm_20' + cudaversion=`$nvcc --version | grep 'release' | cut -d' ' -f5 | cut -d',' -f1` +- if [ "$cudaversion" = "9.0" ]; then ++ cudamajversion=`echo $cudaversion | cut -d. -f1` ++ if [ $cudamajversion -ge 9 ]; then + echo "CUDA Version $cudaversion detected" + echo "Configuring for SM3.0, SM5.0, SM5.2, SM5.3, SM6.0, SM6.1 and SM7.0" + nvccflags="$sm30flags $sm50flags $sm52flags $sm53flags $sm60flags $sm61flags $sm70flags -Wno-deprecated-declarations" +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-04-03 20:55:27.031610543 +0200 ++++ amber16/AmberTools/src/configure2 2018-04-03 20:55:19.359682056 +0200 +@@ -3338,7 +3358,7 @@ + if [ "$optimise" = 'no' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -noopt" ; fi + if [ -z "$zlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nozlib" ; fi + if [ -z "$bzlib" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -nobzlib" ; fi +-if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi ++#if [ "$has_fftw3" = 'yes' ]; then CPPTRAJOPTS="$CPPTRAJOPTS -fftw3 --with-fftw3=$CPPTRAJHOME" ; fi + #if [ "$static" = 'yes' ] ; then CPPTRAJOPTS="$CPPTRAJOPTS -static" ; fi + if [ ! -z "$pnetcdf_dir" ] ; then CPPTRAJOPTS="$CPPTRAJOPTS --with-pnetcdf=$pnetcdf_dir" ; fi + if [ -z "$sanderapi_lib" ] ; then +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2017-05-17 09:05:08.644115630 +0200 +@@ -439,12 +439,12 @@ + write(6,*) 'testing a Fortran program' + end program testf + EOF +- $fc $fflags $netcdfinc -o testp$suffix testp.f90 $netcdfflagf > /dev/null 2> compile.err ++ $fc $fflags $netcdffinc -o testp$suffix testp.f90 $netcdfflagf > /dev/null 2> compile.err + if [ ! -e "testp$suffix" ] ; then + status=1 + if [ "$1" = "verbose" ] ; then + echo "Error: Could not compile with NetCDF Fortran interface." +- echo " $fc $fflags $netcdfinc -o testp$suffix testp.f90 $netcdfflagf" ++ echo " $fc $fflags $netcdffinc -o testp$suffix testp.f90 $netcdfflagf" + echo " Compile error follows:" + cat compile.err + echo "" +@@ -545,6 +545,7 @@ + mpi='no' + mtkpp='' + netcdf_dir='' ++netcdf_fort_dir='' + netcdf_flag='' + netcdfstatic='no' + pnetcdf_dir='' +@@ -630,6 +631,7 @@ + --skip-python) skippython='yes' ;; + --with-python) shift; python="$1";; + --with-netcdf) shift; netcdf_dir="$1";; ++ --with-netcdf-fort) shift; netcdf_fort_dir="$1";; + --with-pnetcdf) shift; pnetcdf_dir="$1" ;; + --python-install) shift; python_install="$1";; + -netcdfstatic) netcdfstatic='yes' ;; +@@ -900,7 +902,7 @@ + flibsf="-larpack -llapack -lblas" + # only used when the user requests a static build or when a static build is + # automatically set, eg, windows: +-staticflag='-static' ++staticflag='' + omp_flag= + mpi_flag= + fp_flags= +@@ -1418,7 +1420,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -1737,7 +1739,7 @@ + fi + + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$pmemd_coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2069,7 +2071,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2206,7 +2208,7 @@ + nvcc="$nvcc -use_fast_math -O3 " + fi + if [ "$mpi" = 'yes' ]; then +- mpi_inc=`(mpicc -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` ++ mpi_inc=`(${CC} -show 2>&1) | awk 'BEGIN{i=0} {while (i < NF) {if ( substr($i, 1, 2) == "-I" ) {printf("%s ", $i);}; i++;}}'` + pmemd_cu_includes="$pmemd_cu_includes $mpi_inc" + pmemd_cu_defines="$pmemd_cu_defines -DMPI -DMPICH_IGNORE_CXX_SEEK" + pmemd_coptflags="$coptflags -DMPICH_IGNORE_CXX_SEEK" +@@ -2279,17 +2281,17 @@ + blas=skip + flibs="-larpack " + flibsf="-larpack " +- mkll="$MKL_HOME/lib/32" ++ mkll="$MKL_HOME/mkl/lib/32" + mkl_processor="32" + mkl_procstring="ia32" + mklinterfacelayer='libmkl_intel.a' + if [ "$x86_64" = 'yes' ]; then +- if [ -d "$MKL_HOME/lib/em64t" ]; then +- mkll="$MKL_HOME/lib/em64t" ++ if [ -d "$MKL_HOME/mkl/lib/em64t" ]; then ++ mkll="$MKL_HOME/mkl/lib/em64t" + mkl_processor="em64t" + mkl_procstring="em64t" + else +- mkll="$MKL_HOME/lib/intel64" ++ mkll="$MKL_HOME/mkl/lib/intel64" + mkl_processor="intel64" + mkl_procstring="intel64" + fi +@@ -2715,11 +2717,17 @@ + else + # A NetCDF directory was specified. Check that library exists and compiles + printf "\tUsing external NetCDF in '$netcdf_dir'\n" ++ # Support separate NetCDF-Fortran installation with --with-netcdf-fort ++ if [ ! -e "$netcdf_fort_dir" ]; then ++ netcdf_fort_dir="$netcdf_dir" ++ fi ++ printf "\tUsing external NetCDF-Fortran in '$netcdf_fort_dir'\n" + netcdfinc="-I"$netcdf_dir"/include" ++ netcdffinc="-I"$netcdf_fort_dir"/include" + if [ "${netcdf_dir}" != '/usr' -a "$netcdf_dir" != '/usr/' ]; then + netcdf_flag="-L${netcdf_dir}/lib $netcdf_flag" + fi +- netcdf=$netcdf_dir"/include/netcdf.mod" ++ netcdf=$netcdf_fort_dir"/include/netcdf.mod" + if [ "$netcdfstatic" = 'no' ] ; then + if [ "${netcdf_dir}" != '/usr' -a "${netcdf_dir}" != '/usr/' ]; then + netcdfflagc="-L${netcdf_dir}/lib -lnetcdf" +@@ -2735,7 +2743,7 @@ + echo "Error: '$netcdfflagc' not found." + exit 1 + fi +- netcdfflagf=$netcdf_dir"/lib/libnetcdff.a" ++ netcdfflagf=$netcdf_fort_dir"/lib/libnetcdff.a" + if [ ! -e "$netcdfflagf" ]; then + echo "Error: '$netcdfflagf' not found." + exit 1 +@@ -2755,6 +2763,7 @@ + netcdfflagf='' + netcdfflagc='' + netcdfinc='' ++ netcdffinc='' + fi + + #------------------------------------------------------------------------------ +@@ -3726,7 +3735,7 @@ + NETCDF=$netcdf + NETCDFLIB=$netcdfflagc + NETCDFLIBF=$netcdfflagf +-NETCDFINC=$netcdfinc ++NETCDFINC=$netcdfinc $netcdffinc + PNETCDFLIB=$pnetcdflib + PNETCDFINC=$pnetcdfinc + PNETCDFDEF=$pnetcdfdef +diff -ru amber16.orig/AmberTools/src/nab/nab.c amber16/AmberTools/src/nab/nab.c +--- amber16.orig/AmberTools/src/nab/nab.c 2019-02-28 10:41:07.185332187 -0600 ++++ amber16/AmberTools/src/nab/nab.c 2019-02-28 19:12:13.618946740 -0600 +@@ -22,7 +22,7 @@ + + static void n2c( int, int, char *, int, int, int, char *[], char [], char * ); + static void cc( int, int, int, int, char [], int, char *[], char [] ); +-static int split( char [], char *[], char * ); ++static int split( char [], char ***, char * ); + static int execute( char **, int, int, int ); + + int main( int argc, char *argv[] ) +@@ -128,8 +128,8 @@ + char cpp_ofname[ 256 ]; + + char cmd[ 1024 ]; +- char *fields[ 256 ]; +- int nfields; ++ char **fields; ++ int nfields, i; + int cpp_ofd, n2c_ofd; + int status; + char *amberhome; +@@ -169,7 +169,7 @@ + amberhome, cppstring, amberhome, + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "cpp cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + #ifndef USE_MKSTEMP + if( (cpp_ofd = +@@ -205,7 +205,7 @@ + nodebug ? "-nodebug" : "", + argv[ ac ] ? argv[ ac ] : "" ); + if( cgdopt ) fprintf( stderr, "nab2c cmd: %s\n", cmd ); +- nfields = split( cmd, fields, " " ); ++ nfields = split( cmd, &fields, " " ); + + status = execute( fields, cpp_ofd, n2c_ofd, 2 ); + unlink( cpp_ofname ); +@@ -213,6 +213,10 @@ + unlink( n2c_ofname ); + fprintf( stderr, "nab2c failed!\n" ); exit(1); + } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); + } + } + unlink( n2c_ofname ); +@@ -233,20 +237,28 @@ + { + int ac; + char *dotp, *amberhome; +- char cmd[ 1024 ], word[ 1024 ]; +- char *fields[256]; ++#define WORDSZ 1024 ++ char *cmd, word[ WORDSZ ]; ++ char **fields; ++ int cmd_sz; + int status; +- int nfields; ++ int nfields, i; + + amberhome = (char *) getenv("AMBERHOME"); + if( amberhome == NULL ){ + fprintf( stderr, "AMBERHOME is not set!\n" ); + exit(1); + } ++ cmd_sz = WORDSZ; ++ cmd = malloc(cmd_sz); + sprintf( cmd, "%s -I%s/include", CC, amberhome ); + if( aopt ){ + #ifdef AVSDIR + sprintf( word, " -I%s/include", AVSDIR ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + #else + fprintf( stderr, "-avs not supported.\n" ); +@@ -257,9 +269,17 @@ + dotp = strrchr( argv[ ac ], '.' ); + strcpy( &dotp[ 1 ], "c" ); + sprintf( word, " %s", argv[ ac ] ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + }else if( argv[ ac ] ){ + sprintf( word, " %s", argv[ ac ] ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + } + } +@@ -268,71 +288,100 @@ + if( aopt ){ + sprintf( word, " -L%s/lib -lflow_c -lgeom -lutil", + AVSDIR ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); + } + #endif + sprintf( word, " -L%s/lib -lnab -lcifparse", amberhome ); ++ if (strlen(cmd) + strlen(word) + 1 > cmd_sz) { ++ cmd_sz += WORDSZ; ++ cmd = realloc(cmd, cmd_sz); ++ } + strcat( cmd, word ); +- sprintf( word, " %s ", FLIBS ); +- strcat( cmd, word ); ++ /* FLIBS can be very big and there is no need to copy it into word first. */ ++ /* Make sure there is space enough for the " -lm" too */ ++ if (strlen(cmd) + strlen(FLIBS) + 6 > cmd_sz) { ++ cmd_sz += strlen(FLIBS) + 6; ++ cmd = realloc(cmd, cmd_sz); ++ } ++ strcat( cmd, " " ); ++ strcat( cmd, FLIBS ); + strcat( cmd, " -lm" ); + } + if( cgdopt ) fprintf( stderr, "cc cmd: %s\n", cmd ); +- nfields = split(cmd,fields," "); ++ nfields = split(cmd, &fields, " "); + status = execute(fields, 0, 1, 2); + if (status != 0) { + fprintf(stderr,"cc failed!\n"); exit (1); + } ++ for (i = 0; i < nfields; i++) { ++ free(fields[i]); ++ } ++ free(fields); ++ free(cmd); + } + +-static int split( char str[], char *fields[], char *fsep ) ++static int split( char str[], char ***fields, char *fsep ) + { +- int nf, flen; ++ int nf, flen, maxnf; + char *sp, *fp, *efp, *nfp; + + if( !str ) + return( 0 ); + ++ maxnf = 10; ++ *fields = (char **) malloc(sizeof(char *) * maxnf); + /* Use fsep of white space is special */ + if( strspn( fsep, " \t\n" ) ){ + for( nf = 0, sp = str; ; ){ + fp = sp + strspn( sp, fsep ); + if( !*fp ) + return( nf ); ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (efp = strpbrk( fp, fsep )) ){ + if( !( flen = efp - fp ) ) + return( nf ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, fp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; ++ (*fields)[ nf ] = nfp; + sp = efp; +- fields[++nf] = NULL; ++ (*fields)[++nf] = NULL; + }else{ + flen = strlen( fp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, fp ); +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + return( nf ); + } + } + }else{ + for( nf = 0, sp = str; ; ){ ++ if (nf + 1 > maxnf) { ++ maxnf += 10; ++ *fields = (char **) realloc(*fields, sizeof(char *) * maxnf); ++ } + if( (fp = strchr( sp, *fsep )) ){ + flen = fp - sp; + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strncpy( nfp, sp, flen ); + nfp[ flen ] = '\0'; +- fields[ nf ] = nfp; +- fields[++nf]=NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf]=NULL; + sp = fp + 1; + }else{ + flen = strlen( sp ); + nfp = (char *)malloc( (flen + 1) * sizeof(char) ); + strcpy( nfp, sp ); +- fields[ nf ] = nfp; +- fields[++nf] = NULL; ++ (*fields)[ nf ] = nfp; ++ (*fields)[++nf] = NULL; + return( nf ); + } + } +diff -ru amber16.orig/AmberTools/src/rism/Makefile amber16/AmberTools/src/rism/Makefile +--- amber16.orig/AmberTools/src/rism/Makefile 2018-04-03 21:52:52.811347758 +0200 ++++ amber16/AmberTools/src/rism/Makefile 2018-04-03 21:51:47.999962945 +0200 +@@ -92,7 +92,7 @@ + # ------ Single-Point information ------------------------------------------ + SPSRC=rism3d.snglpnt.nab + rism3d.snglpnt$(SFX): $(SPSRC) +- $(BINDIR)/nab $(SPSRC) -lfftw3 -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) ++ $(BINDIR)/nab $(SPSRC) $(FLIBS_FFTW3) -o $(BINDIR)/rism3d.snglpnt$(SFX) $(CUSTOMBUILDFLAGS) + rism3d.snglpnt.MPI$(SFX): $(SPSRC) + $(BINDIR)/mpinab -v $(SPSRC) -o $(BINDIR)/rism3d.snglpnt.MPI$(SFX) $(CUSTOMBUILDFLAGS) + # -------------------------------------------------------------------------- +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2018-04-03 20:55:27.031610543 +0200 ++++ amber16/AmberTools/src/configure2 2018-04-03 21:38:41.383450159 +0200 +@@ -920,83 +920,6 @@ + if [ "$noX11" = "true" ]; then + make_xleap="skip_xleap" + xhome='' +-else +- if [ -d /usr/X11R6/lib ]; then +- xhome='/usr/X11R6' +- elif [ -d /usr/X11/lib ]; then # location for MacOSX 10.11 +- xhome='/usr/X11' +- elif [ -d /usr/lib/x86_64-linux-gnu ]; then +- xhome='/usr' +- elif [ -f /usr/lib/i386-linux-gnu/libX11.a ]; then +- xhome='/usr' +- elif [ -f /usr/lib/libX11.a -o -f /usr/lib/libX11.so \ +- -o -f /usr/lib/libX11.dll.a \ +- -o -f /usr/lib64/libX11.a -o -f /usr/lib64/libX11.so ]; then +- xhome='/usr' +- elif [ -f /opt/local/lib/libX11.a -o -f /opt/local/lib/libX11.dylib ]; then +- xhome='/opt/local' +- else +- echo "Could not find the X11 libraries; you may need to edit config.h" +- echo " to set the XHOME and XLIBS variables." +- fi +- +- if [ "$xhome" != "/usr" ]; then +- # Do not add -L/usr/lib to linker. This is always in the standard path +- # and could cause issues trying to build MPI when /usr has an MPI +- # installed that you *don't* want to use. +- xlibs="-L$xhome/lib" +- if [ "$x86_64" = 'yes' ]; then +- xlibs="-L$xhome/lib64 $xlibs" +- fi +- fi +- if [ -d /usr/lib/x86_64-linux-gnu ]; then +- xlibs="-L/usr/lib/x86_64-linux-gnu $xlibs" +- fi +-fi +-#-------------------------------------------------------------------------- +-# Check if the X11 library files for XLEaP are present: +-#-------------------------------------------------------------------------- +-if [ "$noX11" = "false" ]; then +- if [ -r "$xhome/lib/libXt.a" -o -r "$xhome/lib/libXt.dll.a" \ +- -o -r "$xhome/lib/libXt.dylib" \ +- -o -r /usr/lib/x86_64-linux-gnu/libXt.a \ +- -o -r /usr/lib/x86_64-linux-gnu/libXt.so \ +- -o -r /usr/lib/i386-linux-gnu/libXt.a \ +- -o -r /usr/lib/i386-linux-gnu/libXt.so \ +- -o -r /usr/lib/libXt.so \ +- -o -r /usr/lib64/libXt.so \ +- -o -r /usr/X11/lib/libXt.dylib \ +- -o "$x86_64" = 'yes' -a -r "$xhome/lib64/libXt.a" ] +- then +- empty_statement= +- else +- echo "Error: The X11 libraries are not in the usual location !" +- echo " To search for them try the command: locate libXt" +- echo " On new Fedora OS's install the libXt-devel libXext-devel" +- echo " libX11-devel libICE-devel libSM-devel packages." +- echo " On old Fedora OS's install the xorg-x11-devel package." +- echo " On RedHat OS's install the XFree86-devel package." +- echo " On Ubuntu OS's install the xorg-dev and xserver-xorg packages." +- echo +- echo " ...more info for various linuxes at ambermd.org/ubuntu.html" +- echo +- echo " To build Amber without XLEaP, re-run configure with '-noX11:" +- echo " `mod_command_args '' '-noX11'`" +- exit 1 +- fi +- +- if [ -d /usr/include/X11/extensions -o $is_mac = "yes" ] +- then +- empty_statement= +- elif [ "$is_mac" = "no" ]; then +- echo "Error: The X11 extensions headers are not in the usual location!" +- echo " To search for them try the command: locate X11/extensions" +- echo " On new Fedora OSes install libXext-devel" +- echo " On RedHat OSes install libXext-devel" +- echo " To build Amber without XLEaP, re-run configure with '-noX11:" +- echo " `mod_command_args '' '-noX11'`" +- exit 1 +- fi + fi + + #------------------------------------------------------------------------------ +diff -ru amber16.orig/AmberTools/src/cpptraj/configure amber16/AmberTools/src/cpptraj/configure +--- amber16.orig/AmberTools/src/cpptraj/configure 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/cpptraj/configure 2018-12-16 09:13:28.413318032 +0100 +@@ -523,10 +523,10 @@ + XDRFILE=$XDRFILE_TARGET + NETCDFLIB="-lnetcdf" + PNETCDFLIB="" +-BZLIB="-lbz2" +-ZLIB="-lz" +-BLAS="-lblas" +-LAPACK="-llapack" ++BZLIB="-L$EBROOTBZIP2/lib -lbz2" ++ZLIB="-L$EBROOTZLIB/lib -lz" ++BLAS="$LIBBLAS" ++LAPACK="$LIBLAPACK" + ARPACK="-larpack" + FFT_LIB="pub_fft.o" + FFT_LIBDIR="" +@@ -960,13 +960,13 @@ + if [[ $STATIC -eq 2 ]] ; then + # Static linking for specified libraries + if [[ ! -z $BLAS_HOME && ! -z $BLAS ]] ; then +- BLAS="$BLAS_HOME/lib/libblas.a" ++ BLAS="$LIBBLAS" + fi + if [[ ! -z $ARPACK_HOME && ! -z $ARPACK ]] ; then + ARPACK="$ARPACK_HOME/lib/libarpack.a" + fi + if [[ ! -z $LAPACK_HOME && ! -z $LAPACK ]] ; then +- LAPACK="$LAPACK_HOME/lib/liblapack.a" ++ LAPACK="$LIBLAPACK" + fi + if [[ ! -z $NETCDF_HOME && ! -z $NETCDFLIB ]] ; then + NETCDFLIB="$NETCDF_HOME/lib/libnetcdf.a" +diff -ru amber16.orig/AmberTools/src/configure2 amber16/AmberTools/src/configure2 +--- amber16.orig/AmberTools/src/configure2 2017-04-13 15:00:53.000000000 +0200 ++++ amber16/AmberTools/src/configure2 2018-10-06 19:30:27.186868451 +0200 +@@ -3765,7 +3765,7 @@ + PMEMD_FOPTFLAGS=$pmemd_foptflags \$(AMBERBUILDFLAGS) + PMEMD_CC=$cc + PMEMD_COPTFLAGS=$pmemd_coptflags $mpi_flag \$(AMBERBUILDFLAGS) +-PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib ++PMEMD_FLIBSF=$flibs_mkl $win_mpilibs $emillib $flibs_fftw3 + PMEMD_LD=$ld \$(AMBERBUILDFLAGS) + LDOUT=$ldout + PMEMD_GNU_BUG303=$pmemd_gnu_bug303 From dca73e2fe26338b1a920d495e1d9cf8345431041 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Oct 2020 16:40:42 +0200 Subject: [PATCH 571/698] disable EGL in libepoxy-1.5.2-foss-2018a.eb --- .../l/libepoxy/libepoxy-1.5.2-foss-2018a.eb | 25 ++++++++++--------- .../m/Mesa/Mesa-17.3.6-foss-2018a.eb | 4 +-- 2 files changed, 15 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb index 0db3afaae7b..c7cce4c804b 100644 --- a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.2-foss-2018a.eb @@ -1,33 +1,34 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'libepoxy' version = '1.5.2' -homepage = 'http://www.linuxfromscratch.org/blfs/view/svn/x/libepoxy.html' -description = "libepoxy is a library for handling OpenGL function pointer management." +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['https://github.com/anholt/libepoxy/archive/'] -sources = ['%(version)s.tar.gz'] -checksums = ['1ffc3ffe0567f986ff5731d4ef3a3765e0a4f9d642fffdae303362567eecd689'] +source_urls = ['https://github.com/anholt/%(name)s/releases/download/%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['a9562386519eb3fd7f03209f279f697a8cba520d3c155d6e253c3e138beca7d8'] builddependencies = [ + ('Meson', '0.46.1', '-Python-3.6.4'), + ('Ninja', '1.8.2'), ('pkg-config', '0.29.2'), ] dependencies = [ + ('X11', '20180131'), ('Mesa', '17.3.6'), - ('Python', '2.7.14'), ] -preconfigopts = "./autogen.sh && " +configopts = '-Degl=no --libdir %(installdir)s/lib ' sanity_check_paths = { - 'files': [ - 'include/epoxy/egl.h', 'include/epoxy/gl.h', 'include/epoxy/glx.h', - 'lib/libepoxy.la', 'lib/libepoxy.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib'], + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] } moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb index 3929d56fe31..b1f749dd7d9 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-17.3.6-foss-2018a.eb @@ -53,8 +53,8 @@ dependencies = [ ] # GLU is not part anymore of Mesa package! -configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --enable-dri" -configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --enable-egl" +configopts = " --disable-osmesa --enable-gallium-osmesa --enable-gallium-llvm --enable-glx --disable-dri" +configopts += " --disable-gbm --disable-driglx-direct --with-gallium-drivers='swrast,swr' --disable-egl" configopts += " --with-osmesa-bits=32 --enable-texture-float --enable-llvm-shared-libs " buildopts = 'V=1' From 6b4244f3690e935cdc83918d3067875fcabd19d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Oct 2020 17:11:33 +0200 Subject: [PATCH 572/698] No longer require suffix for python > 3.8.6 --- test/easyconfigs/easyconfigs.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 18504d4490e..550405706ee 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -611,11 +611,13 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): # if Python is a dependency, that should be reflected in the versionsuffix # Tkinter is an exception, since its version always matches the Python version anyway + # Python 3.8.6 and later are also excluded, as we consider python 3 the default python # Also whitelist some updated versions of Amber whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies']) + has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] + if LooseVersion(dep['version']) < LooseVersion('3.8.6')) if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn @@ -625,6 +627,12 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): failing_checks.append(msg) else: print('\nNote: Failed non-critical check: ' + msg) + else: + has_recent_python3_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] + if LooseVersion(dep['version']) >= LooseVersion('3.8.6')) + if re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn + failing_checks.append(msg) # require that running of "pip check" during sanity check is enabled via sanity_pip_check if use_pip and easyblock in ['PythonBundle', 'PythonPackage']: From c127ab689bd0107df788585332ca7886528982bc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Oct 2020 17:31:26 +0200 Subject: [PATCH 573/698] adding easyconfigs: ExifTool-12.00-GCCcore-9.3.0.eb --- .../ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb b/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..a80b6ffead2 --- /dev/null +++ b/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PerlModule' + +name = 'ExifTool' +version = '12.00' + +homepage = 'https://owl.phy.queensu.ca/~phil/exiftool/' +description = """Perl module (Image::ExifTool) and program (exiftool) +to read EXIF information from images""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL'] +sources = ['Image-%(name)s-%(version)s.tar.gz'] +checksums = ['d0792cc94ab58a8b3d81b18ccdb8b43848c8fb901b5b7caecdcb68689c6c855a'] + +dependencies = [ + ('Perl', '5.30.2') +] + +options = {'modulename': 'Image::ExifTool'} + +sanity_check_paths = { + 'files': ['bin/exiftool'], + 'dirs': ['lib/perl5/site_perl'], +} + +moduleclass = 'tools' From 9ecb57ae1ceda4a8572677c60b20c08d04efc9ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 17:35:36 +0200 Subject: [PATCH 574/698] stick to official software names for FabIO, Qtconsole, PyOpenCL --- .../FabIO-0.10.2-foss-2019b-Python-3.7.4.eb} | 6 +++--- .../FabIO-0.10.2-fosscuda-2019b-Python-3.7.4.eb} | 6 +++--- .../PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb} | 4 ++-- .../q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb | 2 -- .../Qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb} | 6 +++--- .../Qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb} | 6 +++--- .../s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb | 7 ++----- .../s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb | 9 +++------ 8 files changed, 19 insertions(+), 27 deletions(-) rename easybuild/easyconfigs/f/{fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb => FabIO/FabIO-0.10.2-foss-2019b-Python-3.7.4.eb} (91%) rename easybuild/easyconfigs/f/{fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb => FabIO/FabIO-0.10.2-fosscuda-2019b-Python-3.7.4.eb} (91%) rename easybuild/easyconfigs/p/{pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb => PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb} (95%) rename easybuild/easyconfigs/q/{qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb => Qtconsole/Qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb} (90%) rename easybuild/easyconfigs/q/{qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb => Qtconsole/Qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb} (91%) diff --git a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-foss-2019b-Python-3.7.4.eb similarity index 91% rename from easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-foss-2019b-Python-3.7.4.eb index bf55196baa4..d86bd9a40ab 100644 --- a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-foss-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'fabio' +name = 'FabIO' version = '0.10.2' versionsuffix = '-Python-%(pyver)s' @@ -12,8 +12,8 @@ for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers a toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['fb4dcd0645cbaabbe1d3db59b729cebd72be9b2e3c410e5cdc3b2aa94cc16713'] dependencies = [ diff --git a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-fosscuda-2019b-Python-3.7.4.eb similarity index 91% rename from easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-fosscuda-2019b-Python-3.7.4.eb index e7f49c15ebb..8a9a72212b3 100644 --- a/easybuild/easyconfigs/f/fabio/fabio-0.10.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/f/FabIO/FabIO-0.10.2-fosscuda-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'fabio' +name = 'FabIO' version = '0.10.2' versionsuffix = '-Python-%(pyver)s' @@ -12,8 +12,8 @@ for a total of 20 different file formats (like CBF, EDF, TIFF, ...) and offers a toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['fb4dcd0645cbaabbe1d3db59b729cebd72be9b2e3c410e5cdc3b2aa94cc16713'] dependencies = [ diff --git a/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb similarity index 95% rename from easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb index 5aeecedd1f5..7d86554ef7a 100644 --- a/easybuild/easyconfigs/p/pyopencl/pyopencl-2020.2.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2020.2.2-fosscuda-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'pyopencl' +name = 'PyOpenCL' version = '2020.2.2' versionsuffix = '-Python-%(pyver)s' @@ -26,7 +26,7 @@ exts_list = [ ('pytools', '2020.4', { 'checksums': ['37db39ff11a1b5fc8aec875ae4ddb3d6c21aa0e95bddc9c841aa98e1631ae460'], }), - (name, version, { + ('pyopencl', version, { 'checksums': ['31fcc79fb6862998e98d91a624c0bd4f0ab4c5d418d199912d4d312c64e437ec'], }), ] diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb index c8520d4ec5f..818ca0cb63a 100644 --- a/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/QtPy/QtPy-1.9.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -16,13 +16,11 @@ checksums = ['2db72c44b55d0fe1407be8fba35c838ad0d6d3bb81f23007886dc1fc0f459c8d'] builddependencies = [('binutils', '2.32')] - dependencies = [ ('Python', '3.7.4'), ('PyQt5', '5.13.2', versionsuffix) ] - use_pip = True download_dep_fail = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb similarity index 90% rename from easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb index 208c734bfd9..9fe99bab044 100644 --- a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-foss-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'qtconsole' +name = 'Qtconsole' version = '4.7.7' versionsuffix = '-Python-%(pyver)s' @@ -12,8 +12,8 @@ such as inline figures, proper multiline editing with syntax highlighting, graph toolchain = {'name': 'foss', 'version': '2019b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'] dependencies = [ diff --git a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb similarity index 91% rename from easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb rename to easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb index af3bb2bba32..1e182d772d1 100644 --- a/easybuild/easyconfigs/q/qtconsole/qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-4.7.7-fosscuda-2019b-Python-3.7.4.eb @@ -1,6 +1,6 @@ easyblock = 'PythonPackage' -name = 'qtconsole' +name = 'Qtconsole' version = '4.7.7' versionsuffix = '-Python-%(pyver)s' @@ -12,8 +12,8 @@ such as inline figures, proper multiline editing with syntax highlighting, graph toolchain = {'name': 'fosscuda', 'version': '2019b'} -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] checksums = ['f236ead8711dba0702507dd8fad473c7216a86eefa6098eff8ec4b54f57d7804'] dependencies = [ diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb index e2df5bc0af4..5495126d2a2 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-foss-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ development of data assessment, reduction and analysis applications at synchrotr toolchain = {'name': 'foss', 'version': '2019b'} - dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), @@ -19,11 +18,10 @@ dependencies = [ ('matplotlib', '3.1.1', versionsuffix), ('Mako', '1.1.0'), ('Pillow', '6.2.1'), - ('fabio', '0.10.2', versionsuffix), - ('qtconsole', '4.7.7', versionsuffix), + ('FabIO', '0.10.2', versionsuffix), + ('Qtconsole', '4.7.7', versionsuffix), ] - use_pip = True sanity_pip_check = True @@ -42,5 +40,4 @@ modextrapaths = { 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', } - moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb index 1405be88c1e..954f9158ed7 100644 --- a/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/s/silx/silx-0.13.2-fosscuda-2019b-Python-3.7.4.eb @@ -10,7 +10,6 @@ development of data assessment, reduction and analysis applications at synchrotr toolchain = {'name': 'fosscuda', 'version': '2019b'} - dependencies = [ ('Python', '3.7.4'), ('SciPy-bundle', '2019.10', versionsuffix), @@ -19,12 +18,11 @@ dependencies = [ ('matplotlib', '3.1.1', versionsuffix), ('Mako', '1.1.0'), ('Pillow', '6.2.1'), - ('fabio', '0.10.2', versionsuffix), - ('qtconsole', '4.7.7', versionsuffix), - ('pyopencl', '2020.2.2', versionsuffix), + ('FabIO', '0.10.2', versionsuffix), + ('Qtconsole', '4.7.7', versionsuffix), + ('PyOpenCL', '2020.2.2', versionsuffix), ] - use_pip = True sanity_pip_check = True @@ -43,5 +41,4 @@ modextrapaths = { 'HDF5_PLUGIN_PATH': 'lib/python%(pyshortver)s/site-packages/hdf5plugin/plugins', } - moduleclass = 'vis' From 2c366013d880f4f4b5bdfb4e9b75089652f6bf87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 18:27:00 +0200 Subject: [PATCH 575/698] remove easyconfig for trimAl using goolf toolchain, since it's deprecated --- .../t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb | 38 ------------------- 1 file changed, 38 deletions(-) delete mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb deleted file mode 100644 index 4d9c1f4619a..00000000000 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-goolf-1.7.20.eb +++ /dev/null @@ -1,38 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics - -easyblock = 'MakeCp' - -name = 'trimAl' -version = '1.4.1' - -homepage = 'http://trimal.cgenomics.org/' -description = 'A tool for automated alignment trimming in large-scale phylogenetic analyses' - -toolchain = {'name': 'goolf', 'version': '1.7.20'} - -source_urls = ['https://github.com/scapella/trimal/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] - -start_dir = 'source' - -buildopts = ' CC=${CXX}' - -files_to_copy = [ - (['trimal', 'statal', 'readal'], 'bin'), - 'AUTHORS', - 'CHANGELOG', - 'dataset', - 'LICENSE', - 'README', -] - -sanity_check_paths = { - 'files': ['bin/trimal', 'bin/statal', 'bin/readal'], - 'dirs': [], -} - -moduleclass = 'bio' From 05c700e7141e650603d1b772ff0547e9842b4aa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Oct 2020 18:36:08 +0200 Subject: [PATCH 576/698] Fix missing conditional check of python3 dep variable, fix style --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 550405706ee..624a11ac118 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -617,7 +617,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] - if LooseVersion(dep['version']) < LooseVersion('3.8.6')) + if LooseVersion(dep['version']) < LooseVersion('3.8.6')) if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): msg = "'-Python-%%(pyver)s' should be included in versionsuffix in %s" % ec_fn @@ -629,8 +629,8 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): print('\nNote: Failed non-critical check: ' + msg) else: has_recent_python3_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] - if LooseVersion(dep['version']) >= LooseVersion('3.8.6')) - if re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + if LooseVersion(dep['version']) >= LooseVersion('3.8.6')) + if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn failing_checks.append(msg) From 034940c789bec036f6b949c0aae600763606f96c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 16 Oct 2020 18:44:16 +0200 Subject: [PATCH 577/698] Fix indentation --- test/easyconfigs/easyconfigs.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 624a11ac118..c099f019d68 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -616,7 +616,7 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): whitelist_python_suffix = ['Amber-16-*-2018b-AmberTools-17-patchlevel-10-15.eb', 'Amber-16-intel-2017b-AmberTools-17-patchlevel-8-12.eb'] whitelisted = any(re.match(regex, ec_fn) for regex in whitelist_python_suffix) - has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] + has_python_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] if LooseVersion(dep['version']) < LooseVersion('3.8.6')) if has_python_dep and ec.name != 'Tkinter' and not whitelisted: if not re.search(r'-Python-[23]\.[0-9]+\.[0-9]+', ec['versionsuffix']): @@ -628,9 +628,9 @@ def check_python_packages(self, changed_ecs, added_ecs_filenames): else: print('\nNote: Failed non-critical check: ' + msg) else: - has_recent_python3_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] - if LooseVersion(dep['version']) >= LooseVersion('3.8.6')) - if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): + has_recent_python3_dep = any(dep['name'] == 'Python' for dep in ec['dependencies'] + if LooseVersion(dep['version']) >= LooseVersion('3.8.6')) + if has_recent_python3_dep and re.search(r'-Python-3\.[0-9]+\.[0-9]+', ec['versionsuffix']): msg = "'-Python-%%(pyver)s' should no longer be included in versionsuffix in %s" % ec_fn failing_checks.append(msg) From acc4379180ebff61342bfd59be9268167248e5c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 18:58:18 +0200 Subject: [PATCH 578/698] ad missing binutils build dep --- .../easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb b/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb index a80b6ffead2..8dff80928e4 100644 --- a/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/e/ExifTool/ExifTool-12.00-GCCcore-9.3.0.eb @@ -13,6 +13,8 @@ source_urls = ['https://cpan.metacpan.org/authors/id/E/EX/EXIFTOOL'] sources = ['Image-%(name)s-%(version)s.tar.gz'] checksums = ['d0792cc94ab58a8b3d81b18ccdb8b43848c8fb901b5b7caecdcb68689c6c855a'] +builddependencies = [('binutils', '2.34')] + dependencies = [ ('Perl', '5.30.2') ] From fbb8b550d2d7f53aa74a228d71313e613e335c7a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 16 Oct 2020 19:13:29 +0200 Subject: [PATCH 579/698] BLAS/LAPACK check GPAW patch doesn't check if BLAS and LAPACK actually exist, so it might trigger a `AttributeError: 'NoneType' object has no attribute 'split'` --- .../GPAW-20.1.0-Add-Easybuild-configuration-files.patch | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch index 21fbe69ea7c..e64b4d0f7da 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-Add-Easybuild-configuration-files.patch @@ -45,8 +45,12 @@ index 0000000..5be60fa + libraries += static_eblibs_to_gpawlibs('SCALAPACK_STATIC_LIBS') + +# Add EasyBuild LAPACK/BLAS libs -+libraries += static_eblibs_to_gpawlibs('LAPACK_STATIC_LIBS') -+libraries += static_eblibs_to_gpawlibs('BLAS_STATIC_LIBS') ++lapack = os.getenv('LAPACK_STATIC_LIBS') ++if lapack: ++ libraries += static_eblibs_to_gpawlibs('LAPACK_STATIC_LIBS') ++blas = os.getenv('BLAS_STATIC_LIBS') ++if blas: ++ libraries += static_eblibs_to_gpawlibs('BLAS_STATIC_LIBS') + +# LibXC: +# Use EasyBuild libxc From 4b8f73a0d85769da32393139af4bb1c6b2b3c6d5 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Oct 2020 18:17:10 +0100 Subject: [PATCH 580/698] Fix typo and update to SYSTEM toolchain --- easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb index fa96b1674a7..6fc57aa795b 100644 --- a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb +++ b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb @@ -1,7 +1,7 @@ easyblock = 'PackedBinary' name = 'ORFfinder' -# The only way to get the version id to download the software and run "ORFfinder -version" command +# The only way to get the version is to download the software and run "ORFfinder -version" command # There is no way to download old versions. version = '0.4.3' @@ -12,7 +12,7 @@ description = """ORF finder searches for open reading frames (ORFs) in the sequenced DNA for potential protein encoding segments, verify predicted protein using newly developed SMART BLAST or regular BLASTP.""" -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] sources = [{'filename': '%(name)s-%(version)s.gz', 'download_filename': '%(name)s.gz'}] From 56dc1a5c88394007dd246e39dc6490b24218980d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Oct 2020 18:22:55 +0100 Subject: [PATCH 581/698] Update checksum --- easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb index 6fc57aa795b..715780a46a3 100644 --- a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb +++ b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb @@ -16,7 +16,7 @@ toolchain = SYSTEM source_urls = ['http://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] sources = [{'filename': '%(name)s-%(version)s.gz', 'download_filename': '%(name)s.gz'}] -checksums = ['eff0347277c960c207e7efdf0e5a08889f072dffd12fa6e5a843f06782ee53a8'] +checksums = ['bb676b56f557128e73f68cc852709d1ff7abd1c750d00fd8322de31820969f3c'] postinstallcmds = [ 'mv %(installdir)s/ORFfinder-%(version)s %(installdir)s/ORFfinder', From ec6dc0c0a549bbca7e8988921d959c632eb38300 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Fri, 16 Oct 2020 19:04:04 +0100 Subject: [PATCH 582/698] Add sanity_pip_check --- .../p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb | 2 ++ .../p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb index 7d12920de21..7d4e1487f16 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-8.3.0-Python-3.7.4.eb @@ -34,4 +34,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb index db4f5313e1c..0b8b5f96536 100644 --- a/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/pyEGA3/pyEGA3-3.4.0-GCCcore-9.3.0-Python-3.8.2.eb @@ -34,4 +34,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'bio' From 8b68fd5980516dfa8a2866952704339eabc32a55 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 20:29:55 +0200 Subject: [PATCH 583/698] add easyconfig for Ruby v2.5.1 w/ foss/2018a --- .../r/Ruby/Ruby-2.5.1-foss-2018a.eb | 131 ++++++++++++++++++ 1 file changed, 131 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb new file mode 100644 index 00000000000..a793d8e9b80 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb @@ -0,0 +1,131 @@ +name = 'Ruby' +version = '2.5.1' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'foss', 'version': '2018a'} + +source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dac81822325b79c3ba9532b048c2123357d3310b2b40024202f360251d9829b1'] + +exts_default_options = { + 'source_urls': ['http://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +exts_list = [ + ('ffi', '1.9.25', { + 'checksums': ['f854f08f08190fec772a12e863f33761d02ad3efea3c3afcdeffc8a06313f54a'], + }), + ('childprocess', '0.9.0', { + 'checksums': ['17893660db6562970bc2d74dfa7f0bff1d94af62de81438bf49ded3a8548c128'], + }), + ('json', '2.1.0', { + 'checksums': ['b76fd09b881088c6c64a12721a1528f2f747a1c2ee52fab4c1f60db8af946607'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.11.3', { + 'checksums': ['57b04d4e2806c199bff3663d810db25e019cf88c42cacc0edbb36d3038d6a5ab'], + }), + ('arr-pm', '0.0.10', { + 'checksums': ['0fa2d425a84eeeaf8f95268568e826723b41aeefa14511d1f0ed1368c30bdd1f'], + }), + ('clamp', '1.2.1', { + 'checksums': ['cd041aaf6b4dfd2239cdcfe2c72084d0536b1e7630236353a1d00b0a2e15ca68'], + }), + ('multipart-post', '2.0.0', { + 'checksums': ['3dc44e50d3df3d42da2b86272c568fd7b75c928d8af3cc5f9834e2e5d9586026'], + }), + ('faraday', '0.15.2', { + 'checksums': ['affa23f5e5ee27170cbb5045c580af9b396bac525516c6583661c2bb08038f92'], + }), + ('faraday_middleware', '0.12.2', { + 'checksums': ['2d90093c18c23e7f5a6f602ed3114d2c62abc3f7f959dd3046745b24a863f1dc'], + }), + ('highline', '2.0.0', { + 'checksums': ['74524686caf43dd56465ba847bd2c33b552028cf23973c4f1fbb5e5971f93a19'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.2.2', { + 'checksums': ['c8cc9446bcc51034103c1259ad70b91dc9f5297d13460b2c0cce7e5a93e8d451'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.13.1', { + 'checksums': ['db8613c039b9501e6b2fb85efe4feabb02f55c3365bae52bba35381b89c780e6'], + }), + ('public_suffix', '3.0.2', { + 'checksums': ['3a0168c33fa0b00886423a2ceb21c74199273ccd01bc250360fc8d18600bb0f4'], + }), + ('addressable', '2.4.0', { + 'checksums': ['7abfff765571b0a73549c9a9d2f7e143979cd0c252f7fa4c81e7102a973ef656'], + }), + ('gh', '0.15.1', { + 'checksums': ['ef733f81c17846f217f5ad9616105e9adc337775d41de1cc330133ad25708d3c'], + }), + ('launchy', '2.4.3', { + 'checksums': ['42f52ce12c6fe079bac8a804c66522a0eefe176b845a62df829defe0e37214a4'], + }), + ('ethon', '0.11.0', { + 'checksums': ['88ec7960a8e00f76afc96ed15dcc8be0cb515f963fe3bb1d4e0b5c51f9d7e078'], + }), + ('typhoeus', '1.3.0', { + 'checksums': ['d8d315e067ec9764c61727d77786a7a82309b43c3964416ef476ee65ac09ed06'], + }), + ('websocket', '1.2.8', { + 'checksums': ['1d8155c1cdaab8e8e72587a60e08423c9dd84ee44e4e827358ce3d4c2ccb2138'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.3', { + 'checksums': ['ea7bf591567e391ef262a7c29edaf87c6205204afb5bb39dfa8f08f2e51282a3'], + }), + ('rspec-support', '3.7.1', { + 'checksums': ['4152975a068756076f10c97317e9d2baf10028f3d25c0cb902945569560783da'], + }), + ('rspec-mocks', '3.7.0', { + 'checksums': ['23f7f0039e17f2841edfb51d678ac9e06c056903a7908db967f5618887f2022c'], + }), + ('rspec-expectations', '3.7.0', { + 'checksums': ['7e571848a5cbdb1661187d04e5c1f29287ec80fcb5a395f9994836892a3780bb'], + }), + ('rspec-core', '3.7.1', { + 'checksums': ['526e0b2d22feae638eb99bd746bbb25b18a4869a8f6ce4e8a87dabd1ab5f727f'], + }), + ('rspec', '3.7.0', { + 'checksums': ['0174cfbed780e42aa181227af623e2ae37511f20a2fdfec48b54f6cf4d7a6404'], + }), + ('rack', '2.0.5', { + 'checksums': ['81e3ece3d36e7507ff6a05666cc2ff759bdd08a96aefb8c5fd6c309a8f5d1095'], + }), + ('rack-protection', '2.0.3', { + 'checksums': ['b749d4ee16fb8b92ef644571efed7e79fa6162b712095288b395c61b314aa5fc'], + }), + ('tilt', '2.0.8', { + 'checksums': ['2a3be6c56a8cc6338203c02910e20e858664b633adb550e1103804d75eae4000'], + }), + ('mustermann', '1.0.2', { + 'checksums': ['0f4df2d040ed1ef39b8359670cba5baaf77da8370e5be9108158e53c993b4b1f'], + }), + ('sinatra', '2.0.3', { + 'checksums': ['39d5911273c74b516419d5e99c396fa0405b0187a3d003c3d82d92497029d1cf'], + }), + ('rack-test', '1.0.0', { + 'checksums': ['8116a3ee26f2129ec63a8073f74322be0cb1076405bf9737d4198b8c8b4ee9d0'], + }), + ('bundler', '1.16.2', { + 'checksums': ['3bb53e03db0a8008161eb4c816ccd317120d3c415ba6fee6f90bbc7f7eec8690'], + }), +] + +moduleclass = 'lang' From b1d04d23707c83ac559f40e77803a9d437c4c544 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Fri, 16 Oct 2020 19:30:22 +0000 Subject: [PATCH 584/698] adding builddeps for CMake --- easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb index 5c109893599..2764e7bb0a6 100644 --- a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb @@ -19,7 +19,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/USCiLab/cereal/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['329ea3e3130b026c03a4acc50e168e7daff4e6e661bc6a7dfec0d77b570851d5'] - +builddeps = [('CMake', '3.12.1')] configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' sanity_check_paths = { From 08a837aeee12623774d660be830b581a6b8c9bb1 Mon Sep 17 00:00:00 2001 From: Maxime Boissonneault Date: Fri, 16 Oct 2020 19:55:24 +0000 Subject: [PATCH 585/698] fixed incorrect variable name for CMake --- easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb index 2764e7bb0a6..c814663868c 100644 --- a/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb +++ b/easybuild/easyconfigs/c/Cereal/Cereal-1.3.0.eb @@ -19,7 +19,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/USCiLab/cereal/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['329ea3e3130b026c03a4acc50e168e7daff4e6e661bc6a7dfec0d77b570851d5'] -builddeps = [('CMake', '3.12.1')] +builddependencies = [('CMake', '3.12.1')] configopts = '-DJUST_INSTALL_CEREAL=ON -DSKIP_PERFORMANCE_COMPARISON=ON ' sanity_check_paths = { From 429d7ae8a5bc9861e364e835a2f7be06437e93d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 16 Oct 2020 22:13:30 +0200 Subject: [PATCH 586/698] clean up easyconfigs for FRUIT and FRUIT_processor --- ...b => FRUIT-3.4.3-foss-2018a-Ruby-2.5.1.eb} | 20 ++++++++-------- .../FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb | 23 ++++++++++--------- .../f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch | 2 ++ ..._processor-3.4.3-foss-2018a-Ruby-2.5.1.eb} | 18 +++++---------- ..._processor-3.4.3-intel-2018a-Ruby-2.5.1.eb | 18 +++++---------- ...=> Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.1.eb} | 6 ++--- .../Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb | 6 ++--- 7 files changed, 41 insertions(+), 52 deletions(-) rename easybuild/easyconfigs/f/FRUIT/{FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb => FRUIT-3.4.3-foss-2018a-Ruby-2.5.1.eb} (63%) rename easybuild/easyconfigs/f/FRUIT_processor/{FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb => FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.1.eb} (56%) rename easybuild/easyconfigs/r/Ruby-Tk/{Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb => Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.1.eb} (87%) diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.1.eb similarity index 63% rename from easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb rename to easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.1.eb index d72c08bb902..c98ea9f7530 100644 --- a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.0.eb +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-foss-2018a-Ruby-2.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'ConfigureMake' +easyblock = 'Binary' name = 'FRUIT' version = '3.4.3' -rubyver = '2.5.0' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://fortranxunit.sourceforge.io' description = "FORTRAN Unit Test Framework (FRUIT)" @@ -19,25 +19,23 @@ patches = [ ] checksums = [ '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip - '72f94f3238a8c9d2155147aa19381d745cf533a0f3399484e979b06771217b7b', # fruit_3.4.3-gfortran-fPIC.patch + '65c846156435a51b0b395b614fc636be8920879775ef40a9ca4fbfbe666142f5', # fruit_3.4.3-gfortran-fPIC.patch '6660820c26f647fecd397135d12c61b6ea7b3b2f1d2d7684455036ebc5ead0a4', # fruit_3.4.3-mpi-tests.patch ] builddependencies = [ - ('Ruby', rubyver), + ('Ruby', local_rubyver), ('FRUIT_processor', version, versionsuffix), ] -skipsteps = ['configure'] +extract_sources = True -prebuildopts = 'rake || ' - -preinstallopts = 'mkdir -p %(installdir)s/include && cp src/*.mod %(installdir)s/include && ' -preinstallopts += 'mkdir -p %(installdir)s/lib && cp src/*.a %(installdir)s/lib || ' +install_cmd = "rake && mkdir -p %(installdir)s/{include,lib} && " +install_cmd += "cp src/*.mod %(installdir)s/include/ && cp src/*.a %(installdir)s/lib/" sanity_check_paths = { 'files': ['include/fruit.mod', 'include/fruit_util.mod', 'lib/libfruit.a'], - 'dirs': ['include', 'lib'], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb index fb3ee63850c..9f621dcc011 100644 --- a/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/f/FRUIT/FRUIT-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'ConfigureMake' +easyblock = 'Binary' name = 'FRUIT' version = '3.4.3' -rubyver = '2.5.1' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://fortranxunit.sourceforge.io' description = "FORTRAN Unit Test Framework (FRUIT)" @@ -13,7 +13,10 @@ toolchain = {'name': 'intel', 'version': '2018a'} source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(version)s'] sources = ['fruit_%(version)s.zip'] -patches = ['fruit_%(version)s-ifort-external.patch', 'fruit_%(version)s-mpi-tests.patch'] +patches = [ + 'fruit_%(version)s-ifort-external.patch', + 'fruit_%(version)s-mpi-tests.patch', +] checksums = [ '01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862', # fruit_3.4.3.zip '6f608988078d079ef73f30f47208d2b7d5645b6fc55526790b826f82f8d85b85', # fruit_3.4.3-ifort-external.patch @@ -21,20 +24,18 @@ checksums = [ ] builddependencies = [ - ('Ruby', rubyver), + ('Ruby', local_rubyver), ('FRUIT_processor', version, versionsuffix), ] -skipsteps = ['configure'] - -prebuildopts = 'rake || ' +extract_sources = True -preinstallopts = 'mkdir -p %(installdir)s/include && cp src/*.mod %(installdir)s/include && ' -preinstallopts += 'mkdir -p %(installdir)s/lib && cp src/*.a %(installdir)s/lib || ' +install_cmd = "rake && mkdir -p %(installdir)s/{include,lib} && " +install_cmd += "cp src/*.mod %(installdir)s/include/ && cp src/*.a %(installdir)s/lib/" sanity_check_paths = { 'files': ['include/fruit.mod', 'include/fruit_util.mod', 'lib/libfruit.a'], - 'dirs': ['include', 'lib'], + 'dirs': [], } moduleclass = 'devel' diff --git a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch index 3d5139b51f2..d7be9d171f7 100644 --- a/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch +++ b/easybuild/easyconfigs/f/FRUIT/fruit_3.4.3-gfortran-fPIC.patch @@ -1,3 +1,5 @@ +# build with -fPIC +# S.D. Pinches diff -Nru fruit_3.4.3-orig/rake_base.rb fruit_3.4.3/rake_base.rb --- fruit_3.4.3-orig/rake_base.rb 2017-09-18 10:59:23.000000000 +0200 +++ fruit_3.4.3/rake_base.rb 2019-03-13 16:12:19.000000000 +0100 diff --git a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.1.eb similarity index 56% rename from easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb rename to easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.1.eb index d27f9fbda09..657473cb4fd 100644 --- a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.0.eb +++ b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-foss-2018a-Ruby-2.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'ConfigureMake' +easyblock = 'RubyGem' name = 'FRUIT_processor' version = '3.4.3' -rubyver = '2.5.0' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://fortranxunit.sourceforge.io' description = "FORTRAN Unit Test Framework (FRUIT)" @@ -16,17 +16,11 @@ source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(vers sources = ['fruit_%(version)s.zip'] checksums = ['01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862'] -builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix, toolchain)] +builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix)] -dependencies = [('Ruby', rubyver)] +dependencies = [('Ruby', local_rubyver)] -skipsteps = ['configure', 'build'] - -preinstallopts = 'GEM_HOME=%(installdir)s ' -preinstallopts += 'gem install --bindir %(installdir)s/bin --local ' -preinstallopts += '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem ||' - -modextrapaths = {'GEM_PATH': ''} +gem_file = '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem' sanity_check_paths = { 'files': ['gems/%(namelower)s-%(version)s/lib/%(namelower)s.rb'], diff --git a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb index e17932740e6..e5c6e756470 100644 --- a/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/f/FRUIT_processor/FRUIT_processor-3.4.3-intel-2018a-Ruby-2.5.1.eb @@ -1,10 +1,10 @@ -easyblock = 'ConfigureMake' +easyblock = 'RubyGem' name = 'FRUIT_processor' version = '3.4.3' -rubyver = '2.5.1' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://fortranxunit.sourceforge.io' description = "FORTRAN Unit Test Framework (FRUIT)" @@ -16,17 +16,11 @@ source_urls = ['https://sourceforge.net/projects/fortranxunit/files/fruit_%(vers sources = ['fruit_%(version)s.zip'] checksums = ['01c88d0b8046d809ab317c7b7e4a87ec343fe1c065d408029d83342808929862'] -builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix, toolchain)] +builddependencies = [('Ruby-Tk', '0.2.0', versionsuffix)] -dependencies = [('Ruby', rubyver)] +dependencies = [('Ruby', local_rubyver)] -skipsteps = ['configure', 'build'] - -preinstallopts = 'GEM_HOME=%(installdir)s ' -preinstallopts += 'gem install --bindir %(installdir)s/bin --local ' -preinstallopts += '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem ||' - -modextrapaths = {'GEM_PATH': ''} +gem_file = '%(namelower)s_gem/pkg/%(namelower)s-%(version)s.gem' sanity_check_paths = { 'files': ['gems/%(namelower)s-%(version)s/lib/%(namelower)s.rb'], diff --git a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.1.eb similarity index 87% rename from easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb rename to easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.1.eb index fb1d6461252..92de8031af5 100644 --- a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.0.eb +++ b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-foss-2018a-Ruby-2.5.1.eb @@ -3,8 +3,8 @@ easyblock = 'RubyGem' name = 'Ruby-Tk' version = '0.2.0' -rubyver = '2.5.0' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://github.com/ruby/tk' description = "Ruby Tk interface module using tcltklib" @@ -16,7 +16,7 @@ sources = ['tk-%(version)s.gem'] checksums = ['0d324ae915c20020bea946b1d0b0b35244f16fd2dacc35cf9647b9ac1ea1fc3f'] dependencies = [ - ('Ruby', rubyver), + ('Ruby', local_rubyver), ('Tk', '8.6.8'), ] diff --git a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb index b0f9098d833..627047d9c7f 100644 --- a/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb +++ b/easybuild/easyconfigs/r/Ruby-Tk/Ruby-Tk-0.2.0-intel-2018a-Ruby-2.5.1.eb @@ -3,8 +3,8 @@ easyblock = 'RubyGem' name = 'Ruby-Tk' version = '0.2.0' -rubyver = '2.5.1' -versionsuffix = '-Ruby-%s' % rubyver +local_rubyver = '2.5.1' +versionsuffix = '-Ruby-%s' % local_rubyver homepage = 'https://github.com/ruby/tk' description = "Ruby Tk interface module using tcltklib" @@ -16,7 +16,7 @@ sources = ['tk-%(version)s.gem'] checksums = ['0d324ae915c20020bea946b1d0b0b35244f16fd2dacc35cf9647b9ac1ea1fc3f'] dependencies = [ - ('Ruby', rubyver), + ('Ruby', local_rubyver), ('Tk', '8.6.8'), ] From 2f0b6aec082a1804e4b094f3537ac3a2cf59cd97 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 00:40:09 +0200 Subject: [PATCH 587/698] convert Bsoft-2.0.2-foss-2017b.eb to bundle including build of LibTIFF --- .../b/Bsoft/Bsoft-2.0.2-foss-2017b.eb | 78 +++++++---- .../b/Bsoft/Bsoft-2.0.2_use-eb-packages.patch | 128 ++++++++++++++++++ 2 files changed, 177 insertions(+), 29 deletions(-) create mode 100644 easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2_use-eb-packages.patch diff --git a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb index 3a4495306e2..0c8b7262f8d 100644 --- a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb +++ b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2-foss-2017b.eb @@ -1,11 +1,12 @@ # Authors: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu -easyblock = 'ConfigureMake' +easyblock = 'Bundle' name = 'Bsoft' version = '2.0.2' +local_libtiff_version = '4.0.9' -homepage = 'http://lsbr.niams.nih.gov/bsoft/' +homepage = 'https://lsbr.niams.nih.gov/bsoft/' description = """ Bsoft is a collection of programs and a platform for development of software @@ -17,44 +18,63 @@ description = """ """ toolchain = {'name': 'foss', 'version': '2017b'} -toolchainopts = {'openmp': True} - -# https://lsbr.niams.nih.gov/bsoft/bsoft2_0_2.tgz -source_urls = ['http://lsbr.niams.nih.gov/bsoft/'] -sources = ['%%(namelower)s%s.tgz' % '_'.join(version.split('.'))] +toolchainopts = {'openmp': True, 'pic': True} dependencies = [ - # ('FFTW', '3.3.6'), # FFTW is included in foss/2017b toolchain - ('libjpeg-turbo', '1.5.3'), + ('libjpeg-turbo', '1.5.2'), ('libpng', '1.6.34'), - ('LibTIFF', '4.0.9'), + ('LibTIFF', local_libtiff_version), ('libxml2', '2.9.8'), - ('Tk', '8.6.8') + ('Tk', '8.6.8'), ] -skipsteps = ['configure'] - -prebuildopts = """ - # fix libxml2 include path - sed -e 's,^XMLINC=.*,XMLINC=$EBROOTLIBXML2/include/libxml2,'\ - -i.eb.xmlinc bsoft/bsoft_conf - # fix fftw3 include path - sed -e 's,LIBFFTW/api,LIBFFTW/include,'\ - -i.eb.fftw3inc bsoft/bsoft_conf - # configure - ./bconf --prefix=%(installdir)s --fftw=$EBROOTFFTW --tiff=$EBROOTLIBTIFF\ - --jpeg=$EBROOTLIBJPEGMINTURBO --png=$EBROOTLIBPNG -""" +parallel = 1 + +# Use packages from EB +local_bsoft_configopts = "--fftw=$EBROOTFFTW --jpeg=$EBROOTLIBJPEGMINTURBO --png=$EBROOTLIBPNG" +# Use libraries from LibTIFF already installed in EB +local_bsoft_configopts += " --tiff=$EBROOTLIBTIFF" -# try parallel (EB default) build first then fall back to sequential -buildopts = 'bsoft || make bsoft' +components = [ + # Bsoft needs headers from LibTIFF only available in its source code + ('LibTIFF', local_libtiff_version, { + 'easyblock': 'ConfigureMake', + 'source_urls': ['https://download.osgeo.org/libtiff/'], + 'sources': ['tiff-%s.tar.gz' % local_libtiff_version], + 'checksums': ['6e7bdeec2c310734e734d19aae3a71ebe37a4d842e0e23dbb1b8921c0026cfcd'], + 'start_dir': 'tiff-%s' % local_libtiff_version, + 'configopts': '--enable-ld-version-script', + # skip installation: Bsoft only needs LibTIFF headers at build time and + # those headers are never installed in any case + 'install_cmd': 'true', + }), + (name, version, { + 'easyblock': 'ConfigureMake', + 'source_urls': ['https://lsbr.niams.nih.gov/bsoft/'], + 'sources': ['%%(namelower)s%s.tgz' % '_'.join(version.split('.'))], + 'patches': ['Bsoft-2.0.2_use-eb-packages.patch'], + 'checksums': [ + '1be2e0fcbc61345b488fc6471b73699db57e5b5e6959683582ea6f1b030f1906', # bsoft2_0_2.tgz + 'dfe4e0a68d1b6984edefb32e443f7bc42ae5e520a80a58c3a5b3aa1d9c4b80cb', # Bsoft-2.0.2_use-eb-packages.patch + ], + 'preconfigopts': 'EBBUILDLIBTIFF=%%(builddir)s/tiff-%s' % local_libtiff_version, # use headers in local LibTIFF + 'configure_cmd': './bconf', + 'configopts': local_bsoft_configopts, + 'buildopts': '%(namelower)s', + }), +] + +# Emulate Scripts/postinstall +postinstallcmds = ["cd %%(installdir)s/bin && ln -sf ../tcltk/%s" % x for x in ['bshow', 'bshowX', 'brun', 'brunX']] sanity_check_paths = { - 'files': ['bsoft.bashrc', 'bsetup', 'bin/brun', 'bin/bshow', - 'lib/libbsoft.so', 'lib/libbshow.so'], - 'dirs': [], + 'files': ['bsoft.bashrc', 'bsetup', 'bin/bshell', 'bin/brun', 'bin/brunX', 'bin/bshow', 'bin/bshowX', + 'lib/libbsoft.%s' % SHLIB_EXT, 'lib/libbshow.%s' % SHLIB_EXT], + 'dirs': ['doc', 'parameters', 'tcltk'], } +sanity_check_commands = ["bshell -verb 1 -ico 480,4 -comp 30"] + modextrapaths = { 'BSOFT': '', 'BPARAM': 'parameters', diff --git a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2_use-eb-packages.patch b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2_use-eb-packages.patch new file mode 100644 index 00000000000..38a561b18d5 --- /dev/null +++ b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.2_use-eb-packages.patch @@ -0,0 +1,128 @@ +Adapt configuration scripts of Bsoft to EasyBuild environment +author: Alex Domingo (Vrije Universiteit Brussel) +--- dev.rsc.orig 2018-07-02 20:53:40.000000000 +0200 ++++ dev.rsc 2020-10-16 22:11:09.874568000 +0200 +@@ -38,24 +38,24 @@ + HAVE_FFTW=0 + HAVE_XML=0 + +- if [ -e $LIBFFTW/api/fftw3.h ]; then ++ if [ -e $LIBFFTW/include/fftw3.h ]; then + echo "# FFTW3 found" + HAVE_FFTW=1 + else + echo "# No FFTW3 libraries found!" +- echo "# Looking for: $LIBFFTW/api/fftw3.h" ++ echo "# Looking for: $LIBFFTW/include/fftw3.h" + fi + +- if [ -e $SDK/usr/include/libxml2 ]; then ++ if [ -e $EBROOTLIBXML2/include/libxml2 ]; then + echo "# libxml2 found" + HAVE_XML=1 +- x=`grep -A 3 xmlStrPrintf $SDK/usr/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` ++ x=`grep -A 3 xmlStrPrintf $EBROOTLIBXML2/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` + if [[ $x =~ xmlChar ]]; then + HAVE_XML=2 + fi + else + echo "# No XML library found!" +- echo "# Looking for: $SDK/usr/include/libxml2" ++ echo "# Looking for: $EBROOTLIBXML2/include/libxml2" + fi + + # Optional +@@ -71,13 +71,13 @@ + TCLINC=$TCL/Headers + TKINC=$TK/Headers + elif [[ $SYS =~ Linux ]]; then +- TCL=/usr +- TK=/usr ++ TCL=$EBROOTTCL ++ TK=$EBROOTTK + TCLINC=$TCL/include + TKINC=$TK/include +- if [ -e /usr/include/tk ]; then +- TCLINC=/usr/include/tcl +- TKINC=/usr/include/tk ++ if [ -e $EBROOTTK/include/tk ]; then ++ TCLINC=$EBROOTTCL/include/tcl ++ TKINC=$EBROOTTK/include/tk + fi + fi + +@@ -90,28 +90,28 @@ + TKO="" + fi + +- if [ -e $LIBTIFF/libtiff/tiff.h ]; then ++ if [ -e $EBBUILDLIBTIFF/libtiff/tiff.h ]; then + echo "# libtiff found" + HAVE_TIFF=1 + else + echo "# No TIFF library found! TIFF files will not be supported!" +- echo "# Looking for: $LIBTIFF/libtiff/tiff.h" ++ echo "# Looking for: $EBBUILDLIBTIFF/libtiff/tiff.h" + fi + +- if [ -e $LIBPNG/png.h ]; then ++ if [ -e $LIBPNG/include/png.h ]; then + echo "# libpng found" + HAVE_PNG=1 + else + echo "# No PNG library found! PNG files will not be supported!" +- echo "# Looking for: $LIBPNG/png.h" ++ echo "# Looking for: $LIBPNG/include/png.h" + fi + +- if [ -e $LIBJPEG/jpeglib.h ]; then ++ if [ -e $LIBJPEG/include/jpeglib.h ]; then + echo "# libjpeg found" + HAVE_JPEG=1 + else + echo "# No JPEG library found! JPEG files will not be supported!" +- echo "# Looking for: $LIBJPEG/jpeglib.h" ++ echo "# Looking for: $LIBJPEG/include/jpeglib.h" + fi + + } +--- bsoft/bsoft_conf.orig 2018-07-03 16:38:51.000000000 +0200 ++++ bsoft/bsoft_conf 2020-10-16 23:24:24.158389000 +0200 +@@ -129,7 +129,7 @@ + LIBLIST="" + + +-XMLINC=$SDK/usr/include/libxml2 ++XMLINC=$EBROOTLIBXML2/include/libxml2 + if [ -e $XMLINC ]; then + CFLAGS=$CFLAGS' -DHAVE_XML' + if [ $HAVE_XML == 2 ]; then +@@ -163,7 +163,7 @@ + + if [ $HAVE_TIFF = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_TIFF" +- INCLUDES="$INCLUDES -I$LIBTIFF/libtiff" ++ INCLUDES="$INCLUDES -I$EBBUILDLIBTIFF/libtiff" + # LIBDIR="$LIBDIR -L$LIBTIFF/lib" + # LINKLIBS="$LINKLIBS -ltiff"; + LIBLIST="$LIBLIST $LIBTIFF/lib/libtiff.a" +@@ -171,8 +171,8 @@ + + if [ $HAVE_PNG = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_PNG" +- INCLUDES="$INCLUDES -I$LIBPNG" +-# LIBDIR="$LIBDIR -L$LIBPNG/lib" ++ INCLUDES="$INCLUDES -I$LIBPNG/include" ++ LIBDIR="$LIBDIR -L$EBROOTZLIB/lib" + # LINKLIBS="$LINKLIBS -lz -lpng"; + LINKLIBS="$LINKLIBS -lz"; + LIBLIST="$LIBLIST $LIBPNG/lib/libpng.a" +@@ -180,7 +180,7 @@ + + if [ $HAVE_JPEG = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_JPEG" +- INCLUDES="$INCLUDES -I$LIBJPEG" ++ INCLUDES="$INCLUDES -I$LIBJPEG/include" + # LIBDIR="$LIBDIR -L$LIBJPEG/lib" + # LINKLIBS="$LINKLIBS -ljpeg"; + LIBLIST="$LIBLIST $LIBJPEG/lib/libjpeg.a" From f992f9260e554089a249396a9799d903d6740d72 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 00:40:48 +0200 Subject: [PATCH 588/698] enable PIC in LibTIFF-4.0.9-foss-2017b.eb --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-foss-2017b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-foss-2017b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-foss-2017b.eb index 10dcb118139..ec16609946e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-foss-2017b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-foss-2017b.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2017b'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', From 534cb0afc3bd4561900f0c0f2c4fac446d92a008 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 00:41:10 +0200 Subject: [PATCH 589/698] enable PIC in LibTIFF-4.0.9-GCCcore-6.4.0.eb --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-6.4.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-6.4.0.eb index ba13664037d..64d32331e09 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-6.4.0.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', From 4a17efb669405fc258ed7b419bc2e3f86ff65ad4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 17 Oct 2020 10:47:27 +0200 Subject: [PATCH 590/698] use https source URLs in Ruby 2.5.1 easyconfig --- easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb index a793d8e9b80..4d70edc4886 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-2.5.1-foss-2018a.eb @@ -8,12 +8,12 @@ description = """Ruby is a dynamic, open source programming language with toolchain = {'name': 'foss', 'version': '2018a'} -source_urls = ['http://cache.ruby-lang.org/pub/ruby/'] +source_urls = ['https://cache.ruby-lang.org/pub/ruby/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['dac81822325b79c3ba9532b048c2123357d3310b2b40024202f360251d9829b1'] exts_default_options = { - 'source_urls': ['http://rubygems.org/downloads/'], + 'source_urls': ['https://rubygems.org/downloads/'], 'source_tmpl': '%(name)s-%(version)s.gem', } From d81fd9c8ca2adbcd0ae003ca0505515531563134 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 11:48:02 +0200 Subject: [PATCH 591/698] build LibTIFF enabling PIC --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2017b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018.01.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 1 + 17 files changed, 17 insertions(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb index 2f543e6e918..30d1ba5e1d0 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.2.0.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '8.2.0'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.3.0.eb index 7e5df69176f..be2752e391a 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.10-GCCcore-8.3.0.eb @@ -18,6 +18,7 @@ homepage = 'https://libtiff.gitlab.io/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} source_urls = ['https://download.osgeo.org/libtiff/'] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb index 419d3afe2b6..e39ce099235 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb @@ -7,6 +7,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '5.4.0'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index 76688580b9a..b09324df30e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index a98972105ef..c3ce6c9c3ef 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index fda1e3ceb59..e769608991b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2016a'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index cb758aec726..7c359277acc 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2016b'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb index 49f589e6d45..24cee24b417 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016b'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index bc88218600d..8be02b190db 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb index c1c395504cc..c256cb3752d 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017a'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb index 13cc072a522..bcaafcba6cf 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb @@ -18,6 +18,7 @@ homepage = 'http://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} source_urls = [ 'http://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb index fec76465012..60774abb2b7 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-GCCcore-7.3.0.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '7.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2017b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2017b.eb index 6979ca7f5f4..2bbb83861fa 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2017b.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017b'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018.01.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018.01.eb index 9fc71e1e4dd..6f63dd64add 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018.01.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018.01.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2018.01'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018b.eb index 30f3648fbcd..b8ebfb10f97 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.9-intel-2018b.eb @@ -18,6 +18,7 @@ homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2018b'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index 0e11b9bdee7..afb2bc14767 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -18,6 +18,7 @@ homepage = 'https://libtiff.maptools.org/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '8.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index e147e84dac0..ee0d9664265 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -18,6 +18,7 @@ homepage = 'https://libtiff.maptools.org/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} source_urls = [ 'https://download.osgeo.org/libtiff/', From ee2b895fde40c3c463779a592d2f837a58ea985e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:13:02 +0200 Subject: [PATCH 592/698] move barebones R v3.5.1 to foss/2018b --- ...131-bare.eb => R-3.5.1-foss-2018b-bare.eb} | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) rename easybuild/easyconfigs/r/R/{R-3.5.1-foss-2018a-X11-20180131-bare.eb => R-3.5.1-foss-2018b-bare.eb} (72%) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb similarity index 72% rename from easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb rename to easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb index b6a4f8cbb10..ee8fa2ce1cc 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018a-X11-20180131-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb @@ -1,19 +1,17 @@ ## # This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# +# # Author: Jonas Demeulemeester # The Francis Crick Insitute, London, UK ## name = 'R' version = '3.5.1' -x11ver = '20180131' -versionsuffix = '-X11-%s-bare' % x11ver homepage = 'http://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" -toolchain = {'name': 'foss', 'version': '2018a'} +toolchain = {'name': 'foss', 'version': '2018b'} source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] sources = [SOURCE_TAR_GZ] @@ -23,32 +21,34 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] dependencies = [ - ('X11', x11ver), - ('Mesa', '17.3.6'), + ('X11', '20180604'), + ('Mesa', '18.1.1'), ('libGLU', '9.0.0'), ('cairo', '1.14.12'), ('libreadline', '7.0'), - ('ncurses', '6.0'), + ('ncurses', '6.1'), ('bzip2', '1.0.6'), - ('XZ', '5.2.3'), + ('XZ', '5.2.4'), ('zlib', '1.2.11'), - ('SQLite', '3.21.0'), + ('SQLite', '3.24.0'), ('PCRE', '8.41'), ('libpng', '1.6.34'), # for plotting in R - ('libjpeg-turbo', '1.5.3'), # for plottting in R + ('libjpeg-turbo', '2.0.0'), # for plottting in R ('LibTIFF', '4.0.9'), - ('Java', '1.8.0_162', '', True), # Java bindings are built if Java is found, might as well provide it - ('Tcl', '8.6.8'), # for tcltk + ('Java', '1.8', '', True), ('Tk', '8.6.8'), # for tcltk - ('cURL', '7.58.0'), # for RCurl - ('libxml2', '2.9.7'), # for XML - ('GDAL', '2.2.3', '-Python-3.6.4'), # for rgdal + ('cURL', '7.60.0'), # for RCurl + ('libxml2', '2.9.8'), # for XML + ('GDAL', '2.2.3', '-Python-3.6.6'), # for rgdal ('PROJ', '5.0.0'), # for rgdal ('GMP', '6.1.2'), # for igraph ('NLopt', '2.4.2'), # for nloptr - ('FFTW', '3.3.7'), # for fftw + ('FFTW', '3.3.8'), # for fftw ('libsndfile', '1.0.28'), # for seewave ('ICU', '61.1'), # for rJava & gdsfmt + ('HDF5', '1.10.2'), # for hdf5r + ('UDUNITS', '2.2.26'), # for units + ('GSL', '2.5'), # for RcppGSL # OS dependency should be preferred if the os version is more recent then this version, # it's nice to have an up to date openssl for security reasons # ('OpenSSL', '1.0.2h'), @@ -57,7 +57,7 @@ dependencies = [ osdependencies = [('openssl-devel', 'libssl-dev', 'libopenssl-devel')] configopts = "--with-pic --enable-threads --enable-R-shlib" -# some recommended packages may fail in a parallel build (e.g. Matrix), and we're installing them anyway below +# some recommended packages may fail in a parallel build (e.g. Matrix) configopts += " --with-recommended-packages=no" # specify that at least EasyBuild v3.5.0 is required, From 04c9bfbd0aabb5682b37728d844fa86e5bc2323b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:42:51 +0200 Subject: [PATCH 593/698] fix homepage URL of R-3.5.1-foss-2018b-bare.eb --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb index ee8fa2ce1cc..bd446ada1ad 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb @@ -8,7 +8,7 @@ name = 'R' version = '3.5.1' -homepage = 'http://www.r-project.org/' +homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" toolchain = {'name': 'foss', 'version': '2018b'} From b68e9c46be00a255108cabc38583f89e81c85090 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:43:57 +0200 Subject: [PATCH 594/698] add versionsuffix to R-3.5.1-foss-2018b-bare.eb --- easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb index bd446ada1ad..b6425f1a0f4 100644 --- a/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb +++ b/easybuild/easyconfigs/r/R/R-3.5.1-foss-2018b-bare.eb @@ -7,6 +7,7 @@ name = 'R' version = '3.5.1' +versionsuffix = '-bare' homepage = 'https://www.r-project.org/' description = """R is a free software environment for statistical computing and graphics.""" From f5af98957adf7969cb7e63fa19b3be6ed8d6d044 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:50:04 +0200 Subject: [PATCH 595/698] add missing checksums for LibTIFF v4.0.6 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index b09324df30e..85063921b6c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c'] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index c3ce6c9c3ef..5afe1aec20a 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c'] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index e769608991b..0fec11316a8 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c'] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index 7c359277acc..f74f4ddebe9 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['4d57a50907b510e3049a4bba0d7888930fdfc16ce49f1bf693e5b6247370d68c'] configopts = " --enable-ld-version-script " From 449d2fd15631f2692ca0bec9255f5b4c0b280745 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:50:10 +0200 Subject: [PATCH 596/698] add missing checksums for LibTIFF v4.0.7 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb | 1 + easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb index 24cee24b417..d9510c356e6 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019'] configopts = " --enable-ld-version-script " diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index 8be02b190db..1f5015949ae 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['9f43a2cfb9589e5cecaa66e16bf87f814c945f22df7ba600d63aac4632c4f019'] configopts = " --enable-ld-version-script " From 5e5587672ec675c134c01f4234fc3db233733794 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 12:50:15 +0200 Subject: [PATCH 597/698] add missing checksums for LibTIFF v4.0.8 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb index c256cb3752d..e9917fa3b34 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -25,6 +25,7 @@ source_urls = [ 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] +checksums = ['59d7a5a8ccd92059913f246877db95a2918e6c04fb9d43fd74e5c3390dac2910'] configopts = " --enable-ld-version-script " From c27b3d0e4ace6d45a016a75184fd0652ae05d8ad Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 14:24:14 +0200 Subject: [PATCH 598/698] adding easyconfigs: gettext-0.21-GCCcore-10.2.0.eb, X11-20201008-GCCcore-10.2.0.eb, Tk-8.6.10-GCCcore-10.2.0.eb, Tkinter-3.8.6-GCCcore-10.2.0.eb --- .../g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 32 +++ .../t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb | 40 ++++ .../t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb | 24 ++ .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 210 ++++++++++++++++++ 4 files changed, 306 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..97c0fd67872 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('libxml2', '2.9.10'), + ('ncurses', '6.2'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c72c3a84657 --- /dev/null +++ b/easybuild/easyconfigs/t/Tk/Tk-8.6.10-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Tk' +version = '8.6.10' + +homepage = 'https://www.tcl.tk/' +description = """Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for + building a graphical user interface (GUI) in many different programming languages.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ["https://prdownloads.sourceforge.net/tcl"] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +patches = ['Tk-8.6.4_different-prefix-with-tcl.patch'] +checksums = [ + '63df418a859d0a463347f95ded5cd88a3dd3aaa1ceecaeee362194bc30f3e386', # tk8.6.10-src.tar.gz + '7a6daa8349393af3d340e774aebf07c7410c51e01bc654ceb3679877063b961d', # Tk-8.6.4_different-prefix-with-tcl.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('Tcl', version), + ('X11', '20201008'), + ('zlib', '1.2.11'), +] + +configopts = '--enable-threads --with-tcl=$EBROOTTCL/lib CFLAGS="-I$EBROOTTCL/include"' + +installopts = "&& make install-private-headers" + +postinstallcmds = ["ln -s wish%(version_major_minor)s %(installdir)s/bin/wish"] + +sanity_check_paths = { + 'files': ["bin/wish", "lib/tkConfig.sh", "include/tkInt.h"], + 'dirs': [], +} + +start_dir = 'unix' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d6a03689050 --- /dev/null +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +name = 'Tkinter' +version = '3.8.6' + +homepage = 'https://python.org/' +description = "Tkinter module, built with the Python buildsystem" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/python/%(version)s/'] +sources = ['Python-%(version)s.tgz'] + +builddependencies = [ + ('binutils', '2.35'), + ('libffi', '3.3'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('Tk', '8.6.10'), + ('zlib', '1.2.11'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b5b09e0694b --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -0,0 +1,210 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20201008' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), + ('Bison', '3.7.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('intltool', '0.51.0'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.13.92'), + ('freetype', '2.10.3'), + ('zlib', '1.2.11'), + ('xorg-macros', '1.19.2'), + ('libpciaccess', '0.16'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2020.1', { # 2020-04-14 + 'checksums': ['6265b11b125df2f4853eec4895b14067d5621f813553fa077bebef20d7542418'], + }), + ('libXau', '1.0.9', { # 2019-02-10 + 'checksums': ['1f123d8304b082ad63a9e89376400a3b1d4c29e67e3ea07b3f659cccca690eea'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.14.1', { # 2020-10-08 + 'checksums': ['85cd21e9d9fbc341d0dbf11eace98d55d7db89fda724b0e598855fcddf0944fd'], + }), + ('libxcb', '1.14', { # 2020-02-22 + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2c7fcddd1da34d9b238c9caeda20d3bd7486456fc50b3cc6567185dbd5b0ad02'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.0.1', { # 2020-09-11 + 'easyblock': 'MesonNinja', + 'sources': ['libxkbcommon-%(version)s.tar.xz'], + 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.6.12', { # 2020-08-24 + 'checksums': ['0fce5fc0a24a3dc728174eccd0cb8d6a1b37a2ec1654bd5628c84e5bc200d594'], + }), + ('libXext', '1.3.4', { # 2019-03-16 + 'checksums': ['8ef0789f282826661ff40a8eef22430378516ac580167da35cc948be9041aac1'], + }), + ('libFS', '1.0.8', { # 2019-03-10 + 'checksums': ['e3da723257f4f4c0c629aec402e0a36fbec66a9418f70d24a159cb0470ec83d2'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.0', { # 2019-06-21 + 'checksums': ['d4bee88898fc5e1dc470e361430c72fbc529b9cdbbb6c0ed3affea3a39f97d8d'], + }), + ('libXmu', '1.1.3', { # 2019-03-16 + 'checksums': ['5bd9d4ed1ceaac9ea023d86bf1c1632cd3b172dce4a193a72a94e1d9df87a62e'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.13', { # 2015-05-01 + 'checksums': ['7e74ac3e5f67def549722ff0333d6e6276b8becd9d89615cda011e71238ab694'], + }), + ('libXfixes', '5.0.3', { # 2016-10-04 + 'checksums': ['9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.10', { # 2016-10-04 + 'checksums': ['770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf'], + }), + ('libXcursor', '1.2.0', { # 2019-03-11 + 'checksums': ['ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.4', { # 2019-02-20 + 'checksums': ['895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.4', { # 2019-09-14 + 'checksums': ['74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a'], + }), + ('libXft', '2.3.3', { # 2019-03-16 + 'checksums': ['3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701'], + }), + ('libXi', '1.7.10', { # 2019-06-19 + 'checksums': ['b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3'], + }), + ('libXinerama', '1.1.4', { # 2018-07-05 + 'checksums': ['64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.0', { # 2017-10-11 + 'checksums': ['5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a'], + }), + ('libXtst', '1.2.3', { # 2016-10-04 + 'checksums': ['a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.12', { # 2019-09-24 + 'checksums': ['024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.4', { # 2015-02-24 + 'checksums': ['5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.0', { # 2019-03-16 + 'checksums': ['2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.0', { # 2014-10-15 + 'checksums': ['cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42'], + }), + ('xcb-util-keysyms', '0.4.0', { # 2014-10-01 + 'checksums': ['0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96'], + }), + ('xcb-util-renderutil', '0.3.9', { # 2014-06-13 + 'checksums': ['55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5'], + }), + ('xcb-util-wm', '0.4.1', { # 2014-02-19 + 'checksums': ['038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334'], + }), + ('xcb-util-cursor', '0.1.3', { # 2016-05-12 + 'checksums': ['a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8'], + }), + ('xkeyboard-config', '2.28', { # 2019-10-19 + 'checksums': ['4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff'], + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.3', { # 2015-02-21 + 'checksums': ['f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From af604ecb561ccd5cf87556d5e44801540d25a8e0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 14:45:40 +0200 Subject: [PATCH 599/698] Update checksum in Tkinter --- easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb index d6a03689050..c0154974558 100644 --- a/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/t/Tkinter/Tkinter-3.8.6-GCCcore-10.2.0.eb @@ -9,6 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.python.org/ftp/python/%(version)s/'] sources = ['Python-%(version)s.tgz'] +checksums = ['313562ee9986dc369cd678011bdfd9800ef62fbf7b1496228a18f86b36428c21'] builddependencies = [ ('binutils', '2.35'), From 01514fd9df08d9ffb9cfdf7ea2c0ef9d229fad2b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:36:13 +0200 Subject: [PATCH 600/698] Fix checksum in gettext --- easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb index 97c0fd67872..e0d0f8a84f0 100644 --- a/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21-GCCcore-10.2.0.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -checksums = ['66415634c6e8c3fa8b71362879ec7575e27da43da562c798a8a2f223e6e47f5c'] +checksums = ['c77d0da3102aec9c07f43671e60611ebff89a996ef159497ce8e59d075786b12'] builddependencies = [('binutils', '2.35')] From 5012a2bce1b44d0eedae5d704303d26462ad8ee2 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:50:37 +0200 Subject: [PATCH 601/698] Fix checksum on extension in X11 --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 35 ++++++++++++++++++- 1 file changed, 34 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index b5b09e0694b..3b1816070c9 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -16,6 +16,39 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] +checksums = [ + '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz + '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz + '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz + 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz + '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz + '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz + '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz + '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz + '3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701', # libXft-2.3.3.tar.gz + 'b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3', # libXi-1.7.10.tar.gz + '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz + '3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e', # libXrandr-1.5.2.tar.gz + '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz + 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz + 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz + '024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5', # libXvMC-1.0.12.tar.gz + '715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69', # libXxf86dga-1.1.5.tar.gz + '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz + '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz + '2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3', # libxkbfile-1.1.0.tar.gz + '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz + '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz + 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz + '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz + '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz + '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz + 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz + '4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff', # xkeyboard-config-2.28.tar.gz + 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz + 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz + '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz +] builddependencies = [ ('binutils', '2.35'), @@ -70,7 +103,7 @@ components = [ ('libxkbcommon', '1.0.1', { # 2020-09-11 'easyblock': 'MesonNinja', 'sources': ['libxkbcommon-%(version)s.tar.xz'], - 'checksums': ['57c3630cdc38fb4734cd57fa349e92244f5ae3862813e533cedbd86721a0b6f2'], + 'checksums': ['ab68b25341c99f2218d7cf3dad459c1827f411219901ade05bbccbdb856b6c8d'], 'preconfigopts': '', 'configopts': '-Denable-wayland=false -Denable-docs=false ', }), From 85bde61fe55942e64a3fdeaacbc602247297f300 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 15:52:28 +0200 Subject: [PATCH 602/698] Remove duplicate checksum block in X11 (incorrectly created by inject checksums) --- .../x/X11/X11-20201008-GCCcore-10.2.0.eb | 33 ------------------- 1 file changed, 33 deletions(-) diff --git a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb index 3b1816070c9..041c9f6a6a9 100644 --- a/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/x/X11/X11-20201008-GCCcore-10.2.0.eb @@ -16,39 +16,6 @@ source_urls = [ XORG_DATA_SOURCE + '/xkeyboard-config', XORG_DATA_SOURCE, ] -checksums = [ - '9ab6c13590658501ce4bd965a8a5d32ba4d8b3bb39a5a5bc9901edffc5666570', # libXfixes-5.0.3.tar.gz - '581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c', # libXcomposite-0.4.5.tar.gz - '770527cce42500790433df84ec3521e8bf095dfe5079454a92236494ab296adf', # libXrender-0.9.10.tar.gz - 'ad5b2574fccaa4c3fa67b9874fbed863d29ad230c784e9a08b20692418f6a1f8', # libXcursor-1.2.0.tar.gz - '630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019', # libXdamage-1.1.5.tar.gz - '895ee0986b32fbfcda7f4f25ef6cbacfa760e1690bf59f02085ce0e7d1eebb41', # libfontenc-1.1.4.tar.gz - '59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e', # libXfont-1.5.4.tar.gz - '74e577294c7406b284c50dfcfb5e5d9b3b0cc2d83d33866920ffe1e4860f585a', # libXfont2-2.0.4.tar.gz - '3c3cf88b1a96e49a3d87d67d9452d34b6e25e96ae83959b8d0a980935014d701', # libXft-2.3.3.tar.gz - 'b51e106c445a49409f3da877aa2f9129839001b24697d75a54e5c60507e9a5e3', # libXi-1.7.10.tar.gz - '64de45e18cc76b8e703cb09b3c9d28bd16e3d05d5cd99f2d630de2d62c3acc18', # libXinerama-1.1.4.tar.gz - '3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e', # libXrandr-1.5.2.tar.gz - '5b62feee09f276d74054787df030fceb41034de84174abec6d81c591145e043a', # libXres-1.2.0.tar.gz - 'a0c83acce02d4923018c744662cb28eb0dbbc33b4adc027726879ccf68fbc2c2', # libXtst-1.2.3.tar.gz - 'c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1', # libXv-1.0.11.tar.gz - '024c9ec4f001f037eeca501ee724c7e51cf287eb69ced8c6126e16e7fa9864b5', # libXvMC-1.0.12.tar.gz - '715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69', # libXxf86dga-1.1.5.tar.gz - '5108553c378a25688dcb57dca383664c36e293d60b1505815f67980ba9318a99', # libXxf86vm-1.1.4.tar.gz - '4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925', # libdmx-1.1.4.tar.gz - '2a92adda3992aa7cbad758ef0b8dfeaedebb49338b772c64ddf369d78c1c51d3', # libxkbfile-1.1.0.tar.gz - '7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c', # libxshmfence-1.3.tar.gz - '0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7', # xcb-util-0.4.0.tar.gz - 'cb2c86190cf6216260b7357a57d9100811bb6f78c24576a3a5bfef6ad3740a42', # xcb-util-image-0.4.0.tar.gz - '0807cf078fbe38489a41d755095c58239e1b67299f14460dec2ec811e96caa96', # xcb-util-keysyms-0.4.0.tar.gz - '55eee797e3214fe39d0f3f4d9448cc53cffe06706d108824ea37bb79fcedcad5', # xcb-util-renderutil-0.3.9.tar.gz - '038b39c4bdc04a792d62d163ba7908f4bb3373057208c07110be73c1b04b8334', # xcb-util-wm-0.4.1.tar.gz - 'a322332716a384c94d3cbf98f2d8fe2ce63c2fe7e2b26664b6cea1d411723df8', # xcb-util-cursor-0.1.3.tar.gz - '4424ffaafdf9f09dea69a317709353c4e2b19f69b2405effadce0bac3bdebdff', # xkeyboard-config-2.28.tar.gz - 'e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc', # printproto-1.0.5.tar.gz - 'f6b8cc4ef05d3eafc9ef5fc72819dd412024b4ed60197c0d5914758125817e9c', # libXp-1.0.3.tar.gz - '27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265', # xbitmaps-1.1.2.tar.gz -] builddependencies = [ ('binutils', '2.35'), From 67a97ecd427a9026838904f2821bcf75d381e5be Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 17 Oct 2020 16:55:46 +0200 Subject: [PATCH 603/698] clean up Spyder 4.1.5 easyconfig, drop extensions that are already provided by IPython dependency --- .../Spyder-4.1.5-foss-2020a-Python-3.8.2.eb | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb index 1ad58558b2b..b109e347e47 100644 --- a/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/Spyder/Spyder-4.1.5-foss-2020a-Python-3.8.2.eb @@ -42,10 +42,6 @@ exts_list = [ ('autopep8', '1.5.4', { 'checksums': ['d21d3901cb0da6ebd1e83fc9b0dfbde8b46afc2ede4fe32fbda0c7c6118ca094'], }), - ('backcall', '0.2.0', { - 'use_pip': False, - 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], - }), ('binaryornot', '0.4.4', { 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], }), @@ -61,16 +57,9 @@ exts_list = [ ('decorator', '4.4.2', { 'checksums': ['e3a62f0520172440ca0dcc823749319382e377f37f140a0b99ef45fecb84bfe7'], }), - ('defusedxml', '0.6.0', { - 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], - }), ('diff-match-patch', '20200713', { 'checksums': ['da6f5a01aa586df23dfc89f3827e1cafbb5420be9d87769eeb079ddfd9477a18'], }), - ('entrypoints', '0.3', { - 'use_pip': False, - 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], - }), ('flake8', '3.8.4', { 'checksums': ['aadae8761ec651813c24be05c6f7b4680857ef6afaae4651a4eccaef97ce6c3b'], }), @@ -94,9 +83,6 @@ exts_list = [ ('jinja2-time', '0.2.0', { 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], }), - ('jsonschema', '3.2.0', { - 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], - }), ('jupyterlab_pygments', '0.1.2', { 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], }), @@ -124,9 +110,6 @@ exts_list = [ ('numpydoc', '1.1.0', { 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], }), - ('parso', '0.7.0', { - 'checksums': ['908e9fae2144a076d72ae4e25539143d40b8e3eafbaeae03c1bfe226f4cdf12c'], - }), ('pathtools', '0.1.2', { 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], }), From 8420d182dc629878b8a2e5a37d863e020cacd80e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 17 Oct 2020 16:57:40 +0200 Subject: [PATCH 604/698] enable sanity_pip_check in BDBag easyconfig --- .../easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb index 3da7954f320..84c8901bac4 100644 --- a/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/b/BDBag/BDBag-1.4.1-intel-2018a-Python-3.6.4.eb @@ -34,4 +34,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'data' From 3528f1e3720fbf9b1c07220f481b66c645606ad0 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 17:03:11 +0200 Subject: [PATCH 605/698] adding easyconfigs: Szip-2.1.1-GCCcore-10.2.0.eb, pigz-2.4-GCCcore-10.2.0.eb, gzip-1.10-GCCcore-10.2.0.eb, lz4-1.9.2-GCCcore-10.2.0.eb, zstd-1.4.5-GCCcore-10.2.0.eb --- .../g/gzip/gzip-1.10-GCCcore-10.2.0.eb | 24 ++++++++ .../l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb | 30 ++++++++++ .../p/pigz/pigz-2.4-GCCcore-10.2.0.eb | 55 +++++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb | 29 ++++++++++ .../z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb | 41 ++++++++++++++ 5 files changed, 179 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a046e06c020 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.10-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.10' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c91f74430bf7bc20402e1f657d0b252cb80aa66ba333a25704512af346633c68'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b30c9601128 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.2-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.2' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['658ba6191fa44c92280d4aa2c271b0f4fbc0e34d249578dd05e50e76d0e5efcc'] + +builddependencies = [('binutils', '2.35')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a6603491263 --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.4-GCCcore-10.2.0.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# +# 2.4.0: +# Jonas Demeulemeester +# The Francis Crick Institute +## +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.4' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + 'a4f816222a7b4269bd232680590b579ccc72591f1bb5adafcd7208ca77e14f73', # pigz-2.4.tar.gz + '8de19216a69b6402942f73177c566791f0c7fa4649376029d30d0c537d2195c1', # pigz-2.4_makefile.patch +] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..88e067c36e8 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..af251418cee --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.4.5-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.4.5' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['734d1f565c42f691f8420c8d06783ad818060fc390dee43ae0a89f86d0a4f8c2'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('gzip', '1.10'), + ('XZ', '5.2.5'), + ('lz4', '1.9.2'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 9074c0f29384e19918cbf06d7e9b364c1e5bdb7e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 17:09:02 +0200 Subject: [PATCH 606/698] fix homepage URL in LibTIFF v4.0.6 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb index e39ce099235..53efe127966 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.6' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '5.4.0'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index 85063921b6c..f16422ffec0 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.6' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016a'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index 5afe1aec20a..cdd39b16283 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.6' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index 0fec11316a8..27719d6d0f9 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.6' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2016a'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index f74f4ddebe9..41ab7a772d3 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.6' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2016b'} From d347ce117ec552adf2f82419b6fc9d838eb806f7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 17:09:07 +0200 Subject: [PATCH 607/698] fix homepage URL in LibTIFF v4.0.7 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb index d9510c356e6..b0b53f4506b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.7' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'foss', 'version': '2016b'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index 1f5015949ae..76cd1c43b61 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.7' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017a'} From 19fb9fb717251030494f508410bc49e33335de30 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 17:09:12 +0200 Subject: [PATCH 608/698] fix homepage URL in LibTIFF v4.0.8 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb index e9917fa3b34..0975bf082ae 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.8' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017a'} diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb index bcaafcba6cf..9259181220c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb @@ -14,7 +14,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.0.8' -homepage = 'http://www.remotesensing.org/libtiff/' +homepage = 'https://www.remotesensing.org/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'intel', 'version': '2017b'} From ae7718bef8a1c8105ce0b2759b20652ca119a3c2 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 17 Oct 2020 17:17:01 +0200 Subject: [PATCH 609/698] Add more compression libs --- .../l/LZO/LZO-2.10-GCCcore-10.2.0.eb | 36 +++++++++++++++++ .../z/Zip/Zip-3.0-GCCcore-10.2.0.eb | 40 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2898f75e504 --- /dev/null +++ b/easybuild/easyconfigs/l/LZO/LZO-2.10-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'LZO' +version = '2.10' + +homepage = 'https://www.oberhumer.com/opensource/lzo/' +description = "Portable lossless data compression library" + +source_urls = [homepage + 'download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c0f892943208266f9b6543b3ae308fab6284c5c90e627931446fb49b4221a072'] + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [('binutils', '2.35')] + +configopts = '--enable-shared' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/liblzo2.a', 'lib/liblzo2.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..16af667205d --- /dev/null +++ b/easybuild/easyconfigs/z/Zip/Zip-3.0-GCCcore-10.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Zip' +version = '3.0' + +homepage = 'http://www.info-zip.org/Zip.html' +description = """Zip is a compression and file packaging/archive utility. +Although highly compatible both with PKWARE's PKZIP and PKUNZIP +utilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectives +have been portability and other-than-MSDOS functionality""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +checksums = ['f0e8bb1f9b7eb0b01285495a2699df3a4b766784c1765a8f1aeedf63c0806369'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" IZ_OUR_BZIP2_DIR=$EBROOTBZIP2 ' +buildopts += 'CFLAGS="$CFLAGS -I. -DUNIX -DBZIP2_SUPPORT -DUNICODE_SUPPORT -DLARGE_FILE_SUPPORT" ' +buildopts += 'generic_gcc' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/zip', 'bin/zipcloak', 'bin/zipnote', 'bin/zipsplit'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["zip --version"] + +moduleclass = 'tools' From a28aa6362d0f47543663436dfa7098f29cb8e72b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 18:11:50 +0200 Subject: [PATCH 610/698] fix sources URL in LibTIFF v4.0.6 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb index 53efe127966..a084e08a356 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-GCCcore-5.4.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb index f16422ffec0..900f669eebb 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016a.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb index cdd39b16283..bd4b6e92e9f 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-foss-2016b.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb index 27719d6d0f9..6c968e4df73 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016a.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'intel', 'version': '2016a'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb index 41ab7a772d3..728122d803d 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.6-intel-2016b.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] From 49d066753ec62770cf2a6ac9d3af63c31539a648 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 18:12:00 +0200 Subject: [PATCH 611/698] fix sources URL in LibTIFF v4.0.7 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb index b0b53f4506b..3594e346a39 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-foss-2016b.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb index 76cd1c43b61..cb8c5b536ad 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.7-intel-2017a.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] From 4665d8e096a040939fd3f2e89ef1f39e13a28a4d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Oct 2020 18:12:04 +0200 Subject: [PATCH 612/698] fix sources URL in LibTIFF v4.0.8 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb index 0975bf082ae..408a991c72b 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017a.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'intel', 'version': '2017a'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb index 9259181220c..ad5ab76a66c 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.0.8-intel-2017b.eb @@ -21,7 +21,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'pic': True} source_urls = [ - 'http://download.osgeo.org/libtiff/', + 'https://download.osgeo.org/libtiff/', 'ftp://ftp.remotesensing.org/pub/libtiff/', ] sources = ['tiff-%(version)s.tar.gz'] From 81ec9f5881659b3156083f1a219b9269692b74e4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 18 Oct 2020 09:24:28 +0200 Subject: [PATCH 613/698] xcb-proto: Use SYSTEM toolchains and local_ prefix as needed. --- easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb index 38564e30c77..4670aa60216 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb @@ -9,7 +9,7 @@ latency hiding, direct access to the protocol, improved threading support, and e # even though xcb-proto is installed with configure-make-make install, nothing is actually built; # only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain -toolchain = {'name': 'dummy', 'version': 'dummy'} +toolchain = SYSTEM source_urls = ['http://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] @@ -17,11 +17,11 @@ checksums = ['0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7'] allow_system_deps = [('Python', SYS_PYTHON_VERSION)] -pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[0:2]) sanity_check_paths = { 'files': ['lib/pkgconfig/xcb-proto.pc'], - 'dirs': ['lib/python%s/site-packages/xcbgen' % pyshortver] + 'dirs': ['lib/python%s/site-packages/xcbgen' % local_pyshortver] } moduleclass = 'devel' From 1fba467132bd3e957e6eef1d76639a9c96597b18 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Sun, 18 Oct 2020 09:57:50 +0200 Subject: [PATCH 614/698] libxcb and friends: Use https. --- easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb | 2 +- .../easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb | 2 +- easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb index 242381d83e3..f75f21de178 100644 --- a/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libXau/libXau-1.0.8-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libXau' version = '1.0.8' -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +homepage = "https://www.freedesktop.org/wiki/Software/xlibs" description = """The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display.""" diff --git a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb index c7f421b0a38..0747b23df5e 100644 --- a/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libXdmcp/libXdmcp-1.1.2-GCCcore-6.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'libXdmcp' version = '1.1.2' -homepage = "http://www.freedesktop.org/wiki/Software/xlibs" +homepage = "https://www.freedesktop.org/wiki/Software/xlibs" description = """The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. """ diff --git a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb index 07567190500..2ec01ebf7f2 100644 --- a/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libxcb/libxcb-1.13-GCCcore-6.4.0.eb @@ -3,13 +3,13 @@ easyblock = 'ConfigureMake' name = 'libxcb' version = '1.13' -homepage = 'http://xcb.freedesktop.org/' +homepage = 'https://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" toolchain = {'name': 'GCCcore', 'version': '6.4.0'} -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['https://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['0bb3cfd46dbd90066bf4d7de3cad73ec1024c7325a4a0cbf5f4a0d4fa91155fb'] diff --git a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb index 4670aa60216..c3e29eb967d 100644 --- a/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb +++ b/easybuild/easyconfigs/x/xcb-proto/xcb-proto-1.13.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'xcb-proto' version = '1.13' -homepage = 'http://xcb.freedesktop.org/' +homepage = 'https://xcb.freedesktop.org/' description = """The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.""" @@ -11,7 +11,7 @@ latency hiding, direct access to the protocol, improved threading support, and e # only .py files are installed using Python, and some .xlm flies copied, so OK to use dummy toolchain toolchain = SYSTEM -source_urls = ['http://xcb.freedesktop.org/dist/'] +source_urls = ['https://xcb.freedesktop.org/dist/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['0698e8f596e4c0dbad71d3dc754d95eb0edbb42df5464e0f782621216fa33ba7'] From 627960145a6d2614ca392be659d7b2698de7d73c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 Oct 2020 11:35:35 +0200 Subject: [PATCH 615/698] use https in source URLs for ORFfinder --- easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb index 715780a46a3..21ed4f44399 100644 --- a/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb +++ b/easybuild/easyconfigs/o/ORFfinder/ORFfinder-0.4.3.eb @@ -14,7 +14,7 @@ description = """ORF finder searches for open reading frames (ORFs) in the toolchain = SYSTEM -source_urls = ['http://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] +source_urls = ['https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/ORFfinder/linux-i64/'] sources = [{'filename': '%(name)s-%(version)s.gz', 'download_filename': '%(name)s.gz'}] checksums = ['bb676b56f557128e73f68cc852709d1ff7abd1c750d00fd8322de31820969f3c'] From 6d2d5cdf455f8fec437b3927bf2f8378a2af015e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 Oct 2020 11:50:30 +0200 Subject: [PATCH 616/698] fix checksum of GPAW 20.1.0 patch that was enhanced --- .../easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb index 5f5415c9ab9..49832a9822a 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-foss-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '1231ef113f8c46c1f37bf4e544d792fd75dd8965053f792cac5794cb84af8276', + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb index eae2fe21448..f87fd8a0abd 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-20.1.0-intel-2019b-Python-3.7.4.eb @@ -21,7 +21,7 @@ patches = [ checksums = [ 'c84307eb9943852d78d966c0c8856fcefdefa68621139906909908fb641b8421', # gpaw-20.1.0.tar.gz # GPAW-20.1.0-Add-Easybuild-configuration-files.patch - '1231ef113f8c46c1f37bf4e544d792fd75dd8965053f792cac5794cb84af8276', + 'a12440bf63af70b891a63989b0f048bb8ebf4f60499020ea09259937f04cd042', # GPAW-20.1.0-Wrap-pragma-omp-simd-in-ifdef-_OPENMP-blocks.patch 'bf0e0179ce9261197a10a3a934ce3a8d46489b635a3130a5ceb2fe0fee67bb14', ] From bc391f890d4e16aecbc2615bc7909cb8882eb566 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Z=C3=A1rybnick=C3=BD?= Date: Sun, 18 Oct 2020 12:54:12 +0200 Subject: [PATCH 617/698] GBprocesS: bump to 2.3, remove now redundant fastq-join dependency --- .../fastq-join-1.3.1-intel-2020a.eb | 33 ------------------- ...GBprocesS-2.3-intel-2020a-Python-3.8.2.eb} | 7 ++-- 2 files changed, 3 insertions(+), 37 deletions(-) delete mode 100644 easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb rename easybuild/easyconfigs/g/GBprocesS/{GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb => GBprocesS-2.3-intel-2020a-Python-3.8.2.eb} (86%) diff --git a/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb b/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb deleted file mode 100644 index aba8ecb20d6..00000000000 --- a/easybuild/easyconfigs/f/fastq-join/fastq-join-1.3.1-intel-2020a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'MakeCp' - -name = 'fastq-join' -version = '1.3.1' - -homepage = 'https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html' -description = """ NCIPLOT is a program for revealing non covalent interactions - based on the reduced density gradient. """ - -toolchain = {'name': 'intel', 'version': '2020a'} - -source_urls = ['https://github.com/brwnj/fastq-join/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['1748511a7785ad9944850e81f35c980011f5c6346dec1fb67cc99b3110170690'] - -# Remove hardcoded values -prebuildopts = "sed -i 's/CC=g++//g' Makefile && " -prebuildopts += "sed -i 's/CFLAGS=-O3 -I.//g' Makefile && " - -# Fix failing test (sqrt(-1) is expected to be NaN but is actually -NaN) -prebuildopts += "sed -i 's/n\", dev)/n\", abs(dev))/g' fastq-join.cpp && " - -runtest = 'check' - -files_to_copy = [(['fastq-join'], 'bin')] - -sanity_check_paths = { - 'files': ['bin/fastq-join'], - 'dirs': [], -} -sanity_check_commands = ['fastq-join -h'] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb similarity index 86% rename from easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb index ee7334236af..db57ce63fd5 100644 --- a/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.1.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GBprocesS/GBprocesS-2.3-intel-2020a-Python-3.8.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'GBprocesS' -version = '2.1.1' +version = '2.3' versionsuffix = '-Python-%(pyver)s' homepage = 'https://gbprocess.readthedocs.io/' @@ -16,20 +16,19 @@ toolchain = {'name': 'intel', 'version': '2020a'} source_urls = ['https://gitlab.com/dschaumont/GBprocesS/-/archive/%(version)s/'] sources = ['GBprocesS-%(version)s.tar.gz'] -checksums = ['968e9431160d4c552e85e6478d79e22f3c1d946130917b3cee0a6c602d51e5e1'] +checksums = ['374fa7bc096e0cbc83746f505bea134117debed99b7510cb4123878aeaea9456'] dependencies = [ ('Python', '3.8.2'), ('cutadapt', '2.10', '-Python-%(pyver)s'), ('Biopython', '1.78', versionsuffix), - ('fastq-join', '1.3.1'), ] use_pip = True sanity_pip_check = True download_dep_fail = True -# Tests expect the package to already be installed, but EB runs them beforehand +# The package uses setuptools-scm, so we avoid using the "version" part of it. pretestopts = ( "sed -i 's/" "__version__ = get_distribution(__name__).version/" From ad80a0685734d187ce2534e7bae3b8a820844386 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 14:18:42 +0200 Subject: [PATCH 618/698] adding easyconfigs: re2c-2.0.3-GCCcore-10.2.0.eb, PCRE2-10.35-GCCcore-10.2.0.eb, double-conversion-3.1.5-GCCcore-10.2.0.eb, PCRE-8.44-GCCcore-10.2.0.eb, DBus-1.13.18-GCCcore-10.2.0.eb, libGLU-9.0.1-GCCcore-10.2.0.eb, GLib-2.66.1-GCCcore-10.2.0.eb, NASM-2.15.05-GCCcore-10.2.0.eb, libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb, snappy-1.1.8-GCCcore-10.2.0.eb, NSPR-4.29-GCCcore-10.2.0.eb, NSS-3.57-GCCcore-10.2.0.eb, JasPer-2.0.14-GCCcore-10.2.0.eb --- .../d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 42 +++++++++++++++ .../double-conversion-3.1.5-GCCcore-10.2.0.eb | 38 ++++++++++++++ .../g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb | 52 +++++++++++++++++++ .../j/JasPer/JasPer-2.0.14-GCCcore-10.2.0.eb | 35 +++++++++++++ .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 ++++++++++ .../libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 42 +++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb | 37 +++++++++++++ .../n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb | 28 ++++++++++ .../n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 49 +++++++++++++++++ .../p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb | 45 ++++++++++++++++ .../p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb | 28 ++++++++++ .../r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb | 25 +++++++++ .../s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb | 29 +++++++++++ 13 files changed, 477 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0073dcb0f0d --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.13.18' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('expat', '2.2.9'), +] + +configopts = '--without-systemdsystemunitdir' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..23fc1b1e9fb --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.1.5-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.1.5' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a63ecb93182134ba4293fd5f22d6e08ca417caafa244afaa751cbfddf6415b13'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +build_type = 'Release' + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..f45c527ed46 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.66.1-GCCcore-10.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.66.1' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a269ffe69fbcc3a21ff1acb1b6146b2a5723499d6e2de33ae16ccb6d2438ef60'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.8.6'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('libffi', '3.3'), + ('gettext', '0.21'), + ('libxml2', '2.9.10'), + ('PCRE', '8.44'), + ('util-linux', '2.36'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..460a679974c --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-2.0.14-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '2.0.14' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.ece.uvic.ca/~frodo/jasper/software/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a1f61e55afe8b4ce8115e1508c5d7cb314d56dfcc2dd323f90c072f88ccf57b'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..84bcd5868f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.1' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ +# ('Mesa', '20.0.2'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..5ab669488d2 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.0.5' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('binutils', '2.35'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..16ff10f655e --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-90.html +## + +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a796b4e4211 --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.29-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.29' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['22286bdb8059d74632cc7c2865c139e63953ecfb33bf4362ab58827e86e92582'] + +builddependencies = [('binutils', '2.35')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0f2b08e1b55 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.57' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', +] +checksums = [ + '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz + '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch + '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch +] + +builddependencies = [('binutils', '2.35')] +dependencies = [ + ('NSPR', '4.29'), + ('zlib', '1.2.11'), +] + +# building in parallel fails +parallel = 1 + +# fix for not being able to find header files +buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['lib/libnss.a'], + 'dirs': ['bin', 'include/dbm', 'include/nss'], +} + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1dec4bf1fa6 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.44-GCCcore-10.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.44' + +homepage = 'https://www.pcre.org/' + +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.pcre.org/pub/pcre/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aecafd4af3bd0f3935721af77b889d9024b2e01d96b58471bd91a3063fb47728'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +configopts = """\ + --enable-utf\ + --enable-unicode-properties\ + --enable-pcre16\ + --enable-pcre32\ +""" + +sanity_check_paths = { + 'files': ['bin/pcre-config', 'include/pcre.h', + 'share/man/man3/pcre.3', 'lib/libpcre32.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'share/doc/pcre/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..af6d2eaca84 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.35' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax + and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.sourceforge.net/pcre'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8fdcef8c8f4cd735169dd0225fd010487970c1bcadd49e9b90e26c7250a33dc9'] + +builddependencies = [('binutils', '2.35')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dba73c221fe --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-2.0.3-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '2.0.3' + +homepage = 'https://re2c.org/' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['b2bc1eb8aaaa21ff2fcd26507b7e6e72c5e3d887e58aa515c2155fb17d744278'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4397a7c9873 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.8-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.8' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['16b677f07832a612b0836178db7f374e414f94657c138e6993cbfc5dcc58651f'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +configopts = ['', '-DBUILD_SHARED_LIBS=ON'] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [''] +} + +moduleclass = 'lib' From a122c811371c8087bff0b58e5015baf2ff887008 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 14:41:59 +0200 Subject: [PATCH 619/698] Fix checksum in libjpeg-turbo --- .../l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb index 5ab669488d2..1214eaa1d24 100644 --- a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.0.5-GCCcore-10.2.0.eb @@ -16,7 +16,7 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['33dd8547efd5543639e890efbf2ef52d5a21df81faf41bb940657af916a23406'] +checksums = ['16f8f6f2715b3a38ab562a84357c793dd56ae9899ce130563c72cd93d8357b5d'] builddependencies = [ ('CMake', '3.18.4'), From 241fca23fdd23c1d9e1c369537fb311b8270d3cb Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:02:28 +0200 Subject: [PATCH 620/698] Remove incomplete easyconfig --- .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb deleted file mode 100644 index 84bcd5868f0..00000000000 --- a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libGLU' -version = '9.0.1' - -homepage = 'https://mesa.freedesktop.org/archive/glu/' -description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://mesa.freedesktop.org/archive/glu/'] -sources = ['glu-%(version)s.tar.gz'] -checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] - -builddependencies = [('binutils', '2.35')] - -dependencies = [ -# ('Mesa', '20.0.2'), -] - -sanity_check_paths = { - 'files': ['lib/libGLU.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'vis' From 929419e0fcc0af43e658ee19df54db106228f474 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:16:56 +0200 Subject: [PATCH 621/698] Drop seemingly outdated patch from NSS --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 0f2b08e1b55..a0e6062edb3 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -13,7 +13,6 @@ source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_ sources = [SOURCELOWER_TAR_GZ] patches = [ 'NSS-3.39_pkgconfig.patch', - '%(name)s-%(version)s_fix_kremlin_ppc64le.patch', ] checksums = [ '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz From a59cd6ea680da98a609b5d83c68357f192e01e5e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 15:25:01 +0200 Subject: [PATCH 622/698] Update checksums in NSS 3.57 --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index a0e6062edb3..528d1249552 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -15,9 +15,8 @@ patches = [ 'NSS-3.39_pkgconfig.patch', ] checksums = [ - '75348b3b3229362486c57a880db917da1f96ef4eb639dc9cc2ff17d72268459c', # nss-3.51.tar.gz + '55a86c01be860381d64bb4e5b94eb198df9b0f098a8af0e58c014df398bdc382', # nss-3.57.tar.gz '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774', # NSS-3.39_pkgconfig.patch - '2fc7bd556737d34a62c06f86899863b7071b71943ffb4facfb413a087b8bee2e', # NSS-3.51_fix_kremlin_ppc64le.patch ] builddependencies = [('binutils', '2.35')] From 5f8619505b00d4c27d9362201842d85d535650e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 18 Oct 2020 17:33:29 +0200 Subject: [PATCH 623/698] Update easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb index 16ff10f655e..27a05a06c8e 100644 --- a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-10.2.0.eb @@ -23,7 +23,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['34fd26c70a277a9fdd54cb5ecf389badedaf48047b269d1008fbc819b24e80bc'] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] builddependencies = [ ('binutils', '2.35'), From 91fd58d66da3b066a95f26b62302b6158746939b Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 18:02:44 +0200 Subject: [PATCH 624/698] adding easyconfigs: git-2.28.0-GCCcore-10.2.0-nodocs.eb --- .../g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb new file mode 100644 index 00000000000..d47acd98a74 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.28.0' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com/' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7d84f5d6f48e95b467a04a8aa1d474e0d21abc7877998af945568d2634fea46a'] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('cURL', '7.72.0'), + ('expat', '2.2.9'), + ('gettext', '0.21'), + ('Perl', '5.32.0'), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From e0e71aae0c389b4788130d6e200ee8d4ad5da498 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 18 Oct 2020 19:19:11 +0200 Subject: [PATCH 625/698] Update easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb index 0073dcb0f0d..83b477ea363 100644 --- a/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DBus/DBus-1.13.18-GCCcore-10.2.0.eb @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} source_urls = ['https://dbus.freedesktop.org/releases/dbus'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['7588649b56dd257c6a5f85a8c45aa2dfdf9e99f4de3983710f452081ca43eca6'] +checksums = ['8078f5c25e34ab907ce06905d969dc8ef0ccbec367e1e1707c7ecf8460f4254e'] builddependencies = [ ('binutils', '2.35'), From d4683288a3da7f27b10dc87a5a550ba8907e4fc6 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 19:59:15 +0200 Subject: [PATCH 626/698] Include comment on NSS test suite --- easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb index 528d1249552..06357048174 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.57-GCCcore-10.2.0.eb @@ -34,6 +34,8 @@ buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] From 4c9391d74a57d43ff95a7f77c651547aa144f461 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Oct 2020 20:02:10 +0200 Subject: [PATCH 627/698] fix source URL of lavaan-0.6-2-intel-2018a-R-3.4.4.eb --- .../easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb index bdddde13f4c..ff7e9c87961 100644 --- a/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb +++ b/easybuild/easyconfigs/l/lavaan/lavaan-0.6-2-intel-2018a-R-3.4.4.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2018a'} source_urls = [ 'https://cran.r-project.org/src/contrib/', - 'https://cran.r-project.org/src/contrib/Archive/$(name)s/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s/', ] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['91d5aea1468394f9e2bda773ab51f8a16a198bfc1d8474c1c48bcaba87f9c0be'] From ee0bb41f5e5c2cef68e3b6e47dcf7d279840e59c Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 20:23:19 +0200 Subject: [PATCH 628/698] Fix checksum --- easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb index d47acd98a74..0ca0d915f44 100644 --- a/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.28.0-GCCcore-10.2.0-nodocs.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/git/git/archive'] sources = ['v%(version)s.tar.gz'] -checksums = ['7d84f5d6f48e95b467a04a8aa1d474e0d21abc7877998af945568d2634fea46a'] +checksums = ['02016d16dbce553699db5c9c04f6d13a3f50727c652061b7eb97a828d045e534'] builddependencies = [ ('binutils', '2.35'), From 4d1ce162ed6b050970e35580389f7f3c70baad3f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 22:43:34 +0200 Subject: [PATCH 629/698] adding easyconfigs: LLVM-11.0.0-GCCcore-10.2.0.eb --- .../l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..88f9f8de51b --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-11.0.0-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +name = 'LLVM' +version = '11.0.0' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'cstd': 'gnu++11'} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['913f68c898dfb4a03b397c5e11c6a2f39d0f22ed7665c9cefa87a34423a72469'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), + ('Python', '3.8.6'), +] + +dependencies = [ + ('ncurses', '6.2'), + ('zlib', '1.2.11'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +moduleclass = 'compiler' From 2f711f4b77796a9ee09c3d69c8c3824151fc9ec7 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sun, 18 Oct 2020 23:12:37 +0200 Subject: [PATCH 630/698] adding easyconfigs: APR-1.7.0-GCCcore-10.2.0.eb, APR-util-1.6.1-GCCcore-10.2.0.eb, utf8proc-2.5.0-GCCcore-10.2.0.eb, SCons-4.0.1-GCCcore-10.2.0.eb, Serf-1.3.9-GCCcore-10.2.0.eb, Subversion-1.14.0-GCCcore-10.2.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb | 32 ++++++++++++ .../a/APR/APR-1.7.0-GCCcore-10.2.0.eb | 22 +++++++++ .../s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb | 35 +++++++++++++ .../s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 39 +++++++++++++++ .../Subversion-1.14.0-GCCcore-10.2.0.eb | 49 +++++++++++++++++++ .../utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb | 30 ++++++++++++ 6 files changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4934bcbe299 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.33.0'), + ('expat', '2.2.9'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c3a8371d342 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.35')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..6a8b8a9de33 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'SCons' +version = '4.0.1' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['SCons-3.0.4_fix-pip-install.patch'] +checksums = [ + '722ed104b5c624ecdc89bd4e02b094d2b14d99d47b5d0501961e47f579a2007c', # scons-4.0.1.tar.gz + 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch +] + +builddependencies = [('binutils', '2.35')] + +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'dirs': [], +} + +# no Python module to import during sanity check +options = {'modulename': False} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..710686c4a78 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '2.7.18'), # Serfs build scripts are python 2 only + ('SCons', '4.0.1'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + # OS dependency should be preferred if the os version is more recent then this version, + # it is nice to have an up to date openssl for security reasons + # ('OpenSSL', '1.1.1h'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fac1a9e08c5 --- /dev/null +++ b/easybuild/easyconfigs/s/Subversion/Subversion-1.14.0-GCCcore-10.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'Subversion' +version = '1.14.0' + +homepage = 'https://subversion.apache.org/' +description = " Subversion is an open source version control system." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://apache.belnet.be/%(namelower)s', + 'http://www.eu.apache.org/dist/%(namelower)s', + 'http://www.us.apache.org/dist/%(namelower)s', + 'https://archive.apache.org/dist/%(namelower)s', +] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Subversion-1.12.0-no_swig.patch'] +checksums = [ + '6ba8e218f9f97a83a799e58a3c6da1221d034b18d9d8cbbcb6ec52ab11722102', # subversion-1.14.0.tar.bz2 + '539ea2118f958d152d78438c81649eb727ff0b2e8491295702ee98e1f922041f', # Subversion-1.12.0-no_swig.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Autotools', '20200321'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('SQLite', '3.33.0'), + ('zlib', '1.2.11'), + ('lz4', '1.9.2'), + ('utf8proc', '2.5.0'), + ('Serf', '1.3.9'), +] + +preconfigopts = './autogen.sh && ' + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-apr-util=$EBROOTAPRMINUTIL/bin/apu-1-config " +configopts += "--with-zlib=$EBROOTZLIB --with-lz4=$EBROOTLZ4 --with-serf=$EBROOTSERF" + +sanity_check_paths = { + 'files': ["bin/svn", "bin/svnversion"], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..28be3ea21de --- /dev/null +++ b/easybuild/easyconfigs/u/utf8proc/utf8proc-2.5.0-GCCcore-10.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'utf8proc' +version = '2.5.0' + +homepage = 'https://github.com/JuliaStrings/utf8proc' +description = """utf8proc is a small, clean C library that provides Unicode normalization, case-folding, +and other operations for data in the UTF-8 encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/JuliaStrings/utf8proc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4e8dfc898cfd062493cb7f42d95d70ccdd3a4cd4d90bec0c71b47cca688f1be'] + +builddependencies = [ + ('binutils', '2.35'), + ('CMake', '3.18.4'), +] + +separate_build_dir = True + +configopts = ['', '-DBUILD_SHARED_LIBS=true'] + +sanity_check_paths = { + 'files': ['include/utf8proc.h', 'lib/libutf8proc.a', 'lib/libutf8proc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 7d85f6da3499d345a8cf1e5ffb499551a00fa280 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 00:44:56 +0200 Subject: [PATCH 631/698] Drop python2 --- .../easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb | 6 ++---- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 8 ++++++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb index 6a8b8a9de33..ed589a49fb1 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.0.1-GCCcore-10.2.0.eb @@ -10,22 +10,20 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['SCons-3.0.4_fix-pip-install.patch'] checksums = [ '722ed104b5c624ecdc89bd4e02b094d2b14d99d47b5d0501961e47f579a2007c', # scons-4.0.1.tar.gz - 'c632a50184edbb0dc032943fd717e832577d4ad407eb7743e5331eddb842a69f', # SCons-3.0.4_fix-pip-install.patch ] builddependencies = [('binutils', '2.35')] -multi_deps = {'Python': ['3.8.6', '2.7.18']} +dependencies = [('Python', '3.8.6')] download_dep_fail = True use_pip = True sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/scons', 'bin/scons-time', 'bin/sconsign'], + 'files': ['bin/scons', 'bin/sconsign'], 'dirs': [], } diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb index 710686c4a78..d58e4465206 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -10,11 +10,15 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://archive.apache.org/dist/%(namelower)s'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc'] +patches =['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] builddependencies = [ ('binutils', '2.35'), - ('Python', '2.7.18'), # Serfs build scripts are python 2 only + ('Python', '3.8.6'), ('SCons', '4.0.1'), ] From c03de11e9c4285df4682cb2f0c49042f84088c17 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 00:46:45 +0200 Subject: [PATCH 632/698] adding easyconfigs: libGLU-9.0.1-GCCcore-10.2.0.eb, libdrm-2.4.102-GCCcore-10.2.0.eb, libglvnd-1.2.0-GCCcore-10.2.0.eb, libunwind-1.4.0-GCCcore-10.2.0.eb, Mako-1.1.3-GCCcore-10.2.0.eb, Mesa-20.2.1-GCCcore-10.2.0.eb --- .../l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb | 27 +++++++ .../l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb | 22 ++++++ .../libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb | 31 ++++++++ .../libunwind-1.4.0-GCCcore-10.2.0.eb | 36 +++++++++ .../m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb | 27 +++++++ .../m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 73 +++++++++++++++++++ 6 files changed, 216 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..cea272ad1b3 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.1-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.1' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['f6f484cfcd51e489afe88031afdea1e173aa652697e4c19ddbcb8260579a10f7'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Mesa', '20.2.1'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2aae368ccb1 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb @@ -0,0 +1,22 @@ +name = 'libdrm' +version = '2.4.102' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8bcbf9336c28e393d76c1f16d7e79e394a7fce8a2e929d52d3ad7ad8525ba05b'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [('X11', '20201008')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '--disable-manpages' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..1bba872c7e6 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libglvnd' +version = '1.2.0' + +homepage = 'https://github.com/NVIDIA/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/NVIDIA/libglvnd/releases/download/v%(version)s/'] +sources = ['libglvnd-%(version)s.tar.gz'] +checksums = ['2dacbcfa47b7ffb722cbddc0a4f1bc3ecd71d2d7bb461bceb8e396dc6b81dc6d'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [('X11', '20201008')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..c0a7684fce6 --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.4.0' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +checksums = [ + 'df59c931bd4d7ebfd83ee481c943edf015138089b8e50abed8d9c57ba9338435', # libunwind-1.4.0.tar.gz + '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('XZ', '5.2.5'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..7ac3876f78a --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.1.3-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.1.3' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8195c8c1400ceb53496064314c6736719c6f25e7479cd24c77be3d9361cddc27'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.35')] +multi_deps = {'Python': ['3.8.6', '2.7.18']} + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..218127da186 --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,73 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers are enabled based on system architecture: +# - llvmpipe: the high-performance Gallium LLVM driver +# - swr: Intel's OpenSWR +# Default renderer is llvmpipe. SWR can be enabled by setting the environment +# variable GALLIUM_DRIVER=swr + +name = 'Mesa' +version = '20.2.1' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +patches = ['%(name)s-20.0.2-match-swrast-loosely.patch'] +checksums = [ + 'd1a46d9a3f291bc0e0374600bdcb59844fa3eafaa50398e472a36fc65fd0244a', # mesa-20.2.1.tar.xz + 'e86abc2b9a9ad3e2fc604ad5d9bfe15a62e842e9900365fe7061849ea7438d90', # Mesa-20.0.2-match-swrast-loosely.patch +] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('pkg-config', '0.29.2'), + ('Mako', '1.1.3'), + ('libxml2', '2.9.10'), + ('expat', '2.2.9'), + ('gettext', '0.21'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('zstd', '1.4.5'), + ('libdrm', '2.4.102'), + ('libglvnd', '1.2.0'), + ('libunwind', '1.4.0'), + ('LLVM', '11.0.0'), + ('X11', '20201008'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=gallium -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host +# If you need a different configuration, it possible to override those values by setting your own configopts +# configopts += " -Dgallium-drivers=swrast,swr -Dswr-arches=avx,avx2,skx,knl" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 5304d030e96508dfcbae1b27418d5a14856bfa03 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 01:10:19 +0200 Subject: [PATCH 633/698] include serf python3 patch --- .../s/Serf/Serf-1.3.9_python3_scons.patch | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9_python3_scons.patch diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9_python3_scons.patch b/easybuild/easyconfigs/s/Serf/Serf-1.3.9_python3_scons.patch new file mode 100644 index 00000000000..fd3f3144959 --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9_python3_scons.patch @@ -0,0 +1,22 @@ +# Makes scons script compatible with python3 +# Author: Mikael Öhman +--- SConstruct.orig 2020-10-19 00:08:59.165775221 +0200 ++++ SConstruct 2020-10-19 00:29:58.378134064 +0200 +@@ -166,7 +166,7 @@ + match = re.search('SERF_MAJOR_VERSION ([0-9]+).*' + 'SERF_MINOR_VERSION ([0-9]+).*' + 'SERF_PATCH_VERSION ([0-9]+)', +- env.File('serf.h').get_contents(), ++ str(env.File('serf.h').get_contents()), + re.DOTALL) + MAJOR, MINOR, PATCH = [int(x) for x in match.groups()] + env.Append(MAJOR=str(MAJOR)) +@@ -183,7 +183,7 @@ + + unknown = opts.UnknownVariables() + if unknown: +- print 'Warning: Used unknown variables:', ', '.join(unknown.keys()) ++ print('Warning: Used unknown variables:', ', '.join(unknown.keys())) + + apr = str(env['APR']) + apu = str(env['APU']) From c61c2059e2b4a36ce2a29b2e66ad431606286558 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Mon, 19 Oct 2020 01:35:15 +0200 Subject: [PATCH 634/698] fix style --- easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb index d58e4465206..80f595ab284 100644 --- a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://archive.apache.org/dist/%(namelower)s'] sources = [SOURCELOWER_TAR_BZ2] -patches =['Serf-%(version)s_python3_scons.patch'] +patches = ['Serf-%(version)s_python3_scons.patch'] checksums = [ '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch From db925fda8719aad55d1b257574eecc4666d460dd Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Mon, 19 Oct 2020 11:12:47 +0200 Subject: [PATCH 635/698] Add SHA256 checksum --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 941120cb7bf..ef5317c4953 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -9,7 +9,7 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] -checksums = ['dbc2ed6135009edf28d4e1c2c4f63984'] +checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] dependencies = [ ('GCCcore', local_gccver), From 2cc51f540a71b3c61ba43fc79f1720588a8b6699 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Mon, 19 Oct 2020 11:12:59 +0200 Subject: [PATCH 636/698] Move moduleclass line to end of file --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index ef5317c4953..4bed86b4684 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -21,9 +21,6 @@ dependencies = [ default_cuda_version = None # Use strings like "11.0" or use the command line: --try-amend=default_cuda_version="10.2" -# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' - # NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. # The following list gives examples for the easyconfig # @@ -45,3 +42,6 @@ moduleclass = 'compiler' # module_add_nccl = False # Add NVHPC's NCCL library # module_add_nvshmem = False # Add NVHPC's NVSHMEM library # module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' \ No newline at end of file From 0a1a1a3e88ab382583f87224a14062ce796d4514 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Mon, 19 Oct 2020 11:21:27 +0200 Subject: [PATCH 637/698] Modify CUDA dependency --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 4bed86b4684..2b2ac516b3d 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -14,7 +14,7 @@ checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.34', '', ('GCCcore', local_gccver)), - ('CUDA', '11.0', '', SYSTEM), + ('CUDA', '11.0.2'), # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) ] From ba5505f2c00c781a399ad5470b846dd23600f027 Mon Sep 17 00:00:00 2001 From: Bob Date: Mon, 19 Oct 2020 11:44:46 +0200 Subject: [PATCH 638/698] adding easyconfigs: SeqKit-0.13.2.eb and patches: SeqKit-0.13.2_go-mod.patch --- .../easyconfigs/s/SeqKit/SeqKit-0.13.2.eb | 26 ++ .../s/SeqKit/SeqKit-0.13.2_go-mod.patch | 306 ++++++++++++++++++ 2 files changed, 332 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2.eb create mode 100644 easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2_go-mod.patch diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2.eb b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2.eb new file mode 100644 index 00000000000..19a11821ef8 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'SeqKit' +version = '0.13.2' + +homepage = 'https://bioinf.shenwei.me/seqkit/' +description = """SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation""" + +toolchain = SYSTEM + +github_account = 'shenwei356' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [('SeqKit-0.13.2_go-mod.patch', 1)] +checksums = [ + 'b88def607df69bfd12535ddcfdeb35ed80ba579e7f7dd87ce48342133a297aea', # v0.13.2.tar.gz + '6c68a1b7ee53a09313832db1a580c281c71585aefdf05d3ade9c779c458c55cc', # SeqKit-0.13.2_go-mod.patch +] + +builddependencies = [ + ('Go', '1.14.1'), +] + +installopts = './%(namelower)s' + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2_go-mod.patch b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2_go-mod.patch new file mode 100644 index 00000000000..ecf27fe6d0f --- /dev/null +++ b/easybuild/easyconfigs/s/SeqKit/SeqKit-0.13.2_go-mod.patch @@ -0,0 +1,306 @@ +Add go.mod and go.sum to have reproducible build. +Generated by GoPackage Easyblock. +author: Bob Dröge (University of Groningen) + +diff -ru --new-file seqkit-0.13.2.orig/seqkit/go.mod seqkit-0.13.2/seqkit/go.mod +--- seqkit-0.13.2.orig/go.mod 1970-01-01 01:00:00.000000000 +0100 ++++ seqkit-0.13.2/go.mod 2020-09-10 17:01:03.000000000 +0200 +@@ -0,0 +1,35 @@ ++module github.com/shenwei356/seqkit ++ ++go 1.14 ++ ++require ( ++ github.com/biogo/biogo v1.0.2 ++ github.com/biogo/hts v1.1.0 ++ github.com/bsipos/thist v1.0.0 ++ github.com/cespare/xxhash v1.1.0 ++ github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 // indirect ++ github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 ++ github.com/dustin/go-humanize v1.0.0 ++ github.com/edsrzf/mmap-go v1.0.0 // indirect ++ github.com/fsnotify/fsnotify v1.4.9 ++ github.com/iafan/cwalk v0.0.0-20191125092548-dd7f505d2f66 ++ github.com/klauspost/compress v1.11.0 // indirect ++ github.com/klauspost/pgzip v1.2.5 // indirect ++ github.com/logrusorgru/aurora v2.0.3+incompatible ++ github.com/mattn/go-colorable v0.1.7 ++ github.com/mattn/go-isatty v0.0.12 ++ github.com/mattn/go-runewidth v0.0.9 // indirect ++ github.com/mitchellh/go-homedir v1.1.0 ++ github.com/shenwei356/bio v0.0.0-20200707114446-e0b1f806773e ++ github.com/shenwei356/bpool v0.0.0-20160710042833-f9e0ee4d0403 // indirect ++ github.com/shenwei356/breader v0.0.0-20170924140440-21f0a70fe179 ++ github.com/shenwei356/bwt v0.0.0-20200418151221-ae79c9858c90 ++ github.com/shenwei356/go-logging v0.0.0-20171012171522-c6b9702d88ba ++ github.com/shenwei356/natsort v0.0.0-20190418160752-600d539c017d // indirect ++ github.com/shenwei356/util v0.0.0-20200809113039-4d78997fbf13 ++ github.com/shenwei356/xopen v0.0.0-20181203091311-f4f16ddd3992 ++ github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861 ++ github.com/spf13/cobra v1.0.0 ++ github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 ++ gonum.org/v1/netlib v0.0.0-20200824093956-f0ca4b3a5ef5 // indirect ++) + +diff -ru --new-file seqkit-0.13.2.orig/seqkit/go.sum seqkit-0.13.2/seqkit/go.sum +--- seqkit-0.13.2.orig/go.sum 1970-01-01 01:00:00.000000000 +0100 ++++ seqkit-0.13.2/go.sum 2020-09-10 17:01:16.000000000 +0200 +@@ -0,0 +1,258 @@ ++cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= ++dmitri.shuralyov.com/gpu/mtl v0.0.0-20190408044501-666a987793e9/go.mod h1:H6x//7gZCb22OMCxBHrMx7a5I7Hp++hsVxbQ4BYO7hU= ++github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= ++github.com/BurntSushi/xgb v0.0.0-20160522181843-27f122750802/go.mod h1:IVnqGOEym/WlBOVXweHU+Q+/VP0lqqI8lqeDx9IjBqo= ++github.com/OneOfOne/xxhash v1.2.2 h1:KMrpdQIwFcEqXDklaen+P1axHaj9BSKzvpUUfnHldSE= ++github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= ++github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af h1:wVe6/Ea46ZMeNkQjjBW6xcqyQA/j5e0D6GytH95g0gQ= ++github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw= ++github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc= ++github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= ++github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8= ++github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= ++github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= ++github.com/biogo/biogo v1.0.2 h1:PtMOoOb1ZrSjGMdwDa2VP3Y1QKC5uvWMrU4HThm1uys= ++github.com/biogo/biogo v1.0.2/go.mod h1:p+GFIiT20kY9/fPydaNTQW85a25lBqb0GzoDN5tEoPc= ++github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1 h1:LAHY5JxqhOgJDeDBGKsQ4300qd3sG8C0j5CQS8gD+Kw= ++github.com/biogo/boom v0.0.0-20150317015657-28119bc1ffc1/go.mod h1:fwtxkutinkQcME9Zlywh66T0jZLLjgrwSLY2WxH2N3U= ++github.com/biogo/graph v0.0.0-20150317020928-057c1989faed/go.mod h1:UuyD2swDzTz1ChZTQld42mP5pyePLSDccmGycTpxRew= ++github.com/biogo/hts v1.1.0 h1:J6Na8+e+MYyEpV1B762GUvt4mhtPn3tnQQaxWyKo5rk= ++github.com/biogo/hts v1.1.0/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgOw= ++github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k= ++github.com/bsipos/thist v1.0.0 h1:vZ3W5/ZnT54s4LHeonTCbnzCb20ERlJUnhiwXoGpsbY= ++github.com/bsipos/thist v1.0.0/go.mod h1:7i0xwRua1/bmUxcxi2xAxaFL895rLtOpKUwnw3NrT8I= ++github.com/cespare/xxhash v1.1.0 h1:a6HrQnmkObjyL+Gs60czilIUGqrzKutQD6XZog3p+ko= ++github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc= ++github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= ++github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk= ++github.com/coreos/etcd v3.3.10+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE= ++github.com/coreos/go-semver v0.2.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk= ++github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4= ++github.com/coreos/pkg v0.0.0-20180928190104-399ea9e2e55f/go.mod h1:E3G3o1h8I7cfcXa63jLwjI0eiQQMgzzUDFVpN/nH/eA= ++github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= ++github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548 h1:iwZdTE0PVqJCos1vaoKsclOGD3ADKpshg3SRtYBbwso= ++github.com/cznic/mathutil v0.0.0-20181122101859-297441e03548/go.mod h1:e6NPNENfs9mPDVNRekM7lKScauxd5kXTr1Mfyig6TDM= ++github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8 h1:LpMLYGyy67BoAFGda1NeOBQwqlv7nUXpm+rIVHGxZZ4= ++github.com/cznic/sortutil v0.0.0-20181122101858-f5f958428db8/go.mod h1:q2w6Bg5jeox1B+QkJ6Wp/+Vn0G/bo3f1uY7Fn3vivIQ= ++github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= ++github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ= ++github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no= ++github.com/dustin/go-humanize v1.0.0 h1:VSnTsYCnlFHaM2/igO1h6X3HA71jcobQuxemgkq4zYo= ++github.com/dustin/go-humanize v1.0.0/go.mod h1:HtrtbFcZ19U5GC7JDqmcUSB87Iq5E25KnS6fMYU6eOk= ++github.com/edsrzf/mmap-go v1.0.0 h1:CEBF7HpRnUCSJgGUb5h1Gm7e3VkmVDrR8lvWVLtrOFw= ++github.com/edsrzf/mmap-go v1.0.0/go.mod h1:YO35OhQPt3KJa3ryjFM5Bs14WD66h8eGKpfaBNrHW5M= ++github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90 h1:WXb3TSNmHp2vHoCroCIB1foO/yQ36swABL8aOVeDpgg= ++github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k= ++github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo= ++github.com/fsnotify/fsnotify v1.4.9 h1:hsms1Qyu0jgnwNXIxa+/V/PDsU6CfLf6CNO8H7IWoS4= 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v0.0.0-20170911015856-a32031077861 h1:9z0Ip656Pc+3cj/BpHkErOVg4iE0xcAdvJwfA3hMVzU= ++github.com/smallfish/simpleyaml v0.0.0-20170911015856-a32031077861/go.mod h1:eGZ1jp5PTJ+XVhTErUmw0xyPbgctPFlixWPypUrDkSs= ++github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM= ++github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72 h1:qLC7fQah7D6K1B0ujays3HV9gkFtllcxhzImRR7ArPQ= ++github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA= ++github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ= ++github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE= ++github.com/spf13/cobra v1.0.0 h1:6m/oheQuQ13N9ks4hubMG6BnvwOeaJrqSPLahSnczz8= ++github.com/spf13/cobra v1.0.0/go.mod h1:/6GTrnGXV9HjY+aR4k0oJ5tcvakLuG6EuKReYlHNrgE= ++github.com/spf13/jwalterweatherman v1.0.0/go.mod h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo= ++github.com/spf13/pflag v1.0.3 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= ++github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4= ++github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= ++github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= ++github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= ++github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939 h1:BhIUXV2ySTLrKgh/Hnts+QTQlIbWtomXt3LMdzME0A0= ++github.com/tatsushid/go-prettytable v0.0.0-20141013043238-ed2d14c29939/go.mod h1:omGxs4/6hNjxPKUTjmaNkPzehSnNJOJN6pMEbrlYIT4= ++github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= ++github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= ++github.com/ulikunitz/xz v0.5.6/go.mod h1:2bypXElzHzzJZwzH67Y6wb67pO62Rzfn7BSiF4ABRW8= ++github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= ++github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= ++go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= ++go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= ++go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= ++go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q= ++golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= ++golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= ++golang.org/x/crypto v0.0.0-20190510104115-cbcb75029529/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI= ++golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5 h1:58fnuSXlxZmFdJyvtTFVmVhcMLU6v5fEb/ok4wyqtNU= ++golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI= ++golang.org/x/exp v0.0.0-20180321215751-8460e604b9de/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20180807140117-3d87b88a115f/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20190306152737-a1d7652674e8/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA= ++golang.org/x/exp v0.0.0-20190312203227-4b39c73a6495/go.mod h1:ZjyILWgesfNpC6sMxTJOJm9Kp84zZh5NQWvqDGG3Qr8= ++golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a h1:7Wlg8L54In96HTWOaI4sreLJ6qfyGuvSau5el3fK41Y= ++golang.org/x/exp v0.0.0-20200119233911-0405dc783f0a/go.mod h1:2RIsYlXP63K8oxa1u096TMicItID8zy7Y6sNkU49FU4= ++golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs= ++golang.org/x/image v0.0.0-20190227222117-0694c2d4d067/go.mod h1:kZ7UVZpmo3dzQBMxlp+ypCbDeSB+sBbTgSJuh5dn5js= ++golang.org/x/image v0.0.0-20190802002840-cff245a6509b h1:+qEpEAPhDZ1o0x3tHzZTQDArnOixOzGD9HUJfcg0mb4= ++golang.org/x/image v0.0.0-20190802002840-cff245a6509b/go.mod h1:FeLwcggjj3mMvU+oOTbSwawSJRM1uh48EjtB4UJZlP0= ++golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= ++golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc= ++golang.org/x/mobile v0.0.0-20190312151609-d3739f865fa6/go.mod h1:z+o9i4GpDbdi3rU15maQ/Ox0txvL9dWGYEHz965HBQE= ++golang.org/x/mobile v0.0.0-20190719004257-d2bd2a29d028/go.mod h1:E/iHnbuqvinMTCcRqshq8CkpyQDoeVncDDYHnLhea+o= ++golang.org/x/mod v0.1.0/go.mod h1:0QHyrYULN0/3qlju5TqG8bIK38QM8yzMo5ekMj3DlcY= ++golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= ++golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= ++golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= ++golang.org/x/net v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= ++golang.org/x/net v0.0.0-20190603091049-60506f45cf65/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= ++golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= ++golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= ++golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= ++golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= ++golang.org/x/sys v0.0.0-20190312061237-fead79001313/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20190602015325-4c4f7f33c9ed/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae h1:/WDfKMnPU+m5M4xB+6x4kaepxRw6jWvR5iDRdvjHgy8= ++golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= ++golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= ++golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk= ++golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= ++golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20180525024113-a5b4c53f6e8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190206041539-40960b6deb8e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= ++golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= ++golang.org/x/tools v0.0.0-20190312151545-0bb0c0a6e846/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= ++golang.org/x/tools v0.0.0-20190606050223-4d9ae51c2468/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc= ++golang.org/x/tools v0.0.0-20191012152004-8de300cfc20a/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= ++golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= ++gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4 h1:nYxTaCPaVoJbxx+vMVnsFb6kw5+6aJCx52m/lmM/Vog= ++gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJDxZx5Dpnq+c3wtXuadVZAcxbbBo= ++gonum.org/v1/gonum v0.8.1 h1:wGtP3yGpc5mCLOLeTeBdjeui9oZSz5De0eOjMLC/QuQ= ++gonum.org/v1/gonum v0.8.1/go.mod h1:oe/vMfY3deqTw+1EZJhuvEW2iwGF1bW9wwu7XCu0+v0= ++gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0/go.mod h1:wa6Ws7BG/ESfp6dHfk7C6KdzKA7wR7u/rKwOGE66zvw= ++gonum.org/v1/netlib v0.0.0-20200824093956-f0ca4b3a5ef5 h1:f+MwB6AfpSt3J5u5WH17TOx0eCa2sL26b8D9lfgoK04= ++gonum.org/v1/netlib v0.0.0-20200824093956-f0ca4b3a5ef5/go.mod h1:btLGKT60dpW8TWRO6cDMdlFBmETiIjn20d9poIDla1k= ++gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b h1:Qh4dB5D/WpoUUp3lSod7qgoyEHbDGPUWjIbnqdqqe1k= ++gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZBvf6cAIx93T+c/OS2HFAYskSZc= ++google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= ++google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= ++google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= ++google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= ++gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw= ++gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo= ++gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= ++gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo= ++gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= ++gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++gopkg.in/yaml.v2 v2.2.2 h1:ZCJp+EgiOT7lHqUV2J862kp8Qj64Jo6az82+3Td9dZw= ++gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= ++honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= ++modernc.org/cc v1.0.0/go.mod h1:1Sk4//wdnYJiUIxnW8ddKpaOJCF37yAdqYnkxUpaYxw= ++modernc.org/golex v1.0.0/go.mod h1:b/QX9oBD/LhixY6NDh+IdGv17hgB+51fET1i2kPSmvk= ++modernc.org/mathutil v1.0.0/go.mod h1:wU0vUrJsVWBZ4P6e7xtFJEhFSNsfRLJ8H458uRjg03k= ++modernc.org/strutil v1.1.0/go.mod h1:lstksw84oURvj9y3tn8lGvRxyRC1S2+g5uuIzNfIOBs= ++modernc.org/xc v1.0.0/go.mod h1:mRNCo0bvLjGhHO9WsyuKVU4q0ceiDDDoEeWDJHrNx8I= ++rsc.io/pdf v0.1.1 h1:k1MczvYDUvJBe93bYd7wrZLLUEcLZAuF824/I4e5Xr4= ++rsc.io/pdf v0.1.1/go.mod h1:n8OzWcQ6Sp37PL01nO98y4iUCRdTGarVfzxY20ICaU4= From 75a2f3b35de604a8119510dd513c407c9182cc1d Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 19 Oct 2020 12:29:38 +0200 Subject: [PATCH 639/698] As discussed on EB slack, FLTK should really be at GCCcore level. It is visualization, and likely doesn't benefit from e.g. installation at iccifort level. Thus, there is no reason not to push it down to GCCcore --- .../{FLTK-1.3.5-GCC-9.3.0.eb => FLTK-1.3.5-GCCcore-9.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/FLTK/{FLTK-1.3.5-GCC-9.3.0.eb => FLTK-1.3.5-GCCcore-9.3.0.eb} (95%) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb similarity index 95% rename from easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb rename to easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb index a68c6268969..a96311c4555 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb @@ -11,7 +11,7 @@ description = """FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.""" -toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} source_urls = ['https://fltk.org/pub/%(namelower)s/%(version)s/'] From 852a62e2ea9605f533d0bd2280b078ba279eb6fc Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Mon, 19 Oct 2020 13:01:46 +0200 Subject: [PATCH 640/698] Added binutils as builddep, now that we pushed to GCCcore. It was already failing on my system without it... --- easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb index a96311c4555..b47d9693055 100644 --- a/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/FLTK/FLTK-1.3.5-GCCcore-9.3.0.eb @@ -24,6 +24,10 @@ checksums = [ configopts = '--enable-shared --enable-threads --enable-xft' +builddependencies = [ + ('binutils', '2.34') +] + dependencies = [ ('Mesa', '20.0.2'), ('libGLU', '9.0.1'), From 0a8c4590623dbb3af40c016c833355eb78df588f Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 19 Oct 2020 10:17:26 +0200 Subject: [PATCH 641/698] Score-P v6.0: Improve support for binutils 2.34 Amend ba4957c022a40c96ac5e2f0e5ef577e0c594fd03 to support the binutils 2.34 API in another source-code location. --- .../s/Score-P/Score-P-6.0-gompi-2020a.eb | 2 +- .../Score-P-6.0_binutils_2.34_api_change.patch | 13 +++++++++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb index 497c64d9f05..add15a5eecb 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb @@ -26,7 +26,7 @@ sources = ['scorep-%(version)s.tar.gz'] patches = ['Score-P-6.0_binutils_2.34_api_change.patch'] checksums = [ '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz - 'd5a5208077f60850d61a230c3a2d5e0d46ac0b5ec962904cba3010b9a904b59f', # Score-P-6.0_binutils_2.34_api_change.patch + 'c64a3c0b666a75b114e29a48c8d1f5e420be3674a0fba2b37ecd50630ba2d45c', # Score-P-6.0_binutils_2.34_api_change.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch b/easybuild/easyconfigs/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch index 37d8af47e38..b8d22fd1c53 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0_binutils_2.34_api_change.patch @@ -22,3 +22,16 @@ from upstream repo; fix will be included in releases after v6.0. #endif #include "scorep_unwinding_region.h" +--- a/src/adapters/compiler/scorep_compiler_symbol_table_libbfd.c ++++ b/src/adapters/compiler/scorep_compiler_symbol_table_libbfd.c +@@ -43,6 +43,10 @@ + + #include + ++#ifndef bfd_get_section ++#define bfd_get_section( asymbol ) bfd_asymbol_section( asymbol ) ++#endif ++ + #include + #define SCOREP_DEBUG_MODULE_NAME COMPILER + #include From f4fdf37ac6b840457173e20d1ca93ca5bb767b60 Mon Sep 17 00:00:00 2001 From: Markus Geimer Date: Mon, 19 Oct 2020 10:23:16 +0200 Subject: [PATCH 642/698] Score-P v6.0: Prevent PDT from instrumenting .cu files --- .../s/Score-P/Score-P-6.0-gompi-2020a.eb | 6 +++++- .../s/Score-P/Score-P-6.0-gompic-2019b.eb | 4 +++- .../s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch | 16 ++++++++++++++++ 3 files changed, 24 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb index add15a5eecb..91cbda21537 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompi-2020a.eb @@ -23,10 +23,14 @@ toolchain = {'name': 'gompi', 'version': '2020a'} source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] sources = ['scorep-%(version)s.tar.gz'] -patches = ['Score-P-6.0_binutils_2.34_api_change.patch'] +patches = [ + 'Score-P-6.0_binutils_2.34_api_change.patch', + 'Score-P-6.0_no_PDT_for_CUDA.patch', +] checksums = [ '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz 'c64a3c0b666a75b114e29a48c8d1f5e420be3674a0fba2b37ecd50630ba2d45c', # Score-P-6.0_binutils_2.34_api_change.patch + '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb index fed53023160..96ed8336a4d 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0-gompic-2019b.eb @@ -1,5 +1,5 @@ ## -# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany # Copyright 2020 TU Dresden, Germany # Authors:: Bernd Mohr # Markus Geimer @@ -24,8 +24,10 @@ toolchain = {'name': 'gompic', 'version': '2019b'} source_urls = ['https://www.vi-hps.org/cms/upload/packages/scorep/'] sources = ['scorep-%(version)s.tar.gz'] +patches = ['Score-P-6.0_no_PDT_for_CUDA.patch'] checksums = [ '5dc1023eb766ba5407f0b5e0845ec786e0021f1da757da737db1fb71fc4236b8', # scorep-6.0.tar.gz + '93e3fc5d19a89d14ce98fb772b4d9ddde4191df3ce321c9965602aa12d43fa93', # Score-P-6.0_no_PDT_for_CUDA.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch b/easybuild/easyconfigs/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch new file mode 100644 index 00000000000..24d90a4184a --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-6.0_no_PDT_for_CUDA.patch @@ -0,0 +1,16 @@ +Prevent PDT from instrumenting .cu files; fixes 'make installcheck' when both +PDT and CUDA are enabled. Patch backported from upstream repo; fix will be +included in releases after v6.0. +--- a/src/tools/instrumenter/scorep_instrumenter_pdt.cpp ++++ b/src/tools/instrumenter/scorep_instrumenter_pdt.cpp +@@ -74,6 +74,10 @@ SCOREP_Instrumenter_PdtAdapter::precompile( SCOREP_Instrumenter& instrum + SCOREP_Instrumenter_CmdLine& cmdLine, + const std::string& source_file ) + { ++ if ( is_cuda_file( source_file ) ) ++ { ++ return source_file; ++ } + std::string extension = get_extension( source_file ); + if ( is_fortran_file( source_file ) ) + { From 32487d5a28fe090930664b4459e76cee25ee4326 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 19 Oct 2020 15:22:49 +0000 Subject: [PATCH 643/698] adding easyconfigs: V8-3.2.0-foss-2019b-R-3.6.2.eb --- .../v/V8/V8-3.2.0-foss-2019b-R-3.6.2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/v/V8/V8-3.2.0-foss-2019b-R-3.6.2.eb diff --git a/easybuild/easyconfigs/v/V8/V8-3.2.0-foss-2019b-R-3.6.2.eb b/easybuild/easyconfigs/v/V8/V8-3.2.0-foss-2019b-R-3.6.2.eb new file mode 100644 index 00000000000..e5bb98dae76 --- /dev/null +++ b/easybuild/easyconfigs/v/V8/V8-3.2.0-foss-2019b-R-3.6.2.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'V8' +version = '3.2.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/V8/' +description = """R interface to Google's open source JavaScript engine""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s'] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['f575e07c6fefbc53a96e90bbb41ffdf67794cca797661eb97a6f52348ae20d7c'] + +dependencies = [ + ('R', '3.6.2'), + ('nodejs', '12.16.1'), +] + +installopts = '--configure-vars="INCLUDE_DIR=$CPATH LIB_DIR=$LIBRARY_PATH"' + +sanity_check_paths = { + 'files': ['%(name)s/R/%(name)s'], + 'dirs': ['%(name)s'], +} + +moduleclass = 'lang' From eeedc759578230d2c8153bd17e0c1e3f3d1b1633 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Oct 2020 10:24:39 +0200 Subject: [PATCH 644/698] adding easyconfigs: Bsoft-2.0.7-GCC-9.3.0.eb --- .../b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb | 85 +++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb diff --git a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb new file mode 100644 index 00000000000..d77e648e6be --- /dev/null +++ b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7-GCC-9.3.0.eb @@ -0,0 +1,85 @@ +# Author: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu +# Updated by: Alex Domingo - VUB - http://www.vub.be + +easyblock = 'Bundle' + +name = 'Bsoft' +version = '2.0.7' +local_libtiff_version = '4.1.0' + +homepage = 'https://lsbr.niams.nih.gov/bsoft/' + +description = """ + Bsoft is a collection of programs and a platform for development of software + for image and molecular processing in structural biology. Problems in + structural biology are approached with a highly modular design, allowing fast + development of new algorithms without the burden of issues such as file I/O. + It provides an easily accessible interface, a resource that can be and has + been used in other packages. +""" + +toolchain = {'name': 'GCC', 'version': '9.3.0'} +toolchainopts = {'openmp': True, 'pic': True} + +dependencies = [ + ('FFTW', '3.3.8', '-serial'), + ('libjpeg-turbo', '2.0.4'), + ('libpng', '1.6.37'), + ('LibTIFF', local_libtiff_version), + ('libxml2', '2.9.10'), + ('Tk', '8.6.10'), +] + +parallel = 1 + +# Use packages from EB +local_bsoft_configopts = "--fftw=$EBROOTFFTW --jpeg=$EBROOTLIBJPEGMINTURBO --png=$EBROOTLIBPNG" +# Use libraries from LibTIFF already installed in EB +local_bsoft_configopts += " --tiff=$EBROOTLIBTIFF" + +default_easyblock = 'ConfigureMake' + +components = [ + # Bsoft needs headers from LibTIFF only available in its source code + ('LibTIFF', local_libtiff_version, { + 'source_urls': ['https://download.osgeo.org/libtiff/'], + 'sources': ['tiff-%s.tar.gz' % local_libtiff_version], + 'checksums': ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'], + 'start_dir': 'tiff-%s' % local_libtiff_version, + 'configopts': '--enable-ld-version-script', + # skip installation: Bsoft only needs LibTIFF headers at build time and + # those headers are never installed in any case + 'install_cmd': 'true', + }), + (name, version, { + 'source_urls': ['https://lsbr.niams.nih.gov/bsoft/'], + 'sources': ['%%(namelower)s%s.tgz' % '_'.join(version.split('.'))], + 'patches': ['%(name)s-%(version)s_use-eb-packages.patch'], + 'checksums': [ + 'f86d19b3c843cf8a7dd22871f32aca66ab40546ba3b545f7e4ae95c6ec47379c', # bsoft2_0_7.tgz + '9cb67d30ba8360c08dab01090d084dcfcf5c435ccb1426210bdaabe5ee8c80ed', # Bsoft-2.0.7_use-eb-packages.patch + ], + 'preconfigopts': 'EBBUILDLIBTIFF=%%(builddir)s/tiff-%s' % local_libtiff_version, # use headers in local LibTIFF + 'configure_cmd': './bconf', + 'configopts': local_bsoft_configopts, + 'buildopts': '%(namelower)s', + }), +] + +# Emulate Scripts/postinstall +postinstallcmds = ["cd %%(installdir)s/bin && ln -sf ../tcltk/%s" % x for x in ['bshow', 'bshowX', 'brun', 'brunX']] + +sanity_check_paths = { + 'files': ['bsoft.bashrc', 'bsetup', 'bin/bshell', 'bin/brun', 'bin/brunX', 'bin/bshow', 'bin/bshowX', + 'lib/libbsoft.%s' % SHLIB_EXT, 'lib/libbshow.%s' % SHLIB_EXT], + 'dirs': ['doc', 'parameters', 'tcltk'], +} + +sanity_check_commands = ["bshell -verb 1 -ico 480,4 -comp 30"] + +modextrapaths = { + 'BSOFT': '', + 'BPARAM': 'parameters', +} + +moduleclass = 'bio' From 9ff166bc5d578256e34da665f4eb540abe0cdafe Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Oct 2020 10:29:35 +0200 Subject: [PATCH 645/698] add patch Bsoft-2.0.7_use-eb-packages.patch --- .../b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch | 132 ++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch diff --git a/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch new file mode 100644 index 00000000000..575dee83d7b --- /dev/null +++ b/easybuild/easyconfigs/b/Bsoft/Bsoft-2.0.7_use-eb-packages.patch @@ -0,0 +1,132 @@ +Adapt configuration scripts of Bsoft to EasyBuild environment +author: Alex Domingo (Vrije Universiteit Brussel) +--- dev.rsc.orig 2019-05-09 21:04:05.000000000 +0200 ++++ dev.rsc 2020-10-17 12:35:46.233721000 +0200 +@@ -38,24 +38,24 @@ + HAVE_FFTW=0 + HAVE_XML=0 + +- if [ -e $LIBFFTW/api/fftw3.h ]; then ++ if [ -e $LIBFFTW/include/fftw3.h ]; then + echo "# FFTW3 found" + HAVE_FFTW=1 + else + echo "# No FFTW3 libraries found!" +- echo "# Looking for: $LIBFFTW/api/fftw3.h" ++ echo "# Looking for: $LIBFFTW/include/fftw3.h" + fi + +- if [ -e $SDK/usr/include/libxml2 ]; then ++ if [ -e $EBROOTLIBXML2/include/libxml2 ]; then + echo "# libxml2 found" + HAVE_XML=1 +- x=`grep -A 3 xmlStrPrintf $SDK/usr/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` ++ x=`grep -A 3 xmlStrPrintf $EBROOTLIBXML2/include/libxml2/libxml/xmlstring.h | grep msg | grep xmlChar` + if [[ $x =~ xmlChar ]]; then + HAVE_XML=2 + fi + else + echo "# No XML library found!" +- echo "# Looking for: $SDK/usr/include/libxml2" ++ echo "# Looking for: $EBROOTLIBXML2/include/libxml2" + fi + + # Optional +@@ -71,13 +71,13 @@ + TCLINC=$TCL/Headers + TKINC=$TK/Headers + elif [[ $SYS =~ Linux ]]; then +- TCL=/usr +- TK=/usr ++ TCL=$EBROOTTCL ++ TK=$EBROOTTK + TCLINC=$TCL/include + TKINC=$TK/include +- if [ -e /usr/include/tk ]; then +- TCLINC=/usr/include/tcl +- TKINC=/usr/include/tk ++ if [ -e $EBROOTTK/include/tk ]; then ++ TCLINC=$EBROOTTCL/include/tcl ++ TKINC=$EBROOTTK/include/tk + fi + fi + +@@ -90,28 +90,28 @@ + TKO="" + fi + +- if [ -e $LIBTIFF/libtiff/tiff.h ]; then ++ if [ -e $EBBUILDLIBTIFF/libtiff/tiff.h ]; then + echo "# libtiff found" + HAVE_TIFF=1 + else + echo "# No TIFF library found! TIFF files will not be supported!" +- echo "# Looking for: $LIBTIFF/libtiff/tiff.h" ++ echo "# Looking for: $EBBUILDLIBTIFF/libtiff/tiff.h" + fi + +- if [ -e $LIBPNG/png.h ]; then ++ if [ -e $LIBPNG/include/png.h ]; then + echo "# libpng found" + HAVE_PNG=1 + else + echo "# No PNG library found! PNG files will not be supported!" +- echo "# Looking for: $LIBPNG/png.h" ++ echo "# Looking for: $LIBPNG/include/png.h" + fi + +- if [ -e $LIBJPEG/jpeglib.h ]; then ++ if [ -e $LIBJPEG/include/jpeglib.h ]; then + echo "# libjpeg found" + HAVE_JPEG=1 + else + echo "# No JPEG library found! JPEG files will not be supported!" +- echo "# Looking for: $LIBJPEG/jpeglib.h" ++ echo "# Looking for: $LIBJPEG/include/jpeglib.h" + fi + + } +--- bsoft/bsoft_conf.orig 2019-11-05 20:05:09.000000000 +0100 ++++ bsoft/bsoft_conf 2020-10-17 17:11:31.028913000 +0200 +@@ -129,7 +129,7 @@ + LIBLIST="" + + +-XMLINC=$SDK/usr/include/libxml2 ++XMLINC=$EBROOTLIBXML2/include/libxml2 + if [ -e $XMLINC ]; then + CFLAGS=$CFLAGS' -DHAVE_XML' + if [ $HAVE_XML == 2 ]; then +@@ -163,7 +163,7 @@ + + if [ $HAVE_TIFF = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_TIFF" +- INCLUDES="$INCLUDES -I$LIBTIFF/libtiff" ++ INCLUDES="$INCLUDES -I$EBBUILDLIBTIFF/libtiff" + # LIBDIR="$LIBDIR -L$LIBTIFF/lib" + # LINKLIBS="$LINKLIBS -ltiff"; + LIBLIST="$LIBLIST $LIBTIFF/lib/libtiff.a" +@@ -171,8 +171,8 @@ + + if [ $HAVE_PNG = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_PNG" +- INCLUDES="$INCLUDES -I$LIBPNG" +-# LIBDIR="$LIBDIR -L$LIBPNG/lib" ++ INCLUDES="$INCLUDES -I$LIBPNG/include" ++ LIBDIR="$LIBDIR -L$EBROOTZLIB/lib" + # LINKLIBS="$LINKLIBS -lz -lpng"; + LINKLIBS="$LINKLIBS -lz"; + LIBLIST="$LIBLIST $LIBPNG/lib/libpng.a" +@@ -180,10 +180,10 @@ + + if [ $HAVE_JPEG = 1 ]; then + CFLAGS="$CFLAGS -DHAVE_JPEG" +- INCLUDES="$INCLUDES -I$LIBJPEG" ++ INCLUDES="$INCLUDES -I$LIBJPEG/include" + # LIBDIR="$LIBDIR -L$LIBJPEG/lib" + # LINKLIBS="$LINKLIBS -ljpeg"; +- LIBLIST="$LIBLIST $LIBJPEG/lib/libjpeg.a" ++ LIBLIST="$LIBLIST $LIBJPEG/lib64/libjpeg.a" + fi + + # Tcl/Tk From 43c01b26752437bf49a06112826d83a4d2cf6999 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 19 Oct 2020 22:05:39 +0200 Subject: [PATCH 646/698] {devel,lib,system,tools}[GCCcore/10.2.0] OpenPGM v5.2.122, ZeroMQ v4.3.3, IPython v7.18.1, JupyterLab v2.2.8 ... w/ Python 3.8.6 (#11526) * adding easyconfigs: OpenPGM-5.2.122-GCCcore-10.2.0.eb, ZeroMQ-4.3.3-GCCcore-10.2.0.eb, IPython-7.18.1-GCCcore-10.2.0.eb, libsodium-1.0.18-GCCcore-10.2.0.eb * Add jupyterlab, fix deps and checksums * Add missing checksum to jupyterlab * Revert OpenPGM back to python 2.7.18 build dep. * Use pip for updated terminado * Include JUPYTERLAB_DIR env variable Co-authored-by: c3-micke --- .../IPython/IPython-7.18.1-GCCcore-10.2.0.eb | 144 ++++++++++++++++++ .../JupyterLab-2.2.8-GCCcore-10.2.0.eb | 48 ++++++ .../libsodium-1.0.18-GCCcore-10.2.0.eb | 33 ++++ .../OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb | 37 +++++ .../z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb | 38 +++++ 5 files changed, 300 insertions(+) create mode 100644 easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a4b55345034 --- /dev/null +++ b/easybuild/easyconfigs/i/IPython/IPython-7.18.1-GCCcore-10.2.0.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'IPython' +version = '7.18.1' + +homepage = 'https://ipython.org/index.html' +description = """IPython provides a rich architecture for interactive computing with: + Powerful interactive shells (terminal and Qt-based). + A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. + Support for interactive data visualization and use of GUI toolkits. + Flexible, embeddable interpreters to load into your own projects. + Easy to use, high performance tools for parallel computing.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('ZeroMQ', '4.3.3'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('ipython_genutils', '0.2.0', { + 'checksums': ['eb2e116e75ecef9d4d228fdc66af54269afa26ab4463042e33785b887c628ba8'], + }), + ('ipython', version, { + 'modulename': 'IPython', + 'checksums': ['a331e78086001931de9424940699691ad49dfb457cea31f5471eae7b78222d5e'], + }), + ('pickleshare', '0.7.5', { + 'checksums': ['87683d47965c1da65cdacaf31c8441d12b8044cdec9aca500cd78fc2c683afca'], + }), + ('prompt_toolkit', '3.0.7', { + 'checksums': ['822f4605f28f7d2ba6b0b09a31e25e140871e96364d1d377667b547bb3bf4489'], + }), + ('traitlets', '5.0.4', { + 'checksums': ['86c9351f94f95de9db8a04ad8e892da299a088a64fd283f9f6f18770ae5eae1b'], + }), + ('parso', '0.7.1', { + 'checksums': ['caba44724b994a8a5e086460bb212abc5a8bc46951bf4a9a1210745953622eb9'], + }), + ('jedi', '0.17.2', { + 'checksums': ['86ed7d9b750603e4ba582ea8edc678657fb4007894a12bcf6f4bb97892f31d20'], + }), + ('testpath', '0.4.4', { + 'use_pip': False, + 'checksums': ['60e0a3261c149755f4399a1fff7d37523179a70fdc3abdf78de9fc2604aeec7e'], + }), + ('Send2Trash', '1.5.0', { + 'checksums': ['60001cc07d707fe247c94f74ca6ac0d3255aabcb930529690897ca2a39db28b2'], + }), + ('bleach', '3.2.1', { + 'checksums': ['52b5919b81842b1854196eaae5ca29679a2f2e378905c346d3ca8227c2c66080'], + }), + ('pandocfilters', '1.4.2', { + 'checksums': ['b3dd70e169bb5449e6bc6ff96aea89c5eea8c5f6ab5e207fc2f521a2cf4a0da9'], + }), + ('pyzmq', '19.0.2', { + 'modulename': 'zmq', + 'checksums': ['296540a065c8c21b26d63e3cea2d1d57902373b16e4256afe46422691903a438'], + }), + ('entrypoints', '0.3', { + 'use_pip': False, + 'checksums': ['c70dd71abe5a8c85e55e12c19bd91ccfeec11a6e99044204511f9ed547d48451'], + }), + ('jupyter_core', '4.6.3', { + 'checksums': ['394fd5dd787e7c8861741880bdf8a00ce39f95de5d18e579c74b882522219e7e'], + }), + ('nbformat', '5.0.7', { + 'checksums': ['54d4d6354835a936bad7e8182dcd003ca3dc0cedfee5a306090e04854343b340'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('defusedxml', '0.6.0', { + 'checksums': ['f684034d135af4c6cbb949b8a4d2ed61634515257a67299e5f940fbaa34377f5'], + }), + ('jupyterlab_pygments', '0.1.2', { + 'checksums': ['cfcda0873626150932f438eccf0f8bf22bfa92345b814890ab360d666b254146'], + }), + ('async_generator', '1.10', { + 'checksums': ['6ebb3d106c12920aaae42ccb6f787ef5eefdcdd166ea3d628fa8476abe712144'], + }), + ('nest_asyncio', '1.4.1', { + 'checksums': ['b86c3193abda5b2eeccf8c79894bc71c680369a178f4b068514ac00720b14e01'], + }), + ('nbclient', '0.5.0', { + 'checksums': ['8ad52d27ba144fca1402db014857e53c5a864a2f407be66ca9d74c3a56d6591d'], + }), + ('nbconvert', '6.0.7', { + 'checksums': ['cbbc13a86dfbd4d1b5dee106539de0795b4db156c894c2c5dc382062bbc29002'], + }), + ('tornado', '6.0.4', { + 'checksums': ['0fe2d45ba43b00a41cd73f8be321a44936dc1aba233dee979f17a042b83eb6dc'], + }), + ('terminado', '0.9.1', { + 'checksums': ['3da72a155b807b01c9e8a5babd214e052a0a45a975751da3521a1c3381ce6d76'], + }), + ('jupyter_client', '6.1.7', { + 'checksums': ['49e390b36fe4b4226724704ea28d9fb903f1a3601b6882ce3105221cd09377a1'], + }), + ('backcall', '0.2.0', { + 'checksums': ['5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e'], + }), + ('ipykernel', '5.3.4', { + 'checksums': ['9b2652af1607986a1b231c62302d070bc0534f564c393a5d9d130db9abbbe89d'], + }), + ('prometheus_client', '0.8.0', { + 'checksums': ['c6e6b706833a6bd1fd51711299edee907857be10ece535126a158f911ee80915'], + }), + ('ipywidgets', '7.5.1', { + 'checksums': ['e945f6e02854a74994c596d9db83444a1850c01648f1574adf144fbbabe05c97'], + }), + ('argon2-cffi', '20.1.0', { + 'modulename': 'argon2', + 'checksums': ['d8029b2d3e4b4cea770e9e5a0104dd8fa185c1724a0f01528ae4826a6d25f97d'], + }), + ('notebook', '6.1.4', { + 'checksums': ['687d01f963ea20360c0b904ee7a37c3d8cda553858c8d6e33fd0afd13e89de32'], + }), + ('widgetsnbextension', '3.5.1', { + 'checksums': ['079f87d87270bce047512400efd70238820751a11d2d8cb137a5a5bdbaf255c7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ipython'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/IPython'], +} + +sanity_check_commands = [ + "ipython -h", + "jupyter notebook --help", + "iptest", +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4633201883c --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-2.2.8-GCCcore-10.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '2.2.8' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('json5', '0.9.5', { + 'checksums': ['703cfee540790576b56a92e1c6aaa6c4b0d98971dc358ead83812aa4d06bdb96'], + }), + ('jupyterlab_server', '1.2.0', { + 'checksums': ['5431d9dde96659364b7cc877693d5d21e7b80cea7ae3959ecc2b87518e5f5d8c'], + }), + (name, version, { + 'patches': ['%(name)s-1.2.5_set-app-path-for-easybuild.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + 'c8377bee30504919c1e79949f9fe35443ab7f5c4be622c95307e8108410c8b8c', # jupyterlab-2.2.8.tar.gz + # JupyterLab-1.2.5_set-app-path-for-easybuild.patch + 'a219b1071f37f848f7e79c6800149c0b2386a2b748be43288bc32af8e7dab668', + ], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a9b32bf6280 --- /dev/null +++ b/easybuild/easyconfigs/l/libsodium/libsodium-1.0.18-GCCcore-10.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libsodium' +version = '1.0.18' + +homepage = 'https://doc.libsodium.org/' + +description = """ + Sodium is a modern, easy-to-use software library for encryption, decryption, + signatures, password hashing and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.libsodium.org/libsodium/releases/', + 'https://download.libsodium.org/libsodium/releases/old/', + 'https://download.libsodium.org/libsodium/releases/old/unsupported/', +] +sources = [SOURCE_TAR_GZ] +checksums = ['6f504490b342a4f8a4c4a02fc9b866cbef8622d5df4e5452b46be121e46636c1'] + +builddependencies = [ + ('binutils', '2.35'), +] + +sanity_check_paths = { + 'files': ['include/sodium.h', 'lib/libsodium.so', 'lib/libsodium.a'], + 'dirs': ['include/sodium', 'lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d79856789c3 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenPGM/OpenPGM-5.2.122-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'OpenPGM' +version = '5.2.122' + +homepage = 'https://code.google.com/p/openpgm/' + +description = """ + OpenPGM is an open source implementation of the Pragmatic General Multicast + (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable + and scalable multicast protocol that enables receivers to detect loss, request + retransmission of lost data, or notify an application of unrecoverable loss. + PGM is a receiver-reliable protocol, which means the receiver is responsible + for ensuring all data is received, absolving the sender of reception + responsibility. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/openpgm/'] +sources = ['libpgm-%(version)s.tar.gz'] +checksums = ['6b895f550b95284dcde7189b01e04a9a1c1f94579af31b1eebd32c2207a1ba2c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '2.7.18'), +] + +start_dir = 'pgm' + +sanity_check_paths = { + 'files': ['lib/libpgm.%s' % SHLIB_EXT, 'lib/libpgm.a'], + 'dirs': ['include'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a9ef2d5ea6b --- /dev/null +++ b/easybuild/easyconfigs/z/ZeroMQ/ZeroMQ-4.3.3-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'ZeroMQ' +version = '4.3.3' + +homepage = 'https://www.zeromq.org/' +description = """ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. + It gives you sockets that carry atomic messages across various transports like in-process, + inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, + pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered + products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous + message-processing tasks. It has a score of language APIs and runs on most operating systems.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/zeromq/libzmq/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9d9285db37ae942ed0780c016da87060497877af45094ff9e1a1ca736e3875a2'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('OpenPGM', '5.2.122'), + ('libsodium', '1.0.18'), + ('util-linux', '2.36'), +] + +configopts = '--with-pic --with-pgm --with-libsodium ' + +sanity_check_paths = { + 'files': ['lib/libzmq.%s' % SHLIB_EXT, 'lib/libzmq.a'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'devel' From 5632aa05a11d8d0f597b241cbaf419716f40c0e4 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Tue, 20 Oct 2020 09:03:24 +0200 Subject: [PATCH 647/698] Add note about download location --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 2b2ac516b3d..61a6e75ad9f 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -8,6 +8,8 @@ description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK ( toolchain = SYSTEM +# NVHPC can be downloaded freely from NVIDIA's website at https://developer.nvidia.com/hpc-sdk +# It requires accepting the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] From ed81e92a242ce8ac30cd6e4b407a1ca60596f64e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 20 Oct 2020 09:34:26 +0200 Subject: [PATCH 648/698] adding easyconfigs: Pango-1.47.0-GCCcore-10.2.0.eb, at-spi2-atk-2.38.0-GCCcore-10.2.0.eb, HarfBuzz-2.6.7-GCCcore-10.2.0.eb, at-spi2-core-2.38.0-GCCcore-10.2.0.eb, Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb, ATK-2.36.0-GCCcore-10.2.0.eb, GObject-Introspection-1.66.1-GCCcore-10.2.0.eb, cairo-1.16.0-GCCcore-10.2.0.eb, ICU-67.1-GCCcore-10.2.0.eb, LibTIFF-4.1.0-GCCcore-10.2.0.eb, FriBidi-1.0.10-GCCcore-10.2.0.eb, pixman-0.40.0-GCCcore-10.2.0.eb (#11532) Co-authored-by: c3-micke --- .../a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb | 39 ++++++++++++++++ .../at-spi2-atk-2.38.0-GCCcore-10.2.0.eb | 37 +++++++++++++++ .../at-spi2-core-2.38.0-GCCcore-10.2.0.eb | 39 ++++++++++++++++ .../c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb | 46 +++++++++++++++++++ .../FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb | 34 ++++++++++++++ ...ect-Introspection-1.66.1-GCCcore-10.2.0.eb | 43 +++++++++++++++++ .../Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb | 44 ++++++++++++++++++ .../HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb | 35 ++++++++++++++ .../i/ICU/ICU-67.1-GCCcore-10.2.0.eb | 29 ++++++++++++ .../l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 43 +++++++++++++++++ .../p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb | 41 +++++++++++++++++ .../p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb | 29 ++++++++++++ 12 files changed, 459 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..91ba9a2e476 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.36.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.36.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['fb76247e369402be23f1f5c65d38a9639c1164d934e40f6a9cf3c9e96b652788'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a8e89c30943 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-10.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('DBus', '1.13.18'), + ('at-spi2-core', '2.38.0'), + ('libxml2', '2.9.10'), + ('ATK', '2.36.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..d065df3ef5c --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.38.0-GCCcore-10.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['84e36c3fe66862133f5fe229772b76aa2526e10de5014a3778f2fa46ce550da5'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('DBus', '1.13.18'), + ('X11', '20201008'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..0449c9cee8a --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.16.0-GCCcore-10.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.16.0' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5e7b29b3f113ef870d1e3ecf8adf21f923396401604bda16d44be45e66052331'] + +builddependencies = [ + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('libpng', '1.6.37'), + ('freetype', '2.10.3'), + ('pixman', '0.40.0'), + ('expat', '2.2.9'), + ('GLib', '2.66.1'), + ('X11', '20201008'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..40e6ff91575 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +# Authors:: Jack Perdue - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.10' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7f1c687c7831499bcacae5e8675945a39bacbad16ecaa945e9454a32df653c01'] + +builddependencies = [ + ('Autotools', '20200321'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..152dc3bc8e0 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.66.1-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.66.1' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['dd44a55ee5f426ea22b6b89624708f9e8d53f5cc94e5485c15c87cb30e06161d'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.1'), + ('cairo', '1.16.0'), +] + +dependencies = [ + ('Python', '3.8.6'), + ('GLib', '2.66.1'), + ('libffi', '3.3'), + ('util-linux', '2.36'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2d4114f9681 --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.40.0-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.40.0' + +homepage = 'https://developer.gnome.org/gdk-pixbuf/stable/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['1582595099537ca8ff3b99c6804350b4c058bb8ad67411bbaae024ee7cead4e6'] + +builddependencies = [ + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('binutils', '2.35'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.66.1'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.1.0'), + ('X11', '20201008'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dgir=true " + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..a44e86d5fff --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.6.7-GCCcore-10.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '2.6.7' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://www.freedesktop.org/software/harfbuzz/release/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['49e481d06cdff97bf68d99fa26bdf785331f411614485d892ea4c78eb479b218'] + +builddependencies = [ + ('binutils', '2.35'), + ('GObject-Introspection', '1.66.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('GLib', '2.66.1'), + ('ICU', '67.1'), + ('cairo', '1.16.0'), + ('freetype', '2.10.3'), +] + +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..4b6277c96fd --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-67.1-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '67.1' + +homepage = 'https://icu-project.org/' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['94a80cd6f251a53bd2a997f6f1b5ac6653fe791dfab66e1eb0227740fb86d5dc'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..43be2ea49e0 --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Alan O'Cais (JSC) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/ +## +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.1.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://download.osgeo.org/libtiff/', +] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['5d29f32517dadb6dbcd1255ea5bbc93a2b54b94fbf83653b4d65c7d6775b8634'] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.5') +] + +configopts = " --enable-ld-version-script " + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..815a744fabc --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.47.0-GCCcore-10.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.47.0' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['730db8652fc43188e03218c3374db9d152351f51fc7011b9acae6d0a6c92c367'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('GObject-Introspection', '1.66.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('GLib', '2.66.1'), + ('cairo', '1.16.0'), + ('HarfBuzz', '2.6.7'), + ('FriBidi', '1.0.10'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..21519920c8c --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.40.0-GCCcore-10.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.40.0' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6d200dec3740d9ec4ec8d1180e25779c00bc749f94278c8b9021f5534db223fc'] + +builddependencies = [ + ('binutils', '2.35'), +] + + +sanity_check_paths = { + 'files': ['lib/libpixman-1.so'], + 'dirs': [], +} + +moduleclass = 'vis' From 485bf1d6225faa43e828ab3e60f8e4199a8c9168 Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Tue, 20 Oct 2020 11:08:01 +0200 Subject: [PATCH 649/698] Add commented source_urls --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 61a6e75ad9f..3102e140fcc 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -10,6 +10,8 @@ toolchain = SYSTEM # NVHPC can be downloaded freely from NVIDIA's website at https://developer.nvidia.com/hpc-sdk # It requires accepting the HPC SDK Software License Agreement (https://docs.nvidia.com/hpc-sdk/eula/index.html) +# If you accept the License Agreement, you may also uncomment the following line to automatically download the sources +# source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] From 2f59e942654e22575b25d45861dae85c84909aaf Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Tue, 20 Oct 2020 11:08:50 +0200 Subject: [PATCH 650/698] Fix GCC dependency --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index 3102e140fcc..df22fd12f3e 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -18,7 +18,7 @@ checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.34', '', ('GCCcore', local_gccver)), - ('CUDA', '11.0.2'), + ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) ] From d998a9ed5be57305ed6e97333b790ed03dbb7795 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Oct 2020 12:03:17 +0200 Subject: [PATCH 651/698] adding easyconfigs: Bazel-3.6.0-GCCcore-9.3.0.eb --- .../b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..684308b08e6 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-3.6.0-GCCcore-9.3.0.eb @@ -0,0 +1,25 @@ +name = 'Bazel' +version = '3.6.0' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/bazelbuild/bazel/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +patches = ['%(name)s-3.4.1-fix-grpc-protoc.patch'] +checksums = [ + '3a18f24febb5203f11b0985b27e120ac623058d1d5ca79cd6df992e67d57240a', # bazel-3.6.0-dist.zip + 'f87ad8ad6922fd9c974381ea22b7b0e6502ccad5e532145f179b80d5599e24ac', # Bazel-3.4.1-fix-grpc-protoc.patch +] + +builddependencies = [ + ('binutils', '2.34'), + ('Python', '3.8.2'), + ('Zip', '3.0'), +] +dependencies = [('Java', '11', '', True)] + +moduleclass = 'devel' From cc30d10880d3be6234bab328007b716c0b0df829 Mon Sep 17 00:00:00 2001 From: terjekv Date: Tue, 20 Oct 2020 13:20:30 +0200 Subject: [PATCH 652/698] aarch64-support for Java 1.8. The versionsuffix changes to the power version is to support --try-update-deps as '91-b26-OpenJDK' isn't a testable version. --- easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb | 15 +++++++++++++++ easybuild/easyconfigs/j/Java/Java-1.8.eb | 3 ++- .../j/Java/Java-1.8_191-b26-OpenJDK.eb | 3 ++- 3 files changed, 19 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb new file mode 100644 index 00000000000..22ec074a959 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb @@ -0,0 +1,15 @@ +name = 'Java' +version = '1.8' +versionsuffix = '-aarch64' + +homepage = 'https://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u265-b01/'] +sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_8u265b01.tar.gz'] +checksums = ['87d16dac293d2a9abbb559a277bfaded702f28d1bfdc526f8613bb9cfed84a12'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 05b15f7cfc5..70ff5a44a55 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -16,7 +16,8 @@ toolchain = SYSTEM dependencies = [ ('Java', {'arch=x86_64': '%(version)s.0_241', - 'arch=POWER': '%(version)s_191-b26-OpenJDK'}), + 'arch=POWER': '%(version)s_191-b26-OpenJDK', + 'arch=AArch64': '%(version)s-aarch64'}), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb b/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb index fb57f27e39f..3dc992a0d9c 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8_191-b26-OpenJDK.eb @@ -1,7 +1,8 @@ # This easyconfig was created by the BEAR Software team at the University of Birmingham. name = 'Java' easyblock = 'ConfigureMake' -version = '1.8_191-b26-OpenJDK' +version = '1.8_191' +versionsuffix = '-b26-OpenJDK' homepage = "https://openjdk.java.net/" description = """An open-source implementation of the Java Platform, Standard Edition""" From f39f82aa0f9845e9713f171178443e3deaebed50 Mon Sep 17 00:00:00 2001 From: terjekv Date: Tue, 20 Oct 2020 13:21:46 +0200 Subject: [PATCH 653/698] adding easyconfigs: flatbuffers-1.12.0-GCCcore-9.3.0.eb, giflib-5.2.1-GCCcore-9.3.0.eb, hwloc-1.11.12-GCCcore-9.3.0.eb, JsonCpp-1.9.3-GCCcore-9.3.0.eb, nsync-1.24.0-GCCcore-9.3.0.eb, protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb, TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb --- .../flatbuffers-1.12.0-GCCcore-9.3.0.eb | 29 +++ .../g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb | 28 +++ .../h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb | 48 +++++ .../j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb | 29 +++ .../n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb | 26 +++ ...f-python-3.10.0-foss-2020a-Python-3.8.2.eb | 34 ++++ ...ensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 165 ++++++++++++++++++ 7 files changed, 359 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..c9b52e42459 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-1.12.0-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '1.12.0' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['62f2223fb9181d1d6338451375628975775f7522185266cd5296571ac152bc45'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Ninja', '1.10.0'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..68cf86e8ce3 --- /dev/null +++ b/easybuild/easyconfigs/g/giflib/giflib-5.2.1-GCCcore-9.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'giflib' +version = '5.2.1' + +homepage = 'http://giflib.sourceforge.net/' +description = """giflib is a library for reading and writing gif images. +It is API and ABI compatible with libungif which was in wide use while +the LZW compression algorithm was patented.""" + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['31da5562f44c5f15d63340a09a4fd62b48c45620cd302f77a6d9acf0077879bd'] + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +builddependencies = [('binutils', '2.34')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/giftool'], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..2d2f09d3db1 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '1.11.12' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} +# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake +# cfr. https://github.com/open-mpi/hwloc/issues/315 +toolchainopts = {'vectorize': False} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f1d49433e605dd653a77e1478a78cee095787d554a94afe40d1376bca6708ca5'] + +builddependencies = [ + ('binutils', '2.34'), +] + +dependencies = [ + ('numactl', '2.0.13'), + ('libxml2', '2.9.10'), + ('libpciaccess', '0.16'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..23d023d5575 --- /dev/null +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "CMakeNinja" + +name = 'JsonCpp' +version = '1.9.3' + +homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' +description = """ JsonCpp is a C++ library that allows manipulating JSON values, + including serialization and deserialization to and from strings. It can also preserve existing comment in + unserialization/serialization steps, making it a convenient format to store user input files. """ + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['8593c1d69e703563d94d8c12244e2e18893eeb9a8a9f8aa3d09a327aa45c8f7d'] + +builddependencies = [ + ('CMake', '3.16.4'), + ('Ninja', '1.10.0'), + ('pkg-config', '0.29.2'), + ('binutils', '2.34'), +] + +sanity_check_paths = { + 'files': ['include/json/json.h', 'lib/libjsoncpp.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..21319bfbbbd --- /dev/null +++ b/easybuild/easyconfigs/n/nsync/nsync-1.24.0-GCCcore-9.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeNinja' + +name = 'nsync' +version = '1.24.0' + +homepage = 'https://github.com/google/nsync' +description = """nsync is a C library that exports various synchronization primitives, such as mutexes""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/google/nsync/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['47a6eb2a295be5121a1904a6a775722338a20dc02ee3eec4169ed2c3f203617a'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), + ('Ninja', '1.10.0'), +] + +sanity_check_paths = { + 'files': ['include/nsync.h', 'lib/libnsync.a', 'lib/libnsync_cpp.a'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..c07fb5f0936 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '3.10.0' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/google/protobuf/' +description = """Python Protocol Buffers runtime library.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['db83b5c12c0cd30150bb568e6feb2435c49ce4e68fe2d7b903113f0e221e58fe'] + +dependencies = [ + ('Python', '3.8.2'), + ('protobuf', version) +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +options = {'modulename': 'google.protobuf'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 00000000000..2aa3455633f --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,165 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.3.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [ + ('Bazel', '3.6.0'), + ('protobuf', '3.10.0'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.23.0', '-nodocs'), + ('pybind11', '2.4.3', versionsuffix), +] +dependencies = [ + ('Python', '3.8.2'), + ('h5py', '2.10.0', versionsuffix), + ('cURL', '7.69.1'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '1.12.0'), + ('giflib', '5.2.1'), + ('hwloc', '1.11.12'), + ('ICU', '66.1'), + ('JsonCpp', '1.9.3'), + ('libjpeg-turbo', '2.0.4'), + ('LMDB', '0.9.24'), + ('NASM', '2.14.02'), + ('nsync', '1.24.0'), + ('SQLite', '3.31.1'), + ('PCRE', '8.44'), + ('protobuf-python', '3.10.0', versionsuffix), + ('libpng', '1.6.37'), + ('snappy', '1.1.8'), + ('SWIG', '4.0.1'), + ('zlib', '1.2.11'), +] + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'sanity_pip_check': True, +} +use_pip = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('Markdown', '3.2.2', { + 'checksums': ['1fafe3f1ecabfb514a5285fca634a53c1b32a81cb0feb154264d55bf2ff22c17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('rsa', '4.6', { + 'checksums': ['109ea5a66744dd859bf16fe904b8d8b627adafb9408753161e766a92e7d681fa'], + }), + ('cachetools', '4.1.1', { + 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], + }), + ('google-auth', '1.21.3', { + 'modulename': 'google.auth', + 'checksums': ['31941bf019fb242c04d0de32845da10180788bfddb0de87d78c4bdf55555dda1'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('requests-oauthlib', '1.3.0', { + 'checksums': ['b4261601a71fd721a8bd6d7aa1cc1d6a8a93b4a9f5e96626f8e4d91e8beeaa6a'], + }), + ('google-auth-oauthlib', '0.4.1', { + 'checksums': ['88d2cd115e3391eb85e1243ac6902e76e77c5fe438b7276b297fbe68015458dd'], + }), + ('Werkzeug', '1.0.1', { + 'checksums': ['6c80b1e5ad3665290ea39320b91e1be1e0d5f60652b964a3070216de83d2e47c'], + }), + ('absl-py', '0.10.0', { + 'modulename': 'absl', + 'checksums': ['b20f504a7871a580be5268a18fbad48af4203df5d33dbc9272426cb806245a45'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('grpcio', '1.32.0', { + 'modulename': 'grpc', + 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + }), + ('tensorboard-plugin-wit', '1.7.0', { + 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['ee775f04821185c90d9a0e9c56970ee43d7c41403beb6629385b39517129685b'], + }), + ('tensorboard', '2.3.0', { + 'source_tmpl': 'tensorboard-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['d34609ed83ff01dd5b49ef81031cfc9c166bba0dabd60197024f14df5e8eae5e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('tensorflow-estimator', '2.3.0', { + 'source_tmpl': 'tensorflow_estimator-%(version)s-py2.py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], + }), + ('astor', '0.8.0', { + 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + }), + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + }), + ('opt-einsum', '3.3.0', { + 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('Keras-Preprocessing', '1.1.2', { + 'source_tmpl': 'Keras_Preprocessing-%(version)s.tar.gz', + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.1.0_fix-system-nasm.patch', + 'TensorFlow-2.3.0_fix-json-include-style.patch', + 'TensorFlow-2.3.0_fix-system_absl_py.patch', + 'TensorFlow-2.3.0_fix-system-protobuf.patch', + 'TensorFlow-2.3.0_fix-system-protobuf2.patch', + 'TensorFlow-2.3.0_fix-protoc-build.patch', + 'TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'checksums': [ + 'ee534dd31a811f7a759453567257d1e643f216d8d55a25c32d2fbfff8153a1ac', # v2.3.1.tar.gz + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a', # TensorFlow-2.1.0_fix-cuda-build.patch + # TensorFlow-2.1.0_fix-system-nasm.patch + '6671e40d60edaf1e57b1861aa3b2178d48f9b7dfb5b5c0d44db541116f848f2a', + # TensorFlow-2.3.0_fix-json-include-style.patch + 'e04f5d9aa4c1222393b2cad4b84cd63128ef56eb5cc732d2afbc5d98dfa596a4', + # TensorFlow-2.3.0_fix-system_absl_py.patch + '04e53b637ca64c4804a4a8d636d75e3c09257034b143b70a33bfee09e6ab4b10', + # TensorFlow-2.3.0_fix-system-protobuf.patch + '4407c3f126eb9d3c1658ef8d6ab3a26e7ed2a40ac869dd194d8a1282f6432c1d', + # TensorFlow-2.3.0_fix-system-protobuf2.patch + '74718e007acb7f5f016848218421895a33e9e894620154482deb75408225577d', + # TensorFlow-2.3.0_fix-protoc-build.patch + '78a8390ea5e06dfcfb25f6434721abbe678e37c4ad7f052aad766c4df399bd53', + # TensorFlow-2.3.0_revert-tools-to-exectools-renaming.patch + '1a72f072a764bf66733445ce027c0bad7de7c88092363c0e2a7b91a422608d56', + ], + }), +] + +moduleclass = 'lib' From 30eec8a5501d03deef2d5f478be53ac9111a8356 Mon Sep 17 00:00:00 2001 From: terjekv Date: Tue, 20 Oct 2020 13:53:07 +0200 Subject: [PATCH 654/698] Appease the hound. --- easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 70ff5a44a55..4ea0d1619c5 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -17,7 +17,7 @@ toolchain = SYSTEM dependencies = [ ('Java', {'arch=x86_64': '%(version)s.0_241', 'arch=POWER': '%(version)s_191-b26-OpenJDK', - 'arch=AArch64': '%(version)s-aarch64'}), + 'arch=AArch64': '%(version)s-aarch64'}), ] moduleclass = 'lang' From 687e862a493863c8d32ae0f9fa2f59b1c37b693e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Oct 2020 16:24:25 +0200 Subject: [PATCH 655/698] add newline at end of NVHPC easyconfig to make style tests happy --- easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index df22fd12f3e..5598305050e 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -48,4 +48,4 @@ default_cuda_version = None # Use strings like "11.0" or use the command line: # module_add_cuda = False # Add NVHPC's bundled CUDA # this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) -moduleclass = 'compiler' \ No newline at end of file +moduleclass = 'compiler' From 038179d0ed5db096e336deac62d8146bae5e5b1a Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 20 Oct 2020 18:47:06 +0200 Subject: [PATCH 656/698] adding easyconfigs: OpenRefine-3.4.1-Java-11.eb --- .../o/OpenRefine/OpenRefine-3.4.1-Java-11.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenRefine/OpenRefine-3.4.1-Java-11.eb diff --git a/easybuild/easyconfigs/o/OpenRefine/OpenRefine-3.4.1-Java-11.eb b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-3.4.1-Java-11.eb new file mode 100644 index 00000000000..b2d4b94228b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenRefine/OpenRefine-3.4.1-Java-11.eb @@ -0,0 +1,31 @@ +easyblock = 'PackedBinary' + +name = 'OpenRefine' +version = '3.4.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/OpenRefine/OpenRefine' +description = """OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, + and augment it with data coming from the web.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/OpenRefine/OpenRefine/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['40a95a269131dc84990010644f21c81ea5427779d81aeccc22d85cd361224e99'] + +builddependencies = [ + ('ant', '1.10.8', versionsuffix, True), +] +dependencies = [('Java', '11')] + +install_cmd = "cp -a OpenRefine-%(version)s/* %(installdir)s && cd %(installdir)s && ./refine build" + +sanity_check_paths = { + 'files': ['refine'], + 'dirs': ['server/classes'], +} + +modextrapaths = {'PATH': 'refine'} + +moduleclass = 'tools' From 70f34d49eef2afbb48582cb292c599bd3d484c04 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 20 Oct 2020 18:00:38 +0100 Subject: [PATCH 657/698] adding easyconfigs: stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb, HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb --- .../HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb | 41 +++++++++++++ ...tpipeline-1.7.6-foss-2019b-Python-3.7.4.eb | 61 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb create mode 100644 easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..77bde76ae73 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,41 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonPackage' + +name = 'HTSeq' +version = '0.11.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] + +checksums = ['65c4c13968506c7df92e97124df96fdd041c4476c12a548d67350ba8b436bcfc'] + +builddependencies = [('SWIG', '3.0.12')] + +dependencies = [ + ('Python', '3.7.4'), + ('Pysam', '0.15.3'), + ('SciPy-bundle', '2019.10', versionsuffix), + ('matplotlib', '3.1.1', versionsuffix), +] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +options = {'modulename': '%(name)s'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..40a9f143072 --- /dev/null +++ b/easybuild/easyconfigs/s/stpipeline/stpipeline-1.7.6-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'stpipeline' +version = '1.7.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/SpatialTranscriptomicsResearch/st_pipeline' +description = """The ST Pipeline contains the tools and scripts needed to process + and analyze the raw files generated with the Spatial Transcriptomics method + in FASTQ format to generated datasets for down-stream analysis. The ST + pipeline can also be used to process single cell data as long as a file + with barcodes identifying each cell is provided. The ST Pipeline can also + process RNA-Seq datasets generated with or without UMIs.""" + +toolchain = {'name': 'foss', 'version': '2019b'} + +dependencies = [ + ('Python', '3.7.4'), + ('Pysam', '0.15.3'), + ('scikit-learn', '0.21.3', versionsuffix), + ('Seaborn', '0.10.0', versionsuffix), + ('HTSeq', '0.11.2', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Pympler', '0.7', { + 'checksums': ['7a11e739125a9ce8bf868ded67238a40e8a7bf979bc03005eb8126182e5e274e'], + }), + ('taggd', '0.3.6', { + 'checksums': ['f02604b2b1a553f243b2543012db0ce80e13213ffd2cc439d888ba7a47c34c5e'], + }), + ('regex', '2019.08.19', { + 'checksums': ['587b62d48ca359d2d4f02d486f1f0aa9a20fbaf23a9d4198c4bed72ab2f6c849'], + }), + ('sqlitedict', '1.6.0', { + 'checksums': ['483d6a063c4648dec68d413eb29df74399661f8541dcb3ee926d28fc2f82cb24'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('invoke', '1.3.0', { + 'checksums': ['c52274d2e8a6d64ef0d61093e1983268ea1fc0cd13facb9448c4ef0c9a7ac7da'], + }), + (name, version, { + 'checksums': ['f00a6aaa325c0f5c2386a3fa3bf63fda6269cf6c7eb23c13aa381617996c50d7'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['adjust_matrix_coordinates.py', 'barcode_demux.py', 'convertEnsemblToNames.py', + 'filter_gene_type_matrix.py', 'inv', 'invoke', 'merge_fastq.py', 'multi_qa.py', + 'st_pipeline_run.py', 'st_qa.py', 'taggd_demultiplex.py']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' From 5baff6ef5a649b6b6566bfca5b8f5ff5acc3f888 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Tue, 20 Oct 2020 19:16:09 +0200 Subject: [PATCH 658/698] Switch libdrm to MesonNinja --- .../l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb index 2aae368ccb1..a9b29e1cd1e 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.102-GCCcore-10.2.0.eb @@ -1,3 +1,4 @@ +easyblock = 'MesonNinja' name = 'libdrm' version = '2.4.102' @@ -13,10 +14,18 @@ checksums = ['8bcbf9336c28e393d76c1f16d7e79e394a7fce8a2e929d52d3ad7ad8525ba05b'] builddependencies = [ ('binutils', '2.35'), ('pkg-config', '0.29.2'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), ] dependencies = [('X11', '20201008')] # installing manpages requires an extra build dependency (docbook xsl) -configopts = '--disable-manpages' +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + moduleclass = 'lib' From ad0142be9a3b1134f0db382d9ba295fa1923158d Mon Sep 17 00:00:00 2001 From: terjekv Date: Tue, 20 Oct 2020 19:34:02 +0200 Subject: [PATCH 659/698] Updated dependencies. --- ....3.0.eb => JsonCpp-1.9.4-GCCcore-9.3.0.eb} | 6 ++-- ...-python-3.13.0-foss-2020a-Python-3.8.2.eb} | 4 +-- .../protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb | 29 +++++++++++++++++++ ...ensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 6 ++-- 4 files changed, 37 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/j/JsonCpp/{JsonCpp-1.9.3-GCCcore-9.3.0.eb => JsonCpp-1.9.4-GCCcore-9.3.0.eb} (82%) rename easybuild/easyconfigs/p/protobuf-python/{protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb => protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb} (89%) create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb similarity index 82% rename from easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb rename to easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb index 23d023d5575..287d84a1143 100644 --- a/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.3-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/j/JsonCpp/JsonCpp-1.9.4-GCCcore-9.3.0.eb @@ -1,7 +1,7 @@ easyblock = "CMakeNinja" name = 'JsonCpp' -version = '1.9.3' +version = '1.9.4' homepage = 'https://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html' description = """ JsonCpp is a C++ library that allows manipulating JSON values, @@ -12,7 +12,7 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = ['https://github.com/open-source-parsers/jsoncpp/archive'] sources = ['%(version)s.tar.gz'] -checksums = ['8593c1d69e703563d94d8c12244e2e18893eeb9a8a9f8aa3d09a327aa45c8f7d'] +checksums = ['e34a628a8142643b976c7233ef381457efad79468c67cb1ae0b83a33d7493999'] builddependencies = [ ('CMake', '3.16.4'), @@ -22,7 +22,7 @@ builddependencies = [ ] sanity_check_paths = { - 'files': ['include/json/json.h', 'lib/libjsoncpp.a'], + 'files': ['include/json/json.h', 'lib/libjsoncpp.so'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb similarity index 89% rename from easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb rename to easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb index c07fb5f0936..261c205524f 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.10.0-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-3.13.0-foss-2020a-Python-3.8.2.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'protobuf-python' -version = '3.10.0' +version = '3.13.0' versionsuffix = '-Python-%(pyver)s' homepage = 'https://github.com/google/protobuf/' @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] sources = [{'download_filename': 'protobuf-%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] -checksums = ['db83b5c12c0cd30150bb568e6feb2435c49ce4e68fe2d7b903113f0e221e58fe'] +checksums = ['6a82e0c8bb2bf58f606040cc5814e07715b2094caeba281e2e7d0b0e2e397db5'] dependencies = [ ('Python', '3.8.2'), diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb new file mode 100644 index 00000000000..e7f522b6c01 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-3.13.0-GCCcore-9.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '3.13.0' + +homepage = 'https://github.com/google/protobuf/' +description = """Google Protocol Buffers""" + +toolchain = {'name': 'GCCcore', 'version': '9.3.0'} + +source_urls = ['https://github.com/google/protobuf/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['9b4ee22c250fe31b16f1a24d61467e40780a3fbb9b91c3b65be2a376ed913a1a'] + +builddependencies = [ + ('binutils', '2.34'), + ('CMake', '3.16.4'), +] + +srcdir = 'cmake' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 2aa3455633f..f3d712d6332 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -24,16 +24,16 @@ dependencies = [ ('double-conversion', '3.1.5'), ('flatbuffers', '1.12.0'), ('giflib', '5.2.1'), - ('hwloc', '1.11.12'), + ('hwloc', '2.2.0'), ('ICU', '66.1'), - ('JsonCpp', '1.9.3'), + ('JsonCpp', '1.9.4'), ('libjpeg-turbo', '2.0.4'), ('LMDB', '0.9.24'), ('NASM', '2.14.02'), ('nsync', '1.24.0'), ('SQLite', '3.31.1'), ('PCRE', '8.44'), - ('protobuf-python', '3.10.0', versionsuffix), + ('protobuf-python', '3.13.0', versionsuffix), ('libpng', '1.6.37'), ('snappy', '1.1.8'), ('SWIG', '4.0.1'), From 654cd82591a95f2f4fa19ac4bd23ec05ae2635ab Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Oct 2020 08:39:15 +0200 Subject: [PATCH 660/698] adding easyconfigs: medaka-1.1.3-foss-2019b-Python-3.7.4.eb --- .../medaka-1.1.3-foss-2019b-Python-3.7.4.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb new file mode 100644 index 00000000000..060438597e9 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.1.3-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.1.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2019b'} + +builddependencies = [('Autotools', '20180311')] + +dependencies = [ + ('Python', '3.7.4'), # includes cffi, numpy + # TensorFlow 2.2.0 required by medaka, see requirements.txt + ('TensorFlow', '2.2.0', versionsuffix), + ('Biopython', '1.75', versionsuffix), + ('h5py', '2.10.0', versionsuffix), + # Pysam 0.16.0.1 is strictly required, see requirements.txt + ('Pysam', '0.16.0.1'), + ('SAMtools', '1.10'), + ('minimap2', '2.17'), + ('HTSlib', '1.10.2'), # for tabix, bgzip + ('Racon', '1.4.13'), + ('spoa', '4.0.0'), + ('networkx', '2.4', versionsuffix), + ('edlib', '1.3.8.post1', versionsuffix), + ('pyspoa', '0.0.4', versionsuffix), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('mappy', '2.17', { + 'checksums': ['ed1460efc9c6785df28065b7e93e93c92227f623a181f1a852dca6e6acb1a15f'], + }), + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + ('ont-fast5-api', '3.1.6', { + 'checksums': ['586b819bd48d38f446b33dac4a34f33c1004beeef0baf16ae1253d5fa360b951'], + }), + ('parasail', '1.2', { + 'checksums': ['6ceef978e7d06293c38c9824f76557f3d7e137cb05487be31bf89286f7a8201e'], + }), + ('pyfaidx', '0.5.9.1', { + 'checksums': ['eda8af04ba4da4fd63fdc35a62e0e41dfc06aa1a511728dfbdd7707e3b382855'], + }), + ('xopen', '0.9.0', { + 'checksums': ['1e3918c8a5cd2bd128ba05b3b883ee322349219c99c305e10114638478e3162a'], + }), + ('whatshap', '1.0', { + 'checksums': ['fcf0495793998da94054bdc4c6d6f3f6b145a7befa07ac96275e5e2272979aa2'], + }), + (name, version, { + 'patches': ['medaka-1.1.1_use-SAMtools-dep.patch'], + 'checksums': [ + '7ee7c1e6c6a055a102772a899f32490fc7ebf928731e2b16c5d4d994d1a4d698', # medaka-1.1.3.tar.gz + 'b5b7c69f4c132f632f0a8f775f65a37f19a977aeba7de3880575a6b32586d27e', # medaka-1.1.1_use-SAMtools-dep.patch + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From f2622934e904d7a78d3569f5972a33e27bf38fd9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Oct 2020 09:29:37 +0200 Subject: [PATCH 661/698] whitelist TensorFlow 2.2.0 + Pysam 0.16.0.1 for medaka 1.1.[13] --- test/easyconfigs/easyconfigs.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index c099f019d68..a9258479d1c 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -264,13 +264,13 @@ def check_dep_vars(self, dep, dep_vars): # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), # artic-ncov2019 requires medaka ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), - # medaka 1.1.1 requires TensorFlow 2.2.0 (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); + # medaka 1.1.* requires TensorFlow 2.2.0 (while other 2019b easyconfigs use TensorFlow 2.1.0 as dep); # TensorFlow 2.2.0 is also used as a dep for Horovod 0.19.5 - ('2.2.0;', ['medaka-1.1.1-', 'Horovod-0.19.5-']), + ('2.2.0;', ['medaka-1.1.[13]-', 'Horovod-0.19.5-']), ], - # medaka 1.1.1 requires Pysam 0.16.0.1, + # medaka 1.1.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation - 'Pysam': [('0.16.0.1;', ['medaka-1.1.1-'])], + 'Pysam': [('0.16.0.1;', ['medaka-1.1.[13]-'])], } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From 3513741a0f620b84648dc5a43bb267cb605ab1dc Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 21 Oct 2020 10:22:03 +0100 Subject: [PATCH 662/698] Enable sanity_pip_check --- .../easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb index 77bde76ae73..c6a4660ec07 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-0.11.2-foss-2019b-Python-3.7.4.eb @@ -36,6 +36,8 @@ sanity_check_paths = { sanity_check_commands = ['%(namelower)s-count --help'] +sanity_pip_check = True + options = {'modulename': '%(name)s'} moduleclass = 'bio' From 4bf0c7cf9314758585516141952becd806349b85 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 11:23:45 +0200 Subject: [PATCH 663/698] Include patch for libunwind @ GCC10 --- .../libunwind-1.4.0-GCCcore-10.2.0.eb | 8 +- .../libunwind-1.4.0_weak_symbol_fix.patch | 417 ++++++++++++++++++ 2 files changed, 423 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.4.0_weak_symbol_fix.patch diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb index c0a7684fce6..1073232ea54 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0-GCCcore-10.2.0.eb @@ -14,10 +14,14 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SAVANNAH_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['libunwind-1.3.1_fix_ppc64_fpreg_t.patch'] +patches = [ + 'libunwind-1.3.1_fix_ppc64_fpreg_t.patch', + 'libunwind-1.4.0_weak_symbol_fix.patch', +] checksums = [ 'df59c931bd4d7ebfd83ee481c943edf015138089b8e50abed8d9c57ba9338435', # libunwind-1.4.0.tar.gz '61a507eec7ece286b06be698c742f0016d8c605eaeedf34f451cf1d0e510ec86', # libunwind-1.3.1_fix_ppc64_fpreg_t.patch + 'fdaf565dc8de48d564562a7258d04fe23f594af1741c49a3062f9f60cde220c8', # libunwind-1.4.0_weak_symbol_fix.patch ] builddependencies = [('binutils', '2.35')] @@ -26,7 +30,7 @@ dependencies = [ ('XZ', '5.2.5'), ] -preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd -fno-common" && ' sanity_check_paths = { 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0_weak_symbol_fix.patch b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0_weak_symbol_fix.patch new file mode 100644 index 00000000000..9d7aa9e055c --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.4.0_weak_symbol_fix.patch @@ -0,0 +1,417 @@ +# Fixes link issue on GCC 10 (only needed for 1.4.0, already merged upstream) +# ref: https://github.com/libunwind/libunwind/pull/166 +diff --git a/src/aarch64/Ginit.c b/src/aarch64/Ginit.c +index dec235c82..35389762f 100644 +--- a/src/aarch64/Ginit.c ++++ b/src/aarch64/Ginit.c +@@ -61,13 +61,6 @@ tdep_uc_addr (unw_tdep_context_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -78,7 +71,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/arm/Ginit.c b/src/arm/Ginit.c +index 2720d063a..0bac0d72d 100644 +--- a/src/arm/Ginit.c ++++ b/src/arm/Ginit.c +@@ -57,18 +57,17 @@ tdep_uc_addr (unw_tdep_context_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/coredump/_UPT_get_dyn_info_list_addr.c b/src/coredump/_UPT_get_dyn_info_list_addr.c +index 0d1190556..739ed0569 100644 +--- a/src/coredump/_UPT_get_dyn_info_list_addr.c ++++ b/src/coredump/_UPT_get_dyn_info_list_addr.c +@@ -74,6 +74,11 @@ get_list_addr (unw_addr_space_t as, unw_word_t *dil_addr, void *arg, + + #else + ++/* XXX fix me: there is currently no way to locate the dyn-info list ++ by a remote unwinder. On ia64, this is done via a special ++ unwind-table entry. Perhaps something similar can be done with ++ DWARF2 unwind info. */ ++ + static inline int + get_list_addr (unw_addr_space_t as, unw_word_t *dil_addr, void *arg, + int *countp) +diff --git a/src/hppa/Ginit.c b/src/hppa/Ginit.c +index 461e4b93d..265455a68 100644 +--- a/src/hppa/Ginit.c ++++ b/src/hppa/Ginit.c +@@ -64,13 +64,6 @@ _Uhppa_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -81,7 +74,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/ia64/Ginit.c b/src/ia64/Ginit.c +index b09a2ad57..8601bb3ca 100644 +--- a/src/ia64/Ginit.c ++++ b/src/ia64/Ginit.c +@@ -68,6 +68,7 @@ get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + if (!_U_dyn_info_list_addr) + return -UNW_ENOINFO; + #endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. + *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } +diff --git a/src/mi/Gfind_dynamic_proc_info.c b/src/mi/Gfind_dynamic_proc_info.c +index 98d350128..2e7c62e5e 100644 +--- a/src/mi/Gfind_dynamic_proc_info.c ++++ b/src/mi/Gfind_dynamic_proc_info.c +@@ -49,6 +49,7 @@ local_find_proc_info (unw_addr_space_t as, unw_word_t ip, unw_proc_info_t *pi, + return -UNW_ENOINFO; + #endif + ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. + list = (unw_dyn_info_list_t *) (uintptr_t) _U_dyn_info_list_addr (); + for (di = list->first; di; di = di->next) + if (ip >= di->start_ip && ip < di->end_ip) +diff --git a/src/mips/Ginit.c b/src/mips/Ginit.c +index 3df170c75..bf7a8f5a8 100644 +--- a/src/mips/Ginit.c ++++ b/src/mips/Ginit.c +@@ -69,13 +69,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -86,7 +79,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) (intptr_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/ppc32/Ginit.c b/src/ppc32/Ginit.c +index ba302448a..7b4545580 100644 +--- a/src/ppc32/Ginit.c ++++ b/src/ppc32/Ginit.c +@@ -91,9 +91,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -104,7 +101,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/ppc64/Ginit.c b/src/ppc64/Ginit.c +index 4c88cd6e7..7bfb395a7 100644 +--- a/src/ppc64/Ginit.c ++++ b/src/ppc64/Ginit.c +@@ -95,9 +95,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -108,7 +105,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/ptrace/_UPT_get_dyn_info_list_addr.c b/src/ptrace/_UPT_get_dyn_info_list_addr.c +index cc5ed0441..16671d453 100644 +--- a/src/ptrace/_UPT_get_dyn_info_list_addr.c ++++ b/src/ptrace/_UPT_get_dyn_info_list_addr.c +@@ -71,6 +71,11 @@ get_list_addr (unw_addr_space_t as, unw_word_t *dil_addr, void *arg, + + #else + ++/* XXX fix me: there is currently no way to locate the dyn-info list ++ by a remote unwinder. On ia64, this is done via a special ++ unwind-table entry. Perhaps something similar can be done with ++ DWARF2 unwind info. */ ++ + static inline int + get_list_addr (unw_addr_space_t as, unw_word_t *dil_addr, void *arg, + int *countp) +diff --git a/src/s390x/Ginit.c b/src/s390x/Ginit.c +index f0886ac93..db01743c0 100644 +--- a/src/s390x/Ginit.c ++++ b/src/s390x/Ginit.c +@@ -50,8 +50,6 @@ static struct unw_addr_space local_addr_space; + + unw_addr_space_t unw_local_addr_space = &local_addr_space; + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- + static inline void * + uc_addr (ucontext_t *uc, int reg) + { +@@ -75,11 +73,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -90,7 +83,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/sh/Ginit.c b/src/sh/Ginit.c +index 52988a721..9fe96d2bd 100644 +--- a/src/sh/Ginit.c ++++ b/src/sh/Ginit.c +@@ -58,13 +58,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -75,7 +68,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/tilegx/Ginit.c b/src/tilegx/Ginit.c +index 7564a558b..925e64132 100644 +--- a/src/tilegx/Ginit.c ++++ b/src/tilegx/Ginit.c +@@ -64,13 +64,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -81,7 +74,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) (intptr_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/x86/Ginit.c b/src/x86/Ginit.c +index f6b8dc27d..3cec74a21 100644 +--- a/src/x86/Ginit.c ++++ b/src/x86/Ginit.c +@@ -54,13 +54,6 @@ tdep_uc_addr (ucontext_t *uc, int reg) + + # endif /* UNW_LOCAL_ONLY */ + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -71,7 +64,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + +diff --git a/src/x86_64/Ginit.c b/src/x86_64/Ginit.c +index a865d3385..fd8d418b1 100644 +--- a/src/x86_64/Ginit.c ++++ b/src/x86_64/Ginit.c +@@ -49,13 +49,6 @@ static struct unw_addr_space local_addr_space; + + unw_addr_space_t unw_local_addr_space = &local_addr_space; + +-HIDDEN unw_dyn_info_list_t _U_dyn_info_list; +- +-/* XXX fix me: there is currently no way to locate the dyn-info list +- by a remote unwinder. On ia64, this is done via a special +- unwind-table entry. Perhaps something similar can be done with +- DWARF2 unwind info. */ +- + static void + put_unwind_info (unw_addr_space_t as, unw_proc_info_t *proc_info, void *arg) + { +@@ -66,7 +59,13 @@ static int + get_dyn_info_list_addr (unw_addr_space_t as, unw_word_t *dyn_info_list_addr, + void *arg) + { +- *dyn_info_list_addr = (unw_word_t) &_U_dyn_info_list; ++#ifndef UNW_LOCAL_ONLY ++# pragma weak _U_dyn_info_list_addr ++ if (!_U_dyn_info_list_addr) ++ return -UNW_ENOINFO; ++#endif ++ // Access the `_U_dyn_info_list` from `LOCAL_ONLY` library, i.e. libunwind.so. ++ *dyn_info_list_addr = _U_dyn_info_list_addr (); + return 0; + } + From d95cc78085868d265c02d7644e74a8f64ae69801 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 11:38:51 +0200 Subject: [PATCH 664/698] Update libglvnd to 1.3.2 --- ...core-10.2.0.eb => libglvnd-1.3.2-GCCcore-10.2.0.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/l/libglvnd/{libglvnd-1.2.0-GCCcore-10.2.0.eb => libglvnd-1.3.2-GCCcore-10.2.0.eb} (73%) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb similarity index 73% rename from easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb index 1bba872c7e6..13815c2373d 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -1,16 +1,16 @@ easyblock = 'ConfigureMake' name = 'libglvnd' -version = '1.2.0' +version = '1.3.2' -homepage = 'https://github.com/NVIDIA/libglvnd' +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['https://github.com/NVIDIA/libglvnd/releases/download/v%(version)s/'] -sources = ['libglvnd-%(version)s.tar.gz'] -checksums = ['2dacbcfa47b7ffb722cbddc0a4f1bc3ecd71d2d7bb461bceb8e396dc6b81dc6d'] +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['6332c27f4c792b09a3eb1d7ae18c2d6ff6a0acaf3a746489caf859e659fca2f7'] builddependencies = [ ('binutils', '2.35'), From 31ab26bff83c5f5a36ae21c41ce81cbccb5a701c Mon Sep 17 00:00:00 2001 From: terjekv Date: Wed, 21 Oct 2020 12:07:52 +0200 Subject: [PATCH 665/698] Fix version suffix of Java 1.8 for aarch64. --- .../Java/{Java-1.8-aarch64.eb => Java-1.8-8u265-b01-aarch64.eb} | 2 +- easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/j/Java/{Java-1.8-aarch64.eb => Java-1.8-8u265-b01-aarch64.eb} (93%) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb similarity index 93% rename from easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb rename to easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb index 22ec074a959..b114bbaab8c 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8-aarch64.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb @@ -1,6 +1,6 @@ name = 'Java' version = '1.8' -versionsuffix = '-aarch64' +versionsuffix = '-8u265-b01-aarch64' homepage = 'https://openjdk.java.net' description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index 4ea0d1619c5..a30f115d1c5 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -17,7 +17,7 @@ toolchain = SYSTEM dependencies = [ ('Java', {'arch=x86_64': '%(version)s.0_241', 'arch=POWER': '%(version)s_191-b26-OpenJDK', - 'arch=AArch64': '%(version)s-aarch64'}), + 'arch=AArch64': '%(version)s-8u265-b01-aarch64'}), ] moduleclass = 'lang' From 973fdf9bb5748abc9d83a36333efa738b3c501f1 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 12:56:13 +0200 Subject: [PATCH 666/698] Update libglvnd dependency in Mesa --- easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb index 218127da186..a2dbdd6eb60 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-20.2.1-GCCcore-10.2.0.eb @@ -49,7 +49,7 @@ dependencies = [ ('zlib', '1.2.11'), ('zstd', '1.4.5'), ('libdrm', '2.4.102'), - ('libglvnd', '1.2.0'), + ('libglvnd', '1.3.2'), ('libunwind', '1.4.0'), ('LLVM', '11.0.0'), ('X11', '20201008'), From 2b7caa4932f955880821a7d530b81e8f5d682e10 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Wed, 21 Oct 2020 14:27:04 +0200 Subject: [PATCH 667/698] Switch libglvnd to MesonNinja --- .../easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb index 13815c2373d..d0f0184cab1 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.3.2-GCCcore-10.2.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MesonNinja' name = 'libglvnd' version = '1.3.2' @@ -15,6 +15,8 @@ checksums = ['6332c27f4c792b09a3eb1d7ae18c2d6ff6a0acaf3a746489caf859e659fca2f7'] builddependencies = [ ('binutils', '2.35'), ('pkg-config', '0.29.2'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), ] dependencies = [('X11', '20201008')] From 1da746bc3e87578f96abae1387073a43f440c5b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Oct 2020 15:01:33 +0200 Subject: [PATCH 668/698] adding easyconfigs: OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb --- .../OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb new file mode 100644 index 00000000000..f47bdd4fe14 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.6.3-gompi-2019b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.6.3' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2019b'} + +source_urls = ['http://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5eaa8c5b086bde8514fa4cac345d66b397e02283bc06e44cb6402268a60aeb8'] + +configopts = 'CC="$MPICC" CXX="$MPICC"' + +local_benchmark_dirs = ['libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt']] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From d6e76fc5a8c1f327d48240ef26ae9cd49500abeb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 21 Oct 2020 16:54:37 +0200 Subject: [PATCH 669/698] adding easyconfigs: PLINK-1.9b5-foss-2020a.eb and patches: PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch --- .../p/PLINK/PLINK-1.9b5-foss-2020a.eb | 47 ++++++++++ ...NK-1.9b5_fix_bad_memcmp_and_Makefile.patch | 88 +++++++++++++++++++ 2 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb new file mode 100644 index 00000000000..a8a440c2f5c --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb @@ -0,0 +1,47 @@ +# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Author: Adam Huffman +# The Francis Crick Institute +# Author: Åke Sandgren +# HPC2N, Umeå University + +easyblock = 'ConfigureMake' + +name = 'PLINK' +version = '1.9b5' + +homepage = 'https://www.cog-genomics.org/plink/1.9' +description = """ PLINK is a free, open-source whole genome association analysis toolset, + designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for + steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).""" + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/chrchang/plink-ng/archive'] +sources = [{'download_filename': 'b15c19f.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_fix_bad_memcmp_and_Makefile.patch'] +checksums = [ + 'e00ef16ac5abeb6b4c4d77846bd655fafc62669fbebf8cd2e941f07b3111907e', # PLINK-1.9b5.tar.gz + 'bca77c1142ef6d1cb542295e6273bb5c3719895825470fc0f01b58965a983876', # PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch +] + +dependencies = [('zlib', '1.2.11')] + +start_dir = '1.9' +skipsteps = ['configure'] + +buildopts = '-f Makefile.std CPPFLAGS="-DDYNAMIC_ZLIB" ' +buildopts += 'BLASFLAGS="$LIBLAPACK $LIBBLAS" ZLIB="-lz" ' + +installopts = '-f Makefile.std DESTDIR="" PREFIX="%(installdir)s" ' + +sanity_check_paths = { + 'files': ["bin/plink"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch new file mode 100644 index 00000000000..65aecee5a75 --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5_fix_bad_memcmp_and_Makefile.patch @@ -0,0 +1,88 @@ +Fix some memcmp that where stepping outside of the string. +Fix Makefile.std so the -lm -lpthread -ldl is in LIBS and added at the end of the link line. +Fix a bad #include zlib.h + +Åke Sandgren, 20201021 +diff -ru plink-ng-b15c19f.orig/1.9/dose2plink.c plink-ng-b15c19f/1.9/dose2plink.c +--- plink-ng-b15c19f.orig/1.9/dose2plink.c 2017-11-14 21:16:37.000000000 +0100 ++++ plink-ng-b15c19f/1.9/dose2plink.c 2020-10-21 16:10:16.978526654 +0200 +@@ -96,7 +96,11 @@ + #endif + #endif + +-#include "../zlib-1.2.11/zlib.h" ++#ifdef DYNAMIC_ZLIB ++ #include ++#else ++ #include "../zlib-1.2.11/zlib.h" ++#endif + + #ifdef __APPLE__ + #include +diff -ru plink-ng-b15c19f.orig/1.9/Makefile.std plink-ng-b15c19f/1.9/Makefile.std +--- plink-ng-b15c19f.orig/1.9/Makefile.std 2017-11-14 21:16:37.000000000 +0100 ++++ plink-ng-b15c19f/1.9/Makefile.std 2020-10-21 16:24:14.399023402 +0200 +@@ -32,7 +32,7 @@ + CFLAGS ?= -Wall -O2 + CXXFLAGS ?= -Wall -O2 + BLASFLAGS ?= -L/usr/lib64/atlas -llapack -lcblas -latlas +-LDFLAGS ?= -lm -lpthread -ldl ++LIBS ?= -lm -lpthread -ldl + ZLIB ?= ../zlib-1.2.11/libz.so.1.2.11 + + PREFIX ?= /usr/local +@@ -73,10 +73,10 @@ + all: $(BIN) + + plink: $(OBJS) +- $(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ ++ $(CXX) $(OBJS) $(LDFLAGS_EXTRA) $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ $(LIBS) + + plinkw: $(OBJS) +- gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ ++ gfortran -O2 $(OBJS) $(LDFLAGS_EXTRA) -Wl,-Bstatic $(BLASFLAGS) $(LDFLAGS) -L. $(ZLIB) -o $@ $(LIBS) + + install: + $(INSTALL) -d $(DESTDIR)$(PREFIX)/bin +diff -ru plink-ng-b15c19f.orig/1.9/plink.c plink-ng-b15c19f/1.9/plink.c +--- plink-ng-b15c19f.orig/1.9/plink.c 2017-11-14 21:16:37.000000000 +0100 ++++ plink-ng-b15c19f/1.9/plink.c 2020-10-21 16:22:48.512204129 +0200 +@@ -6854,7 +6854,7 @@ + sprintf(g_logbuf, "Error: Invalid --flip-scan-window size '%s'.\n", argv[cur_arg + 1]); + goto main_ret_INVALID_CMDLINE_WWA; + } +- } else if (!memcmp(argptr2, "lip-scan-window-kb", 22)) { ++ } else if (!memcmp(argptr2, "lip-scan-window-kb", 19)) { + if (!(calculation_type & CALC_FLIPSCAN)) { + logerrprint("Error: --flip-scan-window-kb must be used with --flip-scan.\n"); + goto main_ret_INVALID_CMDLINE; +@@ -10816,7 +10816,7 @@ + if (retval) { + goto main_ret_1; + } +- } else if (!memcmp(argptr2, "ead-genome-list", 19)) { ++ } else if (!memcmp(argptr2, "ead-genome-list", 16)) { + logerrprint("Error: --read-genome-list flag retired. Use --parallel + Unix cat instead.\n"); + goto main_ret_INVALID_CMDLINE; + } else if (!memcmp(argptr2, "ead-genome-minimal", 19)) { +diff -ru plink-ng-b15c19f.orig/1.9/plink_glm.c plink-ng-b15c19f/1.9/plink_glm.c +--- plink-ng-b15c19f.orig/1.9/plink_glm.c 2017-11-14 21:16:37.000000000 +0100 ++++ plink-ng-b15c19f/1.9/plink_glm.c 2020-10-21 16:33:56.287029270 +0200 +@@ -7821,7 +7821,7 @@ + } + for (param_idx = 1; param_idx < param_ct; param_idx++) { + wptr = strcpya(&(outname_end[1]), &(param_names[param_idx * max_param_name_len])); +- memcpy(wptr, ".mperm.dump.all", 17); ++ memcpy(wptr, ".mperm.dump.all", 16); + if (fopen_checked(outname, "w", &outfile)) { + goto glm_linear_nosnp_ret_OPEN_FAIL; + } +@@ -8605,7 +8605,7 @@ + } + for (param_idx = 1; param_idx < param_ct; param_idx++) { + wptr = strcpya(&(outname_end[1]), &(param_names[param_idx * max_param_name_len])); +- memcpy(wptr, ".mperm.dump.all", 17); ++ memcpy(wptr, ".mperm.dump.all", 16); + if (fopen_checked(outname, "w", &outfile)) { + goto glm_logistic_nosnp_ret_OPEN_FAIL; + } From f12146ee2164e451111c50cdfd45332f996f98de Mon Sep 17 00:00:00 2001 From: terjekv Date: Wed, 21 Oct 2020 18:19:51 +0200 Subject: [PATCH 670/698] Remove old hwloc --- .../h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb | 48 ------------------- 1 file changed, 48 deletions(-) delete mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb deleted file mode 100644 index 2d2f09d3db1..00000000000 --- a/easybuild/easyconfigs/h/hwloc/hwloc-1.11.12-GCCcore-9.3.0.eb +++ /dev/null @@ -1,48 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'hwloc' -version = '1.11.12' - -homepage = 'https://www.open-mpi.org/projects/hwloc/' - -description = """ - The Portable Hardware Locality (hwloc) software package provides a portable - abstraction (across OS, versions, architectures, ...) of the hierarchical - topology of modern architectures, including NUMA memory nodes, sockets, shared - caches, cores and simultaneous multithreading. It also gathers various system - attributes such as cache and memory information as well as the locality of I/O - devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily - aims at helping applications with gathering information about modern computing - hardware so as to exploit it accordingly and efficiently. -""" - -toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -# need to build with -fno-tree-vectorize to avoid segfaulting lstopo on Intel Skylake -# cfr. https://github.com/open-mpi/hwloc/issues/315 -toolchainopts = {'vectorize': False} - -source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] -sources = [SOURCE_TAR_GZ] -checksums = ['f1d49433e605dd653a77e1478a78cee095787d554a94afe40d1376bca6708ca5'] - -builddependencies = [ - ('binutils', '2.34'), -] - -dependencies = [ - ('numactl', '2.0.13'), - ('libxml2', '2.9.10'), - ('libpciaccess', '0.16'), -] - -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " - -sanity_check_paths = { - 'files': ['bin/lstopo', 'include/hwloc/linux.h', - 'lib/libhwloc.%s' % SHLIB_EXT], - 'dirs': ['share/man/man3'], -} -sanity_check_commands = ['lstopo'] - -moduleclass = 'system' From 9385d947eb6a8b3363adbc64f7ab45a66c61db64 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 21 Oct 2020 20:46:40 +0200 Subject: [PATCH 671/698] adding easyconfigs: ReFrame-3.2.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.2.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb new file mode 100644 index 00000000000..77a03ef8b4b --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.2.eb @@ -0,0 +1,81 @@ +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.2' + +homepage = 'https://github.com/eth-cscs/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +use_pip = True + +exts_list = [ + ('pip', '20.2.4', { + 'checksums': ['85c99a857ea0fb0aedf23833d9be5c40cf253fe24443f0829c7b472e23c364a1'], + 'use_pip': False, + }), + ('setuptools', '50.3.2', { + 'source_tmpl': 'setuptools-%(version)s.zip', + 'checksums': ['ed0519d27a243843b05d82a5e9d01b0b083d9934eaa3d02779a23da18077bd3c'], + }), + ('wheel', '0.35.1', { + 'checksums': ['99a22d87add3f634ff917310a3d87e499f19e663413a52eb9232c447aa646c9f'], + }), + ('zipp', '3.3.1', { + # install via pre-built wheel, because installing zipp from source is a huge mess, + # lots of weird trouble with 0.0.0 being used a a version due to use of setuptools_scm + 'source_tmpl': 'zipp-%(version)s-py3-none-any.whl', + 'checksums': ['16522f69653f0d67be90e8baa4a46d66389145b734345d68a257da53df670903'], + 'unpack_sources': False, + }), + ('attrs', '20.2.0', { + 'modulename': 'attr', + 'checksums': ['26b54ddbbb9ee1d34d5d3668dd37d6cf74990ab23c828c2888dccdceee395594'], + }), + ('importlib_metadata', '2.0.0', { + 'checksums': ['77a540690e24b0305878c37ffd421785a6f7e53c8b5720d211b211de8d0e95da'], + }), + ('pygelf', '0.3.6', { + 'checksums': ['3e5bc59e3b5a754556a76ff2c69fcf2003218ad7b5ff8417482fa1f6a7eba5f9'], + }), + ('pyrsistent', '0.17.3', { + 'checksums': ['2e636185d9eb976a18a8a8e96efce62f2905fea90041958d8cc2a189756ebf3e'], + }), + ('jsonschema', '3.2.0', { + 'checksums': ['c8a85b28d377cc7737e46e2d9f2b4f44ee3c0e1deac6bf46ddefc7187d30797a'], + }), + ('six', '1.15.0', { + 'checksums': ['30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259'], + }), + ('reframe', version, { + 'source_urls': ['https://github.com/eth-cscs/reframe/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['dc7f72e31386e549a874699067666607a72835914fef18c38ae6032ab5e5ed51'], + }), +] + +postinstallcmds = [ + "cd %(builddir)s/reframe/reframe-%(version)s && cp -r tutorials %(installdir)s", +] + +sanity_check_paths = { + 'files': ['bin/reframe'], + 'dirs': ['lib', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +# need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing extensions +modextrapaths = {'PATH': 'bin'} + +moduleclass = 'devel' From 17172c3b5dc034f4431862b1dc17eb5c7fedf370 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 21 Oct 2020 19:58:09 +0100 Subject: [PATCH 672/698] libarchive: add XZ builddep --- .../easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb index 56c058b302a..8c373a125e9 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.3-GCCcore-10.2.0.eb @@ -19,6 +19,7 @@ checksums = ['ee1e749213c108cb60d53147f18c31a73d6717d7e3d2481c157e1b34c881ea39'] builddependencies = [ ('binutils', '2.35'), + ('XZ', '5.2.5'), ] sanity_check_paths = { From 8d8dbd615e2bc20610c83589d039fd8ef1e584e1 Mon Sep 17 00:00:00 2001 From: terjekv Date: Wed, 21 Oct 2020 22:22:11 +0200 Subject: [PATCH 673/698] Ensure consistent versions of protobuf between dependecies. --- .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index f3d712d6332..91fe4cc5ad6 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -12,7 +12,7 @@ toolchainopts = {'usempi': True, 'pic': True} builddependencies = [ ('Bazel', '3.6.0'), - ('protobuf', '3.10.0'), + ('protobuf', '3.13.0'), # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 ('git', '2.23.0', '-nodocs'), ('pybind11', '2.4.3', versionsuffix), From 798888cda031b769fd5740731b8301165217bde9 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 00:26:58 +0200 Subject: [PATCH 674/698] adding easyconfigs: OpenSSL-1.1.1h-GCCcore-10.2.0.eb --- .../OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b233ee7281d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-1.1.1h-GCCcore-10.2.0.eb @@ -0,0 +1,25 @@ +name = 'OpenSSL' +version = '1.1.1h' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.openssl.org/source/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5c9ca8774bd7b03e5784f26ae9e9e6d749c9da2438545077e6b3d755a06595d9'] + +dependencies = [('zlib', '1.2.11')] + +builddependencies = [ + ('Perl', '5.32.0'), + ('binutils', '2.35'), +] + +runtest = 'test' + +moduleclass = 'system' From 6beb85c607d8db1d57bcaec5d44934580e850694 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 00:46:59 +0200 Subject: [PATCH 675/698] adding easyconfigs: configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb, nodejs-12.19.0-GCCcore-10.2.0.eb, JupyterHub-1.1.0-GCCcore-10.2.0.eb --- ...gurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 24 ++++ .../JupyterHub-1.1.0-GCCcore-10.2.0.eb | 113 ++++++++++++++++++ .../n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb | 44 +++++++ 3 files changed, 181 insertions(+) create mode 100644 easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..fe1c075add3 --- /dev/null +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'configurable-http-proxy' +version = '4.2.1' + +homepage = 'https://github.com/jupyterhub/configurable-http-proxy' +description = """HTTP proxy for node.js including a REST API for updating the routing table. + Developed as a part of the Jupyter Hub multi-user server.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('nodejs', '12.19.0'), +] + +source_urls = ['https://github.com/jupyterhub/configurable-http-proxy/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9f95e6893c2b743112b8e591b411a4c109574389253d95a6b5a69109ede53e23'] + +install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..dbd15fbfceb --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -0,0 +1,113 @@ +easyblock = 'PythonBundle' + +name = 'JupyterHub' +version = '1.1.0' + +homepage = 'http://jupyter.org' +description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed + for centralized deployments in companies, university classrooms and research labs.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), + ('IPython', '7.18.1'), + ('Mako', '1.1.3'), + ('configurable-http-proxy', '4.2.1'), +] + +osdependencies = [OS_PKG_OPENSSL_DEV] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('certipy', '0.1.3', { + 'checksums': ['695704b7716b033375c9a1324d0d30f27110a28895c40151a90ec07ff1032859'], + }), + ('pamela', '1.0.0', { + 'checksums': ['65c9389bef7d1bb0b168813b6be21964df32016923aac7515bdf05366acbab6c'], + }), + ('SQLAlchemy', '1.3.20', { + 'checksums': ['d2f25c7f410338d31666d7ddedfa67570900e248b940d186b48461bd4e5569a1'], + }), + ('alembic', '1.4.3', { + 'checksums': ['5334f32314fb2a56d86b4c4dd1ae34b08c03cae4cb888bc699942104d66bc245'], + }), + ('oauthlib', '3.1.0', { + 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], + }), + ('pyOpenSSL', '19.1.0', { + 'modulename': 'OpenSSL', + 'checksums': ['9a24494b2602aaf402be5c9e30a0b82d4a5c67528fe8fb475e3f3bc00dd69507'], + }), + ('python-json-logger', '2.0.1', { + 'modulename': 'pythonjsonlogger', + 'checksums': ['f26eea7898db40609563bed0a7ca11af12e2a79858632706d835a0f961b7d398'], + }), + ('ruamel.yaml', '0.16.12', { + 'checksums': ['076cc0bc34f1966d920a49f18b52b6ad559fbe656a0748e3535cf7b3f29ebf9e'], + }), + ('ruamel.yaml.clib', '0.2.2', { + 'modulename': False, + 'checksums': ['2d24bd98af676f4990c4d715bcdc2a60b19c56a3fb3a763164d2d8ca0e806ba7'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('jupyter-telemetry', '0.1.0', { + 'source_tmpl': 'jupyter_telemetry-%(version)s.tar.gz', + 'checksums': ['445c613ae3df70d255fe3de202f936bba8b77b4055c43207edf22468ac875314'], + }), + ('jupyterhub', version, { + 'checksums': ['852a70225a03abd631b36a207f3ffdf69326a0db4cef539825fde39ec1b713d7'], + }), + ('batchspawner', '1.0.0', { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ, + 'source_urls': ['https://github.com/jupyterhub/batchspawner/archive/']}], + 'checksums': ['207d816480ecb14b6ac19b027d39fcd5aaa993758a3c242d83cd6d3538063f40'], + }), + ('jupyterhub-systemdspawner', '0.14', { + 'modulename': 'systemdspawner', + 'checksums': ['080dd9cd9292266dad35d1efc7aa1af0ed6993d15eadc79bd959d1ee273d1923'], + }), + ('jupyterhub-simplespawner', '0.1', { + 'modulename': 'simplespawner', + 'checksums': ['5fcc295b310dd7a99c0f00226be311121fd99b36a5d127e8685f3ffa29712d0d'], + }), + ('ldap3', '2.8.1', { + 'checksums': ['37d633e20fa360c302b1263c96fe932d40622d0119f1bddcb829b03462eeeeb7'], + }), + ('jupyterhub-ldapauthenticator', '1.3.2', { + 'modulename': 'ldapauthenticator', + 'checksums': ['758081bbdb28b26313bb18c9d8aa2b8fcdc9162e4d3ab196c626567e64f1ab8b'], + }), + ('PyJWT', '1.7.1', { + 'modulename': 'jwt', + 'checksums': ['8d59a976fb773f3e6a39c85636357c4f0e242707394cadadd9814f5cbaa20e96'], + }), + ('jupyterhub-jwtauthenticator-v2', '2.0.2', { + 'modulename': 'jwtauthenticator', + 'checksums': ['9477a606e34c6ff032ee455ffecaf6e13de5e3bce024a2d720f274b421a390c6'], + }), + ('onetimepass', '1.0.1', { + 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], + }), + ('jupyterhub-nativeauthenticator', '0.0.5', { + 'modulename': 'nativeauthenticator', + 'checksums': ['e71b5c3ed1e3af4e307c7a43dce2fb56d4db161ec4fc59764b422cb696606376'], + }), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['bin/jupyterhub'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], +} + +sanity_check_commands = ['jupyterhub --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..b54074a104a --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.19.0-GCCcore-10.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '12.19.0' # LTS on 2020-10-19 +local_libversion = '72' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['1279e49be60d92cf4c1a48c9d92397db4e9284a100bc47689ce7924686bbddd1'] + +builddependencies = [ + ('binutils', '2.35'), + ('Python', '3.8.6'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +modextrapaths = {'CPATH': 'include/node'} + +moduleclass = 'lang' From a52daa760f18a33dc51f6fccc2416c44fbe80d7e Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 01:01:28 +0200 Subject: [PATCH 676/698] Fix sanity checks and missing build deps --- .../configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 4 ++++ .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 ++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb index fe1c075add3..aef22909e62 100644 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -9,6 +9,10 @@ description = """HTTP proxy for node.js including a REST API for updating the ro toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = { + ('binutils', '2.35'), +} + dependencies = [ ('nodejs', '12.19.0'), ] diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index dbd15fbfceb..2bdae502d71 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -108,6 +108,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages/jupyterhub'], } +sanity_pip_check = True + sanity_check_commands = ['jupyterhub --help'] moduleclass = 'tools' From 3098a8968cea0c1cbcc6157eaabb737a5ecdbbc3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 01:27:05 +0200 Subject: [PATCH 677/698] Add sanity_check_paths to configureable http proxy --- .../configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb index aef22909e62..be9c499a5a3 100644 --- a/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/c/configurable-http-proxy/configurable-http-proxy-4.2.1-GCCcore-10.2.0.eb @@ -23,6 +23,11 @@ checksums = ['9f95e6893c2b743112b8e591b411a4c109574389253d95a6b5a69109ede53e23'] install_cmd = 'npm install --no-package-lock -g --prefix %(installdir)s %(version)s.tar.gz' +sanity_check_paths = { + 'files': ['bin/configurable-http-proxy'], + 'dirs': [], +} + sanity_check_commands = ['%(name)s --version'] moduleclass = 'tools' From 0f1e91e0d5df6c6ad8966065cce7a1d65c5ee70f Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 02:12:09 +0200 Subject: [PATCH 678/698] adding easyconfigs: GTK+-3.24.23-GCCcore-10.2.0.eb, libepoxy-1.5.4-GCCcore-10.2.0.eb --- .../g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 69 +++++++++++++++++++ .../libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb | 36 ++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..daf5522a2c4 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -0,0 +1,69 @@ +easyblock = 'Bundle' + +name = 'GTK+' +version = '3.24.23' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [ + ('binutils', '2.35'), + ('GObject-Introspection', '1.66.1'), + ('gettext', '0.21'), + ('pkg-config', '0.29.2'), + ('cairo', '1.16.0'), + ('Perl', '5.32.0'), +] + +dependencies = [ + ('ATK', '2.36.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.40.0'), + ('Pango', '1.47.0'), + ('libepoxy', '1.5.4'), + ('X11', '20201008'), + ('FriBidi', '1.0.10'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '3.38.0', { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['6683a1aaf2430ccd9ea638dd4bfe1002bc92b412050c3dba20e480f979faaf97'], + }), + (name, version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb new file mode 100644 index 00000000000..2bf072bd402 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.4-GCCcore-10.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.4' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['c926fcc606901f3e03e371027056fd478da43e01ce2da7ffc48b5a0de0ca107c'] + +builddependencies = [ + ('binutils', '2.35'), + ('Meson', '0.55.3'), + ('Ninja', '1.10.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20201008'), + ('Mesa', '20.2.1'), +] + +configopts = '-Degl=no --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s' % x for x in ['common.h', 'gl_generated.h', 'gl.h', 'glx_generated.h', 'glx.h']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 2dbc5db2e9c4ed3e913abc9081355ef52a13dc62 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 02:16:50 +0200 Subject: [PATCH 679/698] Fix https url --- .../easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index 2bdae502d71..ac2d8ad3bbe 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' name = 'JupyterHub' version = '1.1.0' -homepage = 'http://jupyter.org' +homepage = 'https://jupyter.org' description = """JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs.""" From 295e6a42e40b8ef29fb8b3bcdcd532a3c5914f77 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Oct 2020 09:23:42 +0200 Subject: [PATCH 680/698] add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 --- .../easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb | 1 + .../easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb index bcfa6755af6..a670e2affb6 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.0-GCCcore-8.2.0.eb @@ -19,6 +19,7 @@ checksums = ['8643d50ed40c759f5412a3af4e353cffbce4fdf3b5cf321cb72cacf06b2d825e'] builddependencies = [ ('binutils', '2.31.1'), + ('XZ', '5.2.4'), ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb index 98b8cd1a8e6..5a9350da514 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.4.2-GCCcore-9.3.0.eb @@ -19,6 +19,7 @@ checksums = ['b60d58d12632ecf1e8fad7316dc82c6b9738a35625746b47ecdcaf4aed176176'] builddependencies = [ ('binutils', '2.34'), + ('XZ', '5.2.5'), ] sanity_check_paths = { From 9c26e331e59b29c90bbd2372f90c8db5df7a423f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Oct 2020 10:52:20 +0200 Subject: [PATCH 681/698] minor updates for extensions in TensorFlow 2.3.1 easyconfig using foss/2020a --- .../TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 91fe4cc5ad6..030dd977135 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -61,9 +61,9 @@ exts_list = [ ('cachetools', '4.1.1', { 'checksums': ['bbaa39c3dede00175df2dc2b03d0cf18dd2d32a7de7beb68072d13043c9edb20'], }), - ('google-auth', '1.21.3', { + ('google-auth', '1.22.1', { 'modulename': 'google.auth', - 'checksums': ['31941bf019fb242c04d0de32845da10180788bfddb0de87d78c4bdf55555dda1'], + 'checksums': ['9c0f71789438d703f77b94aad4ea545afaec9a65f10e6cc1bc8b89ce242244bb'], }), ('oauthlib', '3.1.0', { 'checksums': ['bee41cc35fcca6e988463cacc3bcb8a96224f470ca547e697b604cc697b2f889'], @@ -84,9 +84,9 @@ exts_list = [ ('astunparse', '1.6.3', { 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], }), - ('grpcio', '1.32.0', { + ('grpcio', '1.33.1', { 'modulename': 'grpc', - 'checksums': ['01d3046fe980be25796d368f8fc5ff34b7cf5e1444f3789a017a7fe794465639'], + 'checksums': ['f19782ec5104599382a0f73f2dfea465d0e65f6818bb3c49ca672b97034c64c3'], }), ('tensorboard-plugin-wit', '1.7.0', { 'source_tmpl': 'tensorboard_plugin_wit-%(version)s-py3-none-any.whl', @@ -110,11 +110,11 @@ exts_list = [ 'unpack_sources': False, 'checksums': ['b75e034300ccb169403cf2695adf3368da68863aeb0c14c3760064c713d5c486'], }), - ('astor', '0.8.0', { - 'checksums': ['37a6eed8b371f1228db08234ed7f6cfdc7817a3ed3824797e20cbb11dc2a7862'], + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - ('gast', '0.3.3', { - 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], + ('gast', '0.4.0', { + 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], }), ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', From 58b8c981225d91cbf503c48de7dd2c5e93b09921 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Thu, 22 Oct 2020 11:00:54 +0200 Subject: [PATCH 682/698] Include binutils build dep --- .../j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb index ac2d8ad3bbe..941bc4ae319 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-1.1.0-GCCcore-10.2.0.eb @@ -9,6 +9,10 @@ description = """JupyterHub is a multiuser version of the Jupyter (IPython) note toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = { + ('binutils', '2.35'), +} + dependencies = [ ('Python', '3.8.6'), ('IPython', '7.18.1'), From f7cc517a9b7ac0cb7f9bb76d2372e1c32f96713a Mon Sep 17 00:00:00 2001 From: Andreas Herten Date: Thu, 22 Oct 2020 11:33:38 +0200 Subject: [PATCH 683/698] Remove CUDA dependency and write some comments about it --- .../n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb index df22fd12f3e..ce774da76ab 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb @@ -18,7 +18,6 @@ checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.34', '', ('GCCcore', local_gccver)), - ('CUDA', '11.0.2', '', ('GCC', local_gccver)), # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) ] @@ -28,10 +27,19 @@ default_cuda_version = None # Use strings like "11.0" or use the command line: # NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. # The following list gives examples for the easyconfig # -# Install NVHPC for an associated CUDA version: -# default_cuda_version = "11.0" -# Can also be specified via --try-amend=default_cuda_version="10.2" -# If not given, is tried to be taken from the CUDA module, if the CUDA module is a dependency +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) System CUDA +# Use CUDA or CUDAcore as a dependency, for example +# dependencies = [('CUDA', '11.0.2', '', ('GCC', local_gccver))] +# or +# dependencies = [('CUDAcore', '11.0.2')] +# The parameter default_cuda_version still can be set as above. If not set, it will be deduced from the +# CUDA module # # Define a NVHPC-default Compute Capability # cuda_compute_capabilities = "8.0" From 6a06426170ffeae15dbed0c87375acdf5b53ec0e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 22 Oct 2020 11:58:08 +0200 Subject: [PATCH 684/698] stick to gast 0.3.3, TensorFlow 2.3.1 has a strict version requirement on it --- .../t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb index 030dd977135..1882dc6a1f7 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.3.1-foss-2020a-Python-3.8.2.eb @@ -113,8 +113,8 @@ exts_list = [ ('astor', '0.8.1', { 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], }), - ('gast', '0.4.0', { - 'checksums': ['40feb7b8b8434785585ab224d1568b857edb18297e5a3047f1ba012bc83b42c1'], + ('gast', '0.3.3', { + 'checksums': ['b881ef288a49aa81440d2c5eb8aeefd4c2bb8993d5f50edae7413a85bfdb3b57'], }), ('opt-einsum', '3.3.0', { 'source_tmpl': 'opt_einsum-%(version)s.tar.gz', From 762951a210032c1c217032f310f50e0f96633485 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Oct 2020 15:08:51 +0200 Subject: [PATCH 685/698] Move PLINK down to golf level. --- ...{PLINK-1.9b5-foss-2020a.eb => PLINK-1.9b5-golf-2020a.eb} | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/p/PLINK/{PLINK-1.9b5-foss-2020a.eb => PLINK-1.9b5-golf-2020a.eb} (86%) diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-golf-2020a.eb similarity index 86% rename from easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb rename to easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-golf-2020a.eb index a8a440c2f5c..13024284eb0 100644 --- a/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-foss-2020a.eb +++ b/easybuild/easyconfigs/p/PLINK/PLINK-1.9b5-golf-2020a.eb @@ -1,4 +1,3 @@ -# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild # Author: Pablo Escobar Lopez # Swiss Institute of Bioinformatics # Biozentrum - University of Basel @@ -18,8 +17,7 @@ description = """ PLINK is a free, open-source whole genome association analysis The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).""" -toolchain = {'name': 'foss', 'version': '2020a'} -toolchainopts = {'openmp': True} +toolchain = {'name': 'golf', 'version': '2020a'} source_urls = ['https://github.com/chrchang/plink-ng/archive'] sources = [{'download_filename': 'b15c19f.tar.gz', 'filename': SOURCE_TAR_GZ}] @@ -35,7 +33,7 @@ start_dir = '1.9' skipsteps = ['configure'] buildopts = '-f Makefile.std CPPFLAGS="-DDYNAMIC_ZLIB" ' -buildopts += 'BLASFLAGS="$LIBLAPACK $LIBBLAS" ZLIB="-lz" ' +buildopts += 'BLASFLAGS="$LIBLAPACK_MT $LIBBLAS_MT" ZLIB="-lz" ' installopts = '-f Makefile.std DESTDIR="" PREFIX="%(installdir)s" ' From 4a7265008dc0845b961056145655638d05512970 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Oct 2020 16:09:12 +0200 Subject: [PATCH 686/698] Kratos: Use https for homepage --- .../easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb index 807582f81ac..7df486aa091 100644 --- a/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/k/Kratos/Kratos-6.0-intel-2018a-Python-3.6.4.eb @@ -4,7 +4,7 @@ name = 'Kratos' version = '6.0' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://www.cimne.com/kratos' +homepage = 'https://www.cimne.com/kratos' description = """Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software.""" From ca49b841bcf9639457ee3a30ae4e59f8ead6d795 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 23 Oct 2020 15:26:54 +0200 Subject: [PATCH 687/698] adding easyconfigs: vsc-mympirun-5.2.0.eb --- .../v/vsc-mympirun/vsc-mympirun-5.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb new file mode 100644 index 00000000000..3c9a0d992fc --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.2.0.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.2.0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('pbr', '5.5.1', { + 'checksums': ['5fad80b613c402d5b7df7bd84812548b2a61e9977387a80a5fc5c396492b13c9'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '4.0.2', { + 'checksums': ['dd33eb70232b6118298d516bbcecd26704689c386594f0f3c4f13867b2c56f72'], + }), + ('IPy', '1.00', { + 'modulename': 'IPy', + 'checksums': ['2f2bf658a858d43868d8a4352b3889cf78c66e2ce678b300dcf518c9149ba621'], + }), + ('vsc-install', '0.17.1', { + 'modulename': 'vsc.install', + 'checksums': ['01431ec39054fdc95b4b4bff28fb988fc36f5504e54c37cccccf5f3a76d646a5'], + }), + ('vsc-base', '3.1.4', { + 'modulename': 'vsc.utils', + 'checksums': ['32d85982ff70a3f50a714f2166f8c24c64c7fdc603df7911ad0b7f3f50dd97b1'], + }), + (name, version, { + 'modulename': 'vsc', + 'checksums': ['7d4ce5ec4d9e1e03fc57bf9016e3300f7046b1b30783dcc710555556be6474e8'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +moduleclass = 'tools' From f0f77f68409662d8c53ca7480f897ec8661b46df Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 23 Oct 2020 17:30:07 +0200 Subject: [PATCH 688/698] Add pmix dep to OpenMPI-4*cuda* --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb | 3 +++ .../easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb index 02cdab983ee..a8dc23189a4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb @@ -13,7 +13,10 @@ checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] dependencies = [ ('zlib', '1.2.11'), ('hwloc', '2.2.0'), + ('libevent', '2.1.11'), ('UCX', '1.8.0', '-CUDA-11.0.2'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), ] # to enable SLURM integration (site-specific) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb index 4f474bba1a3..9775ccaefff 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb @@ -13,7 +13,10 @@ checksums = ['6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc'] dependencies = [ ('zlib', '1.2.11'), ('hwloc', '2.2.0'), + ('libevent', '2.1.11'), ('UCX', '1.8.0', '-CUDA-11.0.2'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), ] # to enable SLURM integration (site-specific) From 5b30962766000ea8f13c5201fc85971779c113d6 Mon Sep 17 00:00:00 2001 From: Bob Date: Fri, 23 Oct 2020 17:42:46 +0200 Subject: [PATCH 689/698] adding easyconfigs: breseq-0.35.4-foss-2020a-R-4.0.0.eb --- .../breseq-0.35.4-foss-2020a-R-4.0.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb diff --git a/easybuild/easyconfigs/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb b/easybuild/easyconfigs/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb new file mode 100644 index 00000000000..8ca749f5625 --- /dev/null +++ b/easybuild/easyconfigs/b/breseq/breseq-0.35.4-foss-2020a-R-4.0.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'breseq' +version = '0.35.4' +versionsuffix = '-R-%(rver)s' + + +homepage = 'https://barricklab.org/breseq' +description = "breseq is a computational pipeline for the analysis of short-read re-sequencing data" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/barricklab/breseq/releases/download/v%(version)s/'] +sources = ['breseq-%(version)s-Source.tar.gz'] +checksums = ['762f7b6aac26bddb5a39724e103267bd48d597d74fa7a8006d2bf0bd68fe86b4'] + +dependencies = [ + ('R', '4.0.0'), + ('Bowtie2', '2.4.1'), + ('zlib', '1.2.11'), + ('ncurses', '6.2'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/breseq', 'bin/gdtools'], + 'dirs': [], +} + +# breseq --help exists with non-zero exit code, so use grep +sanity_check_commands = ["breseq --help | grep 'Usage: breseq'"] + +moduleclass = 'bio' From 7baf0ab095f5a3ea5f7f1ce87243b6a357fbfa89 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Fri, 23 Oct 2020 17:47:09 +0200 Subject: [PATCH 690/698] Also fix missing deps in 4.0.5 @ GCCcore 9.3.0 --- easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index 13a296e2e19..128123c01bd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -19,6 +19,8 @@ dependencies = [ ('hwloc', '2.2.0'), ('libevent', '2.1.11'), ('UCX', '1.8.0'), + ('libfabric', '1.11.0'), + ('PMIx', '3.1.5'), ] # disable MPI1 compatibility for now, see what breaks... From 8b7c35d7ef9c302e39cc2ee10dd92e2016a856b3 Mon Sep 17 00:00:00 2001 From: c3-micke Date: Sat, 24 Oct 2020 19:38:48 +0200 Subject: [PATCH 691/698] Rename jupyterhub to JupyterHub --- .../JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb} | 2 +- .../JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb} | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/j/{jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb => JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb} (98%) rename easybuild/easyconfigs/j/{jupyterhub/jupyterhub-0.8.1-foss-2017a-Python-3.6.4.eb => JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb} (99%) diff --git a/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb similarity index 98% rename from easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb rename to easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb index 3484e3c6a6d..4f7acfa8c4c 100755 --- a/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.6.1-foss-2016a-Python-3.5.1.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.6.1-foss-2016a-Python-3.5.1.eb @@ -1,6 +1,6 @@ easyblock = 'Bundle' -name = 'jupyterhub' +name = 'JupyterHub' version = '0.6.1' versionsuffix = '-Python-%(pyver)s' diff --git a/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.8.1-foss-2017a-Python-3.6.4.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb similarity index 99% rename from easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.8.1-foss-2017a-Python-3.6.4.eb rename to easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb index 7a30326a014..adf98f2603e 100644 --- a/easybuild/easyconfigs/j/jupyterhub/jupyterhub-0.8.1-foss-2017a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-0.8.1-foss-2017a-Python-3.6.4.eb @@ -1,6 +1,6 @@ easyblock = 'Bundle' -name = 'jupyterhub' +name = 'JupyterHub' version = '0.8.1' versionsuffix = '-Python-%(pyver)s' From 44f8af7ba2dcd9a87366df32a2563a32e5fd80f9 Mon Sep 17 00:00:00 2001 From: terjekv Date: Mon, 26 Oct 2020 10:19:26 +0100 Subject: [PATCH 692/698] Fix version data. --- .../j/Java/Java-1.8-8u265-b01-aarch64.eb | 15 --------------- easybuild/easyconfigs/j/Java/Java-1.8.eb | 2 +- .../Java/Java-1.8_265-b01-OpenJDK-aarch64.eb | 19 +++++++++++++++++++ 3 files changed, 20 insertions(+), 16 deletions(-) delete mode 100644 easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb diff --git a/easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb deleted file mode 100644 index b114bbaab8c..00000000000 --- a/easybuild/easyconfigs/j/Java/Java-1.8-8u265-b01-aarch64.eb +++ /dev/null @@ -1,15 +0,0 @@ -name = 'Java' -version = '1.8' -versionsuffix = '-8u265-b01-aarch64' - -homepage = 'https://openjdk.java.net' -description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy - Java applications on desktops and servers.""" - -toolchain = SYSTEM - -source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u265-b01/'] -sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_8u265b01.tar.gz'] -checksums = ['87d16dac293d2a9abbb559a277bfaded702f28d1bfdc526f8613bb9cfed84a12'] - -moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8.eb b/easybuild/easyconfigs/j/Java/Java-1.8.eb index a30f115d1c5..5776712d40f 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8.eb @@ -17,7 +17,7 @@ toolchain = SYSTEM dependencies = [ ('Java', {'arch=x86_64': '%(version)s.0_241', 'arch=POWER': '%(version)s_191-b26-OpenJDK', - 'arch=AArch64': '%(version)s-8u265-b01-aarch64'}), + 'arch=AArch64': '%(version)s_265-b01-OpenJDK-aarch64'}), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb new file mode 100644 index 00000000000..eb050ed46d6 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb @@ -0,0 +1,19 @@ +name = 'Java' +local_patch_version = '265' +local_java_version = '8' +version = '1.%s_%s' % (local_java_version, local_patch_version) +versionsuffix = '-b01-OpenJDK-aarch64' + +homepage = 'https://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy + Java applications on desktops and servers.""" + +toolchain = SYSTEM + +#source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u265-b01/'] +source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk%su%s-b01' % (local_java_version, local_patch_version)] +#sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_8u265b01.tar.gz'] +sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_%su%sb01.tar.gz' % (local_java_version, local_patch_version)] +checksums = ['87d16dac293d2a9abbb559a277bfaded702f28d1bfdc526f8613bb9cfed84a12'] + +moduleclass = 'lang' From 64a05d9997571068b1696272179a14a839ae6ce5 Mon Sep 17 00:00:00 2001 From: terjekv Date: Mon, 26 Oct 2020 11:26:31 +0100 Subject: [PATCH 693/698] Remove comments, appease Hound. --- .../easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb index eb050ed46d6..32a3e5f5b75 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb @@ -10,9 +10,8 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM -#source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk8u265-b01/'] -source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk%su%s-b01' % (local_java_version, local_patch_version)] -#sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_8u265b01.tar.gz'] +source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk%su%s-b01' % + (local_java_version, local_patch_version)] sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_%su%sb01.tar.gz' % (local_java_version, local_patch_version)] checksums = ['87d16dac293d2a9abbb559a277bfaded702f28d1bfdc526f8613bb9cfed84a12'] From 14085a91b994cd656c021da8301dce0ab2c35c59 Mon Sep 17 00:00:00 2001 From: terjekv Date: Mon, 26 Oct 2020 12:26:20 +0100 Subject: [PATCH 694/698] Style fix. --- .../easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb index 32a3e5f5b75..ee2effebf2e 100644 --- a/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb +++ b/easybuild/easyconfigs/j/Java/Java-1.8_265-b01-OpenJDK-aarch64.eb @@ -11,7 +11,7 @@ description = """Java Platform, Standard Edition (Java SE) lets you develop and toolchain = SYSTEM source_urls = ['https://github.com/AdoptOpenJDK/openjdk8-binaries/releases/download/jdk%su%s-b01' % - (local_java_version, local_patch_version)] + (local_java_version, local_patch_version)] sources = ['OpenJDK8U-jdk_aarch64_linux_hotspot_%su%sb01.tar.gz' % (local_java_version, local_patch_version)] checksums = ['87d16dac293d2a9abbb559a277bfaded702f28d1bfdc526f8613bb9cfed84a12'] From 2fdbc936ab2ad8b56e20dc9cfde5324e53815381 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 26 Oct 2020 15:20:33 +0100 Subject: [PATCH 695/698] add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 --- .../o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb | 7 ++- .../o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb | 7 ++- .../o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb | 7 ++- ....1.4_openib-device-params-ConnectX-6.patch | 55 +++++++++++++++++++ 4 files changed, 73 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb index 0f8dd1068d6..742cf80152b 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'GCC', 'version': '8.3.0-2.32'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', +] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch + '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb index ce695dd33f4..e60121be567 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', +] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch + '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb index 15f81251ecf..d2dc52abe14 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb @@ -8,11 +8,16 @@ toolchain = {'name': 'gcccuda', 'version': '2019b'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch'] +patches = [ + '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', +] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz # OpenMPI-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', + # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch + '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch new file mode 100644 index 00000000000..2b600b76339 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch @@ -0,0 +1,55 @@ +fixes "WARNING: No preset parameters were found for the device that Open MPI detected" +on a system with ConnectX-6 Mellanox cards (see output of "lspci | grep -i mellanox") + +see https://github.com/open-mpi/ompi/pull/7179 + +From 922e2b69c54b563deeda443e5e810314a0a55ca1 Mon Sep 17 00:00:00 2001 +From: Akshay Venkatesh +Date: Tue, 19 Nov 2019 07:20:28 -0800 +Subject: [PATCH] OPAL/MCA/BTL/OPENIB: Detect ConnectX-6 HCAs + +Detection code was added after openib was removed from master but it is still +addressing a need on release branch 3.1.x. This is reason behind why a commit +from master was not cherry-picked into 3.1.x + +Signed-off-by: Akshay Venkatesh +--- + opal/mca/btl/openib/mca-btl-openib-device-params.ini | 9 +++++++++ + opal/mca/common/verbs/common_verbs_port.c | 4 ++++ + 2 files changed, 13 insertions(+) + +diff --git a/opal/mca/btl/openib/mca-btl-openib-device-params.ini b/opal/mca/btl/openib/mca-btl-openib-device-params.ini +index 51b2470b757..b51a7dcdde7 100644 +--- a/opal/mca/btl/openib/mca-btl-openib-device-params.ini ++++ b/opal/mca/btl/openib/mca-btl-openib-device-params.ini +@@ -190,6 +190,15 @@ max_inline_data = 256 + + ############################################################################ + ++[Mellanox ConnectX6] ++vendor_id = 0x2c9,0x5ad,0x66a,0x8f1,0x1708,0x03ba,0x15b3,0x119f ++vendor_part_id = 4123 ++use_eager_rdma = 1 ++mtu = 4096 ++max_inline_data = 256 ++ ++############################################################################ ++ + [IBM eHCA 4x and 12x] + vendor_id = 0x5076 + vendor_part_id = 0 +diff --git a/opal/mca/common/verbs/common_verbs_port.c b/opal/mca/common/verbs/common_verbs_port.c +index 973a82666ef..56166dcb776 100644 +--- a/opal/mca/common/verbs/common_verbs_port.c ++++ b/opal/mca/common/verbs/common_verbs_port.c +@@ -94,6 +94,10 @@ int opal_common_verbs_port_bw(struct ibv_port_attr *port_attr, + /* 12x */ + *bandwidth *= 12; + break; ++ case 16: ++ /* 16x */ ++ *bandwidth *= 16; ++ break; + default: + /* Who knows? */ + return OPAL_ERR_NOT_FOUND; From be260cf5c0a58bcaa0c11526172de53b2d473405 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 28 Oct 2020 09:38:49 +0800 Subject: [PATCH 696/698] prepare release notes for eb431 --- RELEASE_NOTES | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 104 insertions(+) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 9a859ade5e8..c570340c044 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -6,6 +6,110 @@ These release notes can also be consulted at http://easybuild.readthedocs.org/en The latest version of easybuild-easyconfig provides 10,384 easyconfig files, for 2,059 different software packages, incl. 31 different (compiler) toolchains. +v4.3.1 (October 30th 2020) +-------------------------- + +update/bugfix release + +- added easyconfigs for 2 new toolchains: + - fosscuda/2020a (#11424) and intelculda/2020a (#11425) +- added example easyconfig files for 72 new software packages: + - CAVIAR (#11158), CCfits (#11505), CFDEMcoupling (#6465), COMSOL (#11513), CUDAcore (#11295), Cereal (#11506), + causallift (#11436), chewBBACA (#11418), Dalton (#5808), ESMValTool (#6329), ExifTool (#11521), eSpeak-NG (#11236), + FHI-aims (#11198), FRUIT (#6613), FRUIT_processor (#6631), FabIO (#11517), Flexbar (#11305), festival (#11236), + fetchMG (#11283), GBprocesS (#11512), GDRCopy (#11295), Gaussian (#4247), Genome_Profiler (#6066), groff (#11200), + ILAMB (#11309), kedro (#11436), leidenalg (#11407), libav (#6194), libmo_unpack (#6329), libobjcryst (#11321), + MBROLA (#11236), MDSplus-Java (#10705), MDSplus-Python (#10705), MyCC (#11283), makeinfo (#11368), + mauveAligner (#11395), Nek5000 (#6408), nanomax-analysis-utils (#11517), OPERA-MS (#11410), ORFfinder (#7031), + Pingouin (#11280), Pint (#11151), PyOpenCL (#11517), PyVCF (#10564), phonemizer (#11236), pydantic (#11151), + pyobjcryst (#11321), pyspoa (#11438), QtPy (#11517), Qtconsole (#11517), ReMatCh (#6067), Ruby-Tk (#6613), + rasterio (#11468), rasterstats (#11468), SBCL (#11413), SDL (#6202), SDL2 (#6203), SDL2_image (#6203), + SDL_image (#6202), SUMO (#11435), SeqKit (#11538), SiNVICT (#11404), Statistics-R (#11274), scikit-uplift (#11432), + silx (#11517), sonic (#11236), speech_tools (#11236), tidybayes (#11335), treatSens (#11431), tsne (#11283), + WisecondorX (#11399), wandb (#11450) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.2.1, ABRA2 2.23, ACTC 1.1, APR util, APR util, APR 1.7.0, APR 1.7.0, ASE 3.19.0, ASE 3.19.0, ASE 3.20.1, ATK 2.36.0, AmberTools 17, Anaconda3 2020.07.eb, Autoconf 2.69, Automake 1.15.1, Automake 1.15.1, Automake 1.16.2, Autotools 20200321, astropy 4.0.1, at spi2, at spi2, awscli 2.0.55, BCFtools 1.3.1, BCFtools 1.8, BDBag 1.4.1, BLAST+ 2.10.1, BLAST 2.10.1, BLAT 3.5, Bazel 3.6.0, Biopython 1.78, Boost.Python 1.65.1, Bottleneck 1.3.2, Bsoft 2.0.2, Bsoft 2.0.7, bam readcount, breseq 0.35.4, bx python, bzip2 1.0.8, CAVIAR 2.2, CBLAS 20110120, CBLAS 20110120, CCL 1.12, CCfits 2.5, CD HIT, CFDEMcoupling 3.8.0, CGAL 4.14.3, CMake 3.18.4, COMSOL 5.4.0.225.eb, CUDA 11.0.2, CUDA 11.0.2, CUDAcore 11.0.2.eb, Cereal 1.3.0.eb, CheMPS2 1.8.9, Check 0.15.2, Clang Python, ClustalW2 2.1, cURL 7.72.0, cairo 1.16.0, causallift 1.0.6, check 0.12.0, chewBBACA 2.5.5, configurable http, cuDNN 6.0.21, cuDNN 6.0.21, cuDNN 7.0.5, cuDNN 7.0.5, DB 18.1.40, DBus 1.13.18, DIRAC 19.0, DIRAC 19.0, Dalton 2016, DendroPy 4.4.0, deepdiff 5.0.2, double conversion, ELPA 2019.11.001, ELPA 2019.11.001, ESMValTool 1.1.0, EasyBuild 4.3.0.eb, ExifTool 12.00, eSpeak NG, ecCodes 2.7.3, edlib 1.3.8.post1, FASTX Toolkit, FFTW 3.3.8, FHI aims, FLTK 1.3.5, FLUENT 18.2.eb, FRUIT 3.4.3, FRUIT 3.4.3, FRUIT_processor 3.4.3, FRUIT_processor 3.4.3, FabIO 0.10.2, FabIO 0.10.2, FastANI 1.31, Fiona 1.8.13, Flexbar 3.5.0, FoX 4.1.2, FriBidi 1.0.10, festival 2.5.0, fetchMG 1.0, fetchMG 1.0, flatbuffers 1.12.0, fmt 6.2.1, fmt 7.0.3, fontconfig 2.13.92, fosscuda 2020a.eb, freetype 2.10.3, GATK 4.1.8.1, GBprocesS 2.3, GDRCopy 2.1, GL2PS 1.4.2, GLib 2.66.1, GMP 6.2.0, GObject Introspection, GROMACS 2019.6, GROMACS 2020.3, GTDB Tk, GTK+ 3.24.23, Gaussian 09.e.01, Gaussian 16.A.03, Gdk Pixbuf, Genome_Profiler 2.1, GitPython 2.1.15.eb, Guile 2.2.4, gcccuda 2020a.eb, geopandas 0.7.0, geopandas 0.8.1, gettext 0.21, gettext 0.21.eb, giflib 5.2.1, git 2.28.0, gompic 2020a.eb, gperf 3.1, groff 1.22.4, gzip 1.10, HMMER 3.3.1, HPL 2.3, HPL 2.3, HTSeq 0.11.2, HTSlib 1.8, HarfBuzz 2.6.7, Harminv 1.4.1, Horovod 0.20.3, HyPhy 2.3.13, hwloc 2.2.0, hypothesis 4.39.3, ICU 67.1, IDBA UD, ILAMB 2.5, IPython 7.15.0, IPython 7.18.1, IRkernel 1.1, iccifortcuda 2020a.eb, ichorCNA 0.3.2, igraph 0.8.2, iimpic 2020a.eb, imkl 2020.1.217, impi 2019.7.217, intelcuda 2020a.eb, intltool 0.51.0, JasPer 2.0.14, JsonCpp 1.9.4, JupyterHub 0.6.1, JupyterHub 0.8.1, JupyterHub 1.1.0, JupyterLab 2.2.8, Kratos 6.0, kedro 0.16.5, LAMMPS 7Aug2019, LLVM 11.0.0, LZO 2.10, LibTIFF 4.1.0, Libint 2.6.0, Longshot 0.4.1, lavaan 0.6, leidenalg 0.8.2, libGLU 9.0.1, libXau 1.0.8, libXdmcp 1.1.2, libarchive 3.4.3, libav 11.10, libcircle 0.3, libcircle 0.3, libdrm 2.4.102, libepoxy 1.5.2, libepoxy 1.5.4, libevent 2.1.12, libfabric 1.11.0, libfabric 1.11.0, libffi 3.3, libglvnd 1.3.2, libjpeg turbo, libmo_unpack 3.1.2, libobjcryst 2017.2.3, libpciaccess 0.16, libpng 1.6.37, libsodium 1.0.18, libtirpc 1.2.6, libtool 2.4.6, libunwind 1.4.0, libxcb 1.13, libxml2 2.9.10, libxsmm 1.16.1, lz4 1.9.2, MAFFT 7.453, MAFFT 7.471, MBROLA 3.3, MDSplus Java, MDSplus Python, MDSplus 7.96.12, MDTraj 1.9.4, MEGAHIT 1.2.9, MMseqs2 11, MUMmer 3.23, MUMmer 4.0.0beta2, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, MyCC 2017, makeinfo 6.7, makeinfo 6.7, mauveAligner 4736, medaka 1.1.1, medaka 1.1.3, mpifileutils 0.10, mpifileutils 0.10, mpifileutils 0.10.1, NAMD 2.12, NASM 2.15.05, NFFT 3.5.2, NSPR 4.29, NSS 3.57, Nek5000 17.0, Ninja 1.10.1, nanomax analysis, nanomax analysis, ncurses 6.2.eb, nettle 3.6, networkx 2.4, nglview 2.7.7, nodejs 12.19.0, nsync 1.24.0, numactl 2.0.13, OPERA MS, ORFfinder 0.4.3.eb, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OpenCV 4.2.0, OpenFOAM 2.2.2, OpenImageIO 2.1.12.0, OpenImageIO 2.1.12.0, OpenMPI 4.0.3, OpenMPI 4.0.3, OpenMPI 4.0.5, OpenPGM 5.2.122, OpenRefine 3.4.1, OpenSSL 1.1.1h, PAML 4.9j, PCMSolver 1.2.3, PCRE 8.42, PCRE 8.44, PCRE2 10.35, PLINK 1.9b5, PMIx 3.1.5, PSI4 1.3.1, PSI4 1.3.2, Pango 1.47.0, ParMETIS 4.0.3, ParMETIS 4.0.3, Pingouin 0.3.8, Pint 0.14, PyCUDA 2017.1.1, PyCairo 1.18, PyGEOS 0.8, PyOpenCL 2020.2.2, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, PyRETIS 2.5.0, PyTorch 1.6.0, PyVCF 0.6.8, Pysam 0.16.0.1, Python 2.7.18, Python 3.8.6, pandas 1.1.2, pbs_python 4.6.0, phonemizer 2.2.1, phonopy 2.7.1, picard 2.22.1, pigz 2.4, pigz 2.4, pixman 0.40.0, pkg config, pretty yaml, prodigal 2.6.3, protobuf python, protobuf 3.13.0, pyEGA3 3.4.0, pyEGA3 3.4.0, pydantic 1.6.1, pylift 0.1.5, pyobjcryst 2.1.0.post2, pyspoa 0.0.4, pytest 6.0.1, python igraph, QtPy 1.9.0, Qtconsole 4.7.7, Qtconsole 4.7.7, QuickFF 2.2.4, R 3.4.3, R 3.5.1, R 3.6.2, ReFrame 3.2.eb, ReMatCh 3.2, Ruby Tk, Ruby Tk, Ruby 2.5.1, Rust 1.42.0, rasterio 1.1.7, rasterstats 0.15.0, re2c 2.0.3, SAMtools 1.11, SBCL 2.0.9, SCons 4.0.1, SDL 1.2.15, SDL2 2.0.8, SDL2_image 2.0.3, SDL_image 1.2.12, SQLite 3.33.0, SUMO 1.7.0, ScaLAPACK 2.1.0, SciPy bundle, SeqKit 0.13.2.eb, SeqKit 0.8.1.eb, Serf 1.3.9, Serf 1.3.9, SiNVICT 1.0, Siesta 4.0, Spyder 4.1.5, Spyder 4.1.5, Statistics R, Structure 2.3.4, Subversion 1.14.0, Subversion 1.14.0, Szip 2.1.1, sbt 1.3.13, scikit optimize, scikit uplift, silx 0.13.2, silx 0.13.2, snappy 1.1.8, sonic 20180202, speech_tools 2.5.0, spglib python, spoa 4.0.0, stpipeline 1.7.6, TAMkin 1.2.6, TINKER 8.8.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRIQS 3.0.0, Taiyaki 5.1.0, Taiyaki 5.1.0, Tcl 8.6.10, TensorFlow 2.3.1, TensorFlow 2.3.1, TensorFlow 2.3.1, Tk 8.6.10, Tkinter 2.7.18, Tkinter 3.8.6, Trim_Galore 0.6.6, tidybayes 2.1.1, torchvision 0.7.0, treatSens 3.0, trimAl 1.4.1, tsne 0.1.8, UCX 1.8.0, UCX 1.9.0, UDUNITS 2.2.26, UnZip 6.0, UnZip 6.0, utf8proc 2.5.0, utf8proc 2.5.0, util linux, V8 2.3, V8 2.3, V8 3.2.0, Valgrind 3.16.1, Valgrind 3.16.1, VirtualGL 2.6.2, vsc mympirun, WRF 4.1.3, WisecondorX 1.1.6, wandb 0.8.30, X11 20201008, XGBoost 1.2.0, XZ 5.2.5, Xerces C++, Xvfb 1.20.9, xarray 0.16.1, xcb proto, xorg macros, xprop 1.2.4, ZeroMQ 4.3.3, Zip 3.0, zstd 1.4.5 +- minor enhancements, including: + - use more EasyBuild installed dependencies for TensorFlow 2.2.0 (#11224) + - add additional extensions to R 4.0.0 easyconfig (#11340) + - add additional extensions to Bioconductor 3.11 bundle (#11341) + - make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (#11355) + - add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (#11387) + - add ncurses runtime dependency to Clang easyconfigs built with GCC(core) 8.3.0 (#11415) + - add ncurses runtime dependency to Clang 8.x easyconfigs (#11416) + - add ncurses runtime dependency to Clang 10.x easyconfigs using GCCcore/9.3.0 (#11419) + - add dbarts extension to R 4.0.0 easyconfig (#11430) + - cache M4 source tarball to avoid test failures because of download problems (#11469) + - add reader, elementR, ie2misc, assertive, rdrop2 as extensions to R v4.0.0 easyconfig (#11487) + - add crossmeta extension to Bioconductor 3.11 bundle (#11488) + - build LibTIFF with -fPIC (#11527) + - update Java/1.8 wrapper to also support aarch64 (#11545) +- various bug fixes, including: + - add Python 3 as build dep for Xvfb 1.20.8 easyconfigs (#10745) + - patch out bug in collective primitive in TensorFlow 2.2.0 (#11175) + - add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (#11200) + - add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (#11273) + - add libtirpc as a build dep for HDF to fix installation on RHEL8 (#11279) + - fix build problems with make 4.2.1 on RHEL8 (#11282) + - change $LIBS in Ghostscript 9.27 easyconfig to include location of zlib library to link with (#11291) + - remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (#11307) + - make sure correct zlib is used in recent Ghostscript easyconfigs (#11319) + - remove GLog and GFlags from PyTorch 1.2.0 (#11327), 1.3.1 (#11325), 1.4.0 (#11322) and 1.6.0 (#11323) + - use PyTorch easyblock for PyTorch 1.3.1 (#11325) + - add missing git build dependency for OpenImageIO 2.0.12 (#11328) + - fix HDF 4.2.14 easyconfigs for RHEL8 (#11330) + - add patch to fix installation of LAMMPS 7Aug2019 on AMD Epyc systems (#11334) + - fix dependency on Bowtie of v0.x in seq2HLA easyconfigs (#11339) + - fix installation of Hadoop v2.10.0 on RHEL8 (#11358) + - add patch to fix installation of Sailfish v0.10.1 on RHEL8 (#11364) + - add patch to fix installation of FuSeq v1.1.2 on RHEL8 (#11365) + - really fix make 4.2.1 on RHEL 8 (#11371) + - fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (#11385) + - stick to Python 2 as build dep for Qt5 5.13.1 (#11386) + - add patch for LAME configure script to make it check for correct ncurses symbol (#11388) + - add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (#11390) + - fix Multiwfn 3.6 installation on RHEL8 (#11402) + - fix OpenFOAM 2.3.1-intel-2019b installation on RHEL8 (#11409) + - fix broken worker easyconfigs (#11412) + - fix installation of Bioconductor 3.11 bundle on aarch64 (#11417) + - add patch to libunwind fixing a failure on POWER (#11421) + - fix infinite loop build bug on ppc64le for R 4.0.0 (#11428) + - fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (#11434) + - fix PyVCF easyconfig, only supports Python 2 (#11437) + - in-place update of easyconfig Horovod v0.20.0 to v0.20.3 (#11442) + - add patches to fix miscomputation and performance issues for OpenBLAS easyconfigs using GCC toolchain versions: + - 8.2.0-2.31.1 (#11443), 8.3.0 (#11444), 9.2.0 and 9.3.0 (#11445) + - add missing DB dependency (required for DB_File) to easyconfigs for Perl versions: + - 5.28.1, 5.30.0 and 5.30.2 (#11451) and 5.32.0 (#11452) + - fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (#11453) + - use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (#11454) + - add missing UnZip dependency for Python 3.8.2 (#11458) + - add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (#11464) + - tweak non-MPI DIRAC 19.0 easyconfig to use CMakeMake easyblock + add MPI version of DRAC 19.0 (#11465) + - allow Kent_tools to build when MySQL installed at the OS level (#11471) + - add missing ncurses dep for Clang 5.0.x, 6.0.1, 7.0.x (#11472) + - add missing moduleclass to easyconfigs for: + - Arlequin 3.5.2.2 (#11473), MEGAHIT 1.2.8 (#11474) and 1.2.9 (#11475), PyCUDA 2019.1.2 (#11476) + - fix source for SQLite 3.31.1 (#11483) + - fix worker-1.6.11-intel-2019b installation on RHEL 8.2 (#11498) + - disable libunwind + add xauth component for Xvfb 1.20.9 (#11500) + - fix checksum in NAMD 2.12 easyconfigs + add source URL (#11515) + - add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (#11523) + - backport fixes for Score-P v6.0 (#11540) + - add XZ build dependency for libarchive 3.4.3 (#11556) + - add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (#11561) + - add PMIx and friends as deps to OpenMPI 4.0.3 CUDA variants (and 4.0.5) (#11568) +- other changes: + - add easyconfigs for old cuDNN versions + cleanup in cuDNN-7.0.5-CUDA-9.1.85.eb (#6070) + - update README on constructing source file for MATLAB (#6341) + - remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (#11301) + - make CI sanity check messages less confusing ("is" -> "should be") (#11314) + - in-place update of TensorFlow 2.3.0 easyconfigs to version 2.3.1 (#11375) + - remove extentions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (#11429) + - move FLTK-1.3.5 to GCCcore toolchain (#11539) + - rename jupyterhub to JupyterHub (#11571) + + v4.3.0 (September 13th 2020) ---------------------------- From 1dcbc457012ff9dec7588bb41ad07d92e6ffa00b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Oct 2020 19:38:19 +0100 Subject: [PATCH 697/698] drop versionsuffix + set default_cuda_version + clarify comments w.r.t. using custom CUDA as dependency in NVHPC easyconfig --- ...{NVHPC-20.7-GCC-9.3.0.eb => NVHPC-20.7.eb} | 22 ++++++++++--------- 1 file changed, 12 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/n/NVHPC/{NVHPC-20.7-GCC-9.3.0.eb => NVHPC-20.7.eb} (80%) diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7.eb similarity index 80% rename from easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb rename to easybuild/easyconfigs/n/NVHPC/NVHPC-20.7.eb index 0c2e5ac7950..bfb5c8222c0 100644 --- a/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-20.7.eb @@ -1,7 +1,5 @@ name = 'NVHPC' version = '20.7' -local_gccver = '9.3.0' -versionsuffix = '-GCC-%s' % local_gccver homepage = 'https://developer.nvidia.com/hpc-sdk/' description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" @@ -15,6 +13,7 @@ toolchain = SYSTEM sources = ['nvhpc_2020_%(version_major)s%(version_minor)s_Linux_x86_64_cuda_multi.tar.gz'] checksums = ['a5c5c8726d2210f2310a852c6d6e03c9ef8c75e3643e9c94e24909f5e9c2ea7a'] +local_gccver = '9.3.0' dependencies = [ ('GCCcore', local_gccver), ('binutils', '2.34', '', ('GCCcore', local_gccver)), @@ -22,7 +21,12 @@ dependencies = [ ('numactl', '2.0.13', '', ('GCCcore', local_gccver)) ] -default_cuda_version = None # Use strings like "11.0" or use the command line: --try-amend=default_cuda_version="10.2" +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/20.7/cuda/) +# for NVHPC 20.7, those are: 11.0, 10.2, 10.1; +# this version can be tweaked from the EasyBuild command line with --try-amend=default_cuda_version="10.2" (for example) +default_cuda_version = '11.0' # NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. # The following list gives examples for the easyconfig @@ -33,17 +37,15 @@ default_cuda_version = None # Use strings like "11.0" or use the command line: # default_cuda_version = "11.0" # in this easyconfig file; alternatively, it can be specified through the command line during installation with # --try-amend=default_cuda_version="10.2" -# 2) System CUDA -# Use CUDA or CUDAcore as a dependency, for example -# dependencies = [('CUDA', '11.0.2', '', ('GCC', local_gccver))] -# or +# 2) CUDA provided via EasyBuild +# Use CUDAcore as a dependency, for example # dependencies = [('CUDAcore', '11.0.2')] -# The parameter default_cuda_version still can be set as above. If not set, it will be deduced from the -# CUDA module +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) # # Define a NVHPC-default Compute Capability # cuda_compute_capabilities = "8.0" -# Can also be specified via --cuda-compute-capabilities=8.0 +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 # Only single values supported, not lists of values! # # Options to add/remove things to/from environment module (defaults shown) From f181294c4def20c8c01058ee2d9c77c52665d2cc Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 28 Oct 2020 21:19:02 +0100 Subject: [PATCH 698/698] minor tweaks to EasyBuild v4.3.1 release notes + bump version to 4.3.1 --- RELEASE_NOTES | 93 +++++++++++++++++++++++++-------------------------- setup.py | 2 +- 2 files changed, 46 insertions(+), 49 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index c570340c044..16e797c1806 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,45 +3,52 @@ For more detailed information, please see the git log. These release notes can also be consulted at http://easybuild.readthedocs.org/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 10,384 easyconfig files, for 2,059 different software packages, +The latest version of easybuild-easyconfig provides 10,794 easyconfig files, for 2,134 different software packages, incl. 31 different (compiler) toolchains. -v4.3.1 (October 30th 2020) +v4.3.1 (October 29th 2020) -------------------------- update/bugfix release - added easyconfigs for 2 new toolchains: - - fosscuda/2020a (#11424) and intelculda/2020a (#11425) -- added example easyconfig files for 72 new software packages: - - CAVIAR (#11158), CCfits (#11505), CFDEMcoupling (#6465), COMSOL (#11513), CUDAcore (#11295), Cereal (#11506), - causallift (#11436), chewBBACA (#11418), Dalton (#5808), ESMValTool (#6329), ExifTool (#11521), eSpeak-NG (#11236), - FHI-aims (#11198), FRUIT (#6613), FRUIT_processor (#6631), FabIO (#11517), Flexbar (#11305), festival (#11236), - fetchMG (#11283), GBprocesS (#11512), GDRCopy (#11295), Gaussian (#4247), Genome_Profiler (#6066), groff (#11200), - ILAMB (#11309), kedro (#11436), leidenalg (#11407), libav (#6194), libmo_unpack (#6329), libobjcryst (#11321), - MBROLA (#11236), MDSplus-Java (#10705), MDSplus-Python (#10705), MyCC (#11283), makeinfo (#11368), - mauveAligner (#11395), Nek5000 (#6408), nanomax-analysis-utils (#11517), OPERA-MS (#11410), ORFfinder (#7031), - Pingouin (#11280), Pint (#11151), PyOpenCL (#11517), PyVCF (#10564), phonemizer (#11236), pydantic (#11151), - pyobjcryst (#11321), pyspoa (#11438), QtPy (#11517), Qtconsole (#11517), ReMatCh (#6067), Ruby-Tk (#6613), - rasterio (#11468), rasterstats (#11468), SBCL (#11413), SDL (#6202), SDL2 (#6203), SDL2_image (#6203), - SDL_image (#6202), SUMO (#11435), SeqKit (#11538), SiNVICT (#11404), Statistics-R (#11274), scikit-uplift (#11432), - silx (#11517), sonic (#11236), speech_tools (#11236), tidybayes (#11335), treatSens (#11431), tsne (#11283), - WisecondorX (#11399), wandb (#11450) + - fosscuda/2020a (#11424) and intelcuda/2020a (#11425) + +- added example easyconfig files for 75 new software packages: + - Bsoft (#6551, #11537), causallift (#11436), CAVIAR (#11158), CCfits (#11505), Cereal (#11506), + CFDEMcoupling (#6465), Check (#11295), chewBBACA (#11418), COMSOL (#11513), CUDAcore (#11295), Dalton (#5808), + DIRAC (#11414), ESMValTool (#6329), eSpeak-NG (#11236), ExifTool (#11521), FabIO (#11517), festival (#11236), + fetchMG (#11283), FHI-aims (#11198), Flexbar (#11305), FRUIT (#6613), FRUIT_processor (#6631), Gaussian (#4247), + GBprocesS (#11512), GDRCopy (#11295), Genome_Profiler (#6066), groff (#11200), ILAMB (#11309), kedro (#11436), + leidenalg (#11407), libav (#6194), libmo_unpack (#6329), libobjcryst (#11321), makeinfo (#11368), + mauveAligner (#11395), MBROLA (#11236), MDSplus-Java (#10705), MDSplus-Python (#10705), MyCC (#11283), + nanomax-analysis-utils (#11517), Nek5000 (#6408), NVHPC (#11391), OPERA-MS (#11410), ORFfinder (#7031), + phonemizer (#11236), Pingouin (#11280), Pint (#11151), pydantic (#11151), pyobjcryst (#11321), PyOpenCL (#11517), + pyspoa (#11438), QtPy (#11517), Qtconsole (#11517), rasterio (#11468), rasterstats (#11468), ReMatCh (#6067), + Ruby-Tk (#6613), SBCL (#11413), scikit-uplift (#11432), SDL (#6202), SDL2 (#6203), SDL2_image (#6203), + SDL_image (#6202), SeqKit (#11538), silx (#11517), SiNVICT (#11404), sonic (#11236), speech_tools (#11236), + Statistics-R (#11274), SUMO (#11435), tidybayes (#11335), treatSens (#11431), tsne (#11283), wandb (#11450), + WisecondorX (#11399) - added additional easyconfigs for various supported software packages, including: - - ABINIT 9.2.1, ABRA2 2.23, ACTC 1.1, APR util, APR util, APR 1.7.0, APR 1.7.0, ASE 3.19.0, ASE 3.19.0, ASE 3.20.1, ATK 2.36.0, AmberTools 17, Anaconda3 2020.07.eb, Autoconf 2.69, Automake 1.15.1, Automake 1.15.1, Automake 1.16.2, Autotools 20200321, astropy 4.0.1, at spi2, at spi2, awscli 2.0.55, BCFtools 1.3.1, BCFtools 1.8, BDBag 1.4.1, BLAST+ 2.10.1, BLAST 2.10.1, BLAT 3.5, Bazel 3.6.0, Biopython 1.78, Boost.Python 1.65.1, Bottleneck 1.3.2, Bsoft 2.0.2, Bsoft 2.0.7, bam readcount, breseq 0.35.4, bx python, bzip2 1.0.8, CAVIAR 2.2, CBLAS 20110120, CBLAS 20110120, CCL 1.12, CCfits 2.5, CD HIT, CFDEMcoupling 3.8.0, CGAL 4.14.3, CMake 3.18.4, COMSOL 5.4.0.225.eb, CUDA 11.0.2, CUDA 11.0.2, CUDAcore 11.0.2.eb, Cereal 1.3.0.eb, CheMPS2 1.8.9, Check 0.15.2, Clang Python, ClustalW2 2.1, cURL 7.72.0, cairo 1.16.0, causallift 1.0.6, check 0.12.0, chewBBACA 2.5.5, configurable http, cuDNN 6.0.21, cuDNN 6.0.21, cuDNN 7.0.5, cuDNN 7.0.5, DB 18.1.40, DBus 1.13.18, DIRAC 19.0, DIRAC 19.0, Dalton 2016, DendroPy 4.4.0, deepdiff 5.0.2, double conversion, ELPA 2019.11.001, ELPA 2019.11.001, ESMValTool 1.1.0, EasyBuild 4.3.0.eb, ExifTool 12.00, eSpeak NG, ecCodes 2.7.3, edlib 1.3.8.post1, FASTX Toolkit, FFTW 3.3.8, FHI aims, FLTK 1.3.5, FLUENT 18.2.eb, FRUIT 3.4.3, FRUIT 3.4.3, FRUIT_processor 3.4.3, FRUIT_processor 3.4.3, FabIO 0.10.2, FabIO 0.10.2, FastANI 1.31, Fiona 1.8.13, Flexbar 3.5.0, FoX 4.1.2, FriBidi 1.0.10, festival 2.5.0, fetchMG 1.0, fetchMG 1.0, flatbuffers 1.12.0, fmt 6.2.1, fmt 7.0.3, fontconfig 2.13.92, fosscuda 2020a.eb, freetype 2.10.3, GATK 4.1.8.1, GBprocesS 2.3, GDRCopy 2.1, GL2PS 1.4.2, GLib 2.66.1, GMP 6.2.0, GObject Introspection, GROMACS 2019.6, GROMACS 2020.3, GTDB Tk, GTK+ 3.24.23, Gaussian 09.e.01, Gaussian 16.A.03, Gdk Pixbuf, Genome_Profiler 2.1, GitPython 2.1.15.eb, Guile 2.2.4, gcccuda 2020a.eb, geopandas 0.7.0, geopandas 0.8.1, gettext 0.21, gettext 0.21.eb, giflib 5.2.1, git 2.28.0, gompic 2020a.eb, gperf 3.1, groff 1.22.4, gzip 1.10, HMMER 3.3.1, HPL 2.3, HPL 2.3, HTSeq 0.11.2, HTSlib 1.8, HarfBuzz 2.6.7, Harminv 1.4.1, Horovod 0.20.3, HyPhy 2.3.13, hwloc 2.2.0, hypothesis 4.39.3, ICU 67.1, IDBA UD, ILAMB 2.5, IPython 7.15.0, IPython 7.18.1, IRkernel 1.1, iccifortcuda 2020a.eb, ichorCNA 0.3.2, igraph 0.8.2, iimpic 2020a.eb, imkl 2020.1.217, impi 2019.7.217, intelcuda 2020a.eb, intltool 0.51.0, JasPer 2.0.14, JsonCpp 1.9.4, JupyterHub 0.6.1, JupyterHub 0.8.1, JupyterHub 1.1.0, JupyterLab 2.2.8, Kratos 6.0, kedro 0.16.5, LAMMPS 7Aug2019, LLVM 11.0.0, LZO 2.10, LibTIFF 4.1.0, Libint 2.6.0, Longshot 0.4.1, lavaan 0.6, leidenalg 0.8.2, libGLU 9.0.1, libXau 1.0.8, libXdmcp 1.1.2, libarchive 3.4.3, libav 11.10, libcircle 0.3, libcircle 0.3, libdrm 2.4.102, libepoxy 1.5.2, libepoxy 1.5.4, libevent 2.1.12, libfabric 1.11.0, libfabric 1.11.0, libffi 3.3, libglvnd 1.3.2, libjpeg turbo, libmo_unpack 3.1.2, libobjcryst 2017.2.3, libpciaccess 0.16, libpng 1.6.37, libsodium 1.0.18, libtirpc 1.2.6, libtool 2.4.6, libunwind 1.4.0, libxcb 1.13, libxml2 2.9.10, libxsmm 1.16.1, lz4 1.9.2, MAFFT 7.453, MAFFT 7.471, MBROLA 3.3, MDSplus Java, MDSplus Python, MDSplus 7.96.12, MDTraj 1.9.4, MEGAHIT 1.2.9, MMseqs2 11, MUMmer 3.23, MUMmer 4.0.0beta2, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, MyCC 2017, makeinfo 6.7, makeinfo 6.7, mauveAligner 4736, medaka 1.1.1, medaka 1.1.3, mpifileutils 0.10, mpifileutils 0.10, mpifileutils 0.10.1, NAMD 2.12, NASM 2.15.05, NFFT 3.5.2, NSPR 4.29, NSS 3.57, Nek5000 17.0, Ninja 1.10.1, nanomax analysis, nanomax analysis, ncurses 6.2.eb, nettle 3.6, networkx 2.4, nglview 2.7.7, nodejs 12.19.0, nsync 1.24.0, numactl 2.0.13, OPERA MS, ORFfinder 0.4.3.eb, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OSU Micro, OpenCV 4.2.0, OpenFOAM 2.2.2, OpenImageIO 2.1.12.0, OpenImageIO 2.1.12.0, OpenMPI 4.0.3, OpenMPI 4.0.3, OpenMPI 4.0.5, OpenPGM 5.2.122, OpenRefine 3.4.1, OpenSSL 1.1.1h, PAML 4.9j, PCMSolver 1.2.3, PCRE 8.42, PCRE 8.44, PCRE2 10.35, PLINK 1.9b5, PMIx 3.1.5, PSI4 1.3.1, PSI4 1.3.2, Pango 1.47.0, ParMETIS 4.0.3, ParMETIS 4.0.3, Pingouin 0.3.8, Pint 0.14, PyCUDA 2017.1.1, PyCairo 1.18, PyGEOS 0.8, PyOpenCL 2020.2.2, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, PyRETIS 2.5.0, PyTorch 1.6.0, PyVCF 0.6.8, Pysam 0.16.0.1, Python 2.7.18, Python 3.8.6, pandas 1.1.2, pbs_python 4.6.0, phonemizer 2.2.1, phonopy 2.7.1, picard 2.22.1, pigz 2.4, pigz 2.4, pixman 0.40.0, pkg config, pretty yaml, prodigal 2.6.3, protobuf python, protobuf 3.13.0, pyEGA3 3.4.0, pyEGA3 3.4.0, pydantic 1.6.1, pylift 0.1.5, pyobjcryst 2.1.0.post2, pyspoa 0.0.4, pytest 6.0.1, python igraph, QtPy 1.9.0, Qtconsole 4.7.7, Qtconsole 4.7.7, QuickFF 2.2.4, R 3.4.3, R 3.5.1, R 3.6.2, ReFrame 3.2.eb, ReMatCh 3.2, Ruby Tk, Ruby Tk, Ruby 2.5.1, Rust 1.42.0, rasterio 1.1.7, rasterstats 0.15.0, re2c 2.0.3, SAMtools 1.11, SBCL 2.0.9, SCons 4.0.1, SDL 1.2.15, SDL2 2.0.8, SDL2_image 2.0.3, SDL_image 1.2.12, SQLite 3.33.0, SUMO 1.7.0, ScaLAPACK 2.1.0, SciPy bundle, SeqKit 0.13.2.eb, SeqKit 0.8.1.eb, Serf 1.3.9, Serf 1.3.9, SiNVICT 1.0, Siesta 4.0, Spyder 4.1.5, Spyder 4.1.5, Statistics R, Structure 2.3.4, Subversion 1.14.0, Subversion 1.14.0, Szip 2.1.1, sbt 1.3.13, scikit optimize, scikit uplift, silx 0.13.2, silx 0.13.2, snappy 1.1.8, sonic 20180202, speech_tools 2.5.0, spglib python, spoa 4.0.0, stpipeline 1.7.6, TAMkin 1.2.6, TINKER 8.8.1, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, TRIQS 3.0.0, Taiyaki 5.1.0, Taiyaki 5.1.0, Tcl 8.6.10, TensorFlow 2.3.1, TensorFlow 2.3.1, TensorFlow 2.3.1, Tk 8.6.10, Tkinter 2.7.18, Tkinter 3.8.6, Trim_Galore 0.6.6, tidybayes 2.1.1, torchvision 0.7.0, treatSens 3.0, trimAl 1.4.1, tsne 0.1.8, UCX 1.8.0, UCX 1.9.0, UDUNITS 2.2.26, UnZip 6.0, UnZip 6.0, utf8proc 2.5.0, utf8proc 2.5.0, util linux, V8 2.3, V8 2.3, V8 3.2.0, Valgrind 3.16.1, Valgrind 3.16.1, VirtualGL 2.6.2, vsc mympirun, WRF 4.1.3, WisecondorX 1.1.6, wandb 0.8.30, X11 20201008, XGBoost 1.2.0, XZ 5.2.5, Xerces C++, Xvfb 1.20.9, xarray 0.16.1, xcb proto, xorg macros, xprop 1.2.4, ZeroMQ 4.3.3, Zip 3.0, zstd 1.4.5 + - ABINIT 9.2.1, ASE 3.20.1, Autotools 20200321, Bazel 3.6.0, Biopython 1.78, CCL 1.12, CMake 3.18.4, CUDA 11.0.2, + cURL 7.72.0, deepdiff 5.0.2, fmt 7.0.3, GATK 4.1.8.1, GLib 2.66.1, GROMACS 2020.3, GTK+ 3.24.23, git 2.28.0, + HMMER 3.3.1, Horovod 0.20.3, ICU 67.1, IPython 7.18.1, ichorCNA 0.3.2, JupyterHub 1.1.0, JupyterLab 2.2.8, + LLVM 11.0.0, libarchive 3.4.3, libcircle 0.3, libevent 2.1.12, libfabric 1.11.0, libglvnd 1.3.2, libunwind 1.4.0, + libxcb 1.13, MAFFT 7.471, MDSplus 7.96.12, MEGAHIT 1.2.9, MMseqs2 11-e1a1c, Mako 1.1.3, Mesa 20.2.1, Meson 0.55.3, + medaka 1.1.3, mpifileutils 0.10.1, NASM 2.15.05, NSPR 4.29, NSS 3.57, Ninja 1.10.1, nettle 3.6, nglview 2.7.7, + nodejs 12.19.0, OpenImageIO 2.1.12.0, OpenRefine 3.4.1, OpenSSL 1.1.1h, PCRE2 10.35, PSI4 1.3.2, Pango 1.47.0, + PyGEOS 0.8, PyOpenGL 3.1.5, PyQt5 5.15.1, PyQtGraph 0.11.0, PyRETIS 2.5.0, Python 3.8.6, pandas 1.1.2, + phonopy 2.7.1, picard 2.22.1, pixman 0.40.0, protobuf 3.13.0, pyEGA3 3.4.0, pytest 6.0.1, ReFrame 3.2. re2c 2.0.3, + SAMtools 1.11, SCons 4.0.1, SQLite 3.33.0, Spyder 4.1.5, Subversion 1.14.0, sbt 1.3.13, spglib-python 1.16.0, + spoa 4.0.0, TINKER 8.8.1, TRIQS 3.0.0, Taiyaki 5.1.0, TensorFlow 2.3.1, Tkinter 2.7.18 + 3.8.6, torchvision 0.7.0, + UCX 1.9.0, V8 3.2.0, VirtualGL 2.6.2, vsc mympirun 5.2.0 X11 20201008, XGBoost 1.2.0, + XZ 5.2.5, Xerces-C++ 3.2.3, xarray 0.16.1, ZeroMQ 4.3.3, zstd 1.4.5 - minor enhancements, including: - use more EasyBuild installed dependencies for TensorFlow 2.2.0 (#11224) - - add additional extensions to R 4.0.0 easyconfig (#11340) - - add additional extensions to Bioconductor 3.11 bundle (#11341) + - add additional extensions to R 4.0.0 easyconfig (#11340, #11430, #11487) + - add additional extensions to Bioconductor 3.11 bundle (#11341, #11488) - make libtirpc easier to use as replacement of rpc in glibc (for RHEL8) (#11355) - - add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (#11387) - - add ncurses runtime dependency to Clang easyconfigs built with GCC(core) 8.3.0 (#11415) - - add ncurses runtime dependency to Clang 8.x easyconfigs (#11416) - - add ncurses runtime dependency to Clang 10.x easyconfigs using GCCcore/9.3.0 (#11419) - - add dbarts extension to R 4.0.0 easyconfig (#11430) - - cache M4 source tarball to avoid test failures because of download problems (#11469) - - add reader, elementR, ie2misc, assertive, rdrop2 as extensions to R v4.0.0 easyconfig (#11487) - - add crossmeta extension to Bioconductor 3.11 bundle (#11488) + - add libevent, libfabric and PMIx dependencies to OpenMPI 4.0.3 (for foss/2020a & iomkl/2020a) (#11387, #11568) - build LibTIFF with -fPIC (#11527) - update Java/1.8 wrapper to also support aarch64 (#11545) - various bug fixes, including: @@ -50,7 +57,7 @@ update/bugfix release - add missing groff build dependency for Perl (provides nroff tool requires to install man pages) (#11200) - add pocl dependency to GDAL easyconfig using fosscuda/2019b toolchain to make sure it builds on POWER (#11273) - add libtirpc as a build dep for HDF to fix installation on RHEL8 (#11279) - - fix build problems with make 4.2.1 on RHEL8 (#11282) + - fix build problems with make 4.2.1 on RHEL8 (#11282, #11371) - change $LIBS in Ghostscript 9.27 easyconfig to include location of zlib library to link with (#11291) - remove --no-dist-info configuration option for SIP in recent PyQt5 easyconfigs (#11307) - make sure correct zlib is used in recent Ghostscript easyconfigs (#11319) @@ -63,50 +70,40 @@ update/bugfix release - fix installation of Hadoop v2.10.0 on RHEL8 (#11358) - add patch to fix installation of Sailfish v0.10.1 on RHEL8 (#11364) - add patch to fix installation of FuSeq v1.1.2 on RHEL8 (#11365) - - really fix make 4.2.1 on RHEL 8 (#11371) - - fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (#11385) - - stick to Python 2 as build dep for Qt5 5.13.1 (#11386) + - fix installation of Qt5 5.14.1 on top of zlib provided by Gentoo + stick to Python 2 as build dep (#11385, #11386) - add patch for LAME configure script to make it check for correct ncurses symbol (#11388) - add protobuf-python as a dependency and corresponding sanity check to PyTorch 1.6 (#11390) - fix Multiwfn 3.6 installation on RHEL8 (#11402) - - fix OpenFOAM 2.3.1-intel-2019b installation on RHEL8 (#11409) + - fix OpenFOAM 2.3.1 installation with intel/2019b on RHEL8 (#11409) - fix broken worker easyconfigs (#11412) + - add ncurses runtime dependency to Clang easyconfigs (#11415, #11416, #11419, #11472) - fix installation of Bioconductor 3.11 bundle on aarch64 (#11417) - add patch to libunwind fixing a failure on POWER (#11421) - fix infinite loop build bug on ppc64le for R 4.0.0 (#11428) - fix compilation of Qt5 v5.12.3 and v5.13.1 on Ubuntu 20.04 (#11434) - fix PyVCF easyconfig, only supports Python 2 (#11437) - - in-place update of easyconfig Horovod v0.20.0 to v0.20.3 (#11442) - - add patches to fix miscomputation and performance issues for OpenBLAS easyconfigs using GCC toolchain versions: - - 8.2.0-2.31.1 (#11443), 8.3.0 (#11444), 9.2.0 and 9.3.0 (#11445) - - add missing DB dependency (required for DB_File) to easyconfigs for Perl versions: - - 5.28.1, 5.30.0 and 5.30.2 (#11451) and 5.32.0 (#11452) + - add patches to fix miscomputation (on POWER) and performance issues for OpenBLAS (#11443, #11444, #11445) + - add missing DB dependency (required for DB_File) to easyconfigs for Perl (#11451, #11452) - fix dbarts extension in R v4.0.0 easyconfigs for non-x86_64 (#11453) - use Homebrew source mirror to auto-download sources for DB v18.1.25 and v18.1.32 (#11454) - add missing UnZip dependency for Python 3.8.2 (#11458) - add support for building OpenBLAS on ARM TSV110 with GCC 8.3 (#11464) - - tweak non-MPI DIRAC 19.0 easyconfig to use CMakeMake easyblock + add MPI version of DRAC 19.0 (#11465) - allow Kent_tools to build when MySQL installed at the OS level (#11471) - - add missing ncurses dep for Clang 5.0.x, 6.0.1, 7.0.x (#11472) - add missing moduleclass to easyconfigs for: - Arlequin 3.5.2.2 (#11473), MEGAHIT 1.2.8 (#11474) and 1.2.9 (#11475), PyCUDA 2019.1.2 (#11476) - fix source for SQLite 3.31.1 (#11483) - - fix worker-1.6.11-intel-2019b installation on RHEL 8.2 (#11498) - - disable libunwind + add xauth component for Xvfb 1.20.9 (#11500) + - fix installation of worker 1.6.11 with intel/2019b on RHEL 8.2 (#11498) - fix checksum in NAMD 2.12 easyconfigs + add source URL (#11515) - add BLAS/LAPACK check to GPAW patch adding EasyBuild configuration files (#11523) - backport fixes for Score-P v6.0 (#11540) - - add XZ build dependency for libarchive 3.4.3 (#11556) - add XZ build dep to easyconfigs for libarchive v3.4.0 and v3.4.2 (#11561) - - add PMIx and friends as deps to OpenMPI 4.0.3 CUDA variants (and 4.0.5) (#11568) + - add patch for OpenMPI 3.1.4 adding device parameters for ConnectX-6 (#11575) - other changes: - - add easyconfigs for old cuDNN versions + cleanup in cuDNN-7.0.5-CUDA-9.1.85.eb (#6070) - update README on constructing source file for MATLAB (#6341) - remove easyconfigs for Taiyaki that depend on PyTorch 1.3.1, since latest version still requires PyTorch 1.2.0 (#11301) - - make CI sanity check messages less confusing ("is" -> "should be") (#11314) - - in-place update of TensorFlow 2.3.0 easyconfigs to version 2.3.1 (#11375) + - make CI error messages less confusing ("is" -> "should be") (#11314) - remove extentions from R-bundle-Bioconductor 3.11 easyconfigs that are also included in R 4.0.0 (#11429) - - move FLTK-1.3.5 to GCCcore toolchain (#11539) + - cache M4 source tarball to avoid test failures because of download problems (#11469) - rename jupyterhub to JupyterHub (#11571) diff --git a/setup.py b/setup.py index 1c737902693..15bca61be59 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.3.1.dev0' +VERSION = '4.3.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2])