Fix HOMME build issues with SCORPIO 1.6.3 #6429

jayeshkrishna · 2024-05-17T14:32:38Z

Fixes standalone HOMME build issues with SCORPIO 1.6.3
(Also see PR #6329)

[BFB]

Removing reference to piolib_mod module since its no longer available. Using the function directly from pio module instead.

SCORPIO no longer exports build directory with the library targets. Adding path to SCORPIO include directory for HOMME standalone builds

jayeshkrishna · 2024-05-17T14:33:22Z

This PR fixes build issues seen in the nightlies with HOMME_P24.f19_g16_rx1.A (standalone HOMME tests)

github-actions · 2024-05-17T14:36:17Z

PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6429/
on branch `gh-pages` at 2024-06-01 00:24 UTC

whannah1 · 2024-05-17T16:49:00Z

I just tested a merge of this branch with current master on chrysalis and got this configuration error trying to build homme_tool:

-- Could NOT find PnetCDF_C (missing: PnetCDF_C_LIBRARY PnetCDF_C_INCLUDE_DIR)
-- Could not find PnetCDF library, disabling support for PnetCDF
-- Disabling support for ADIOS (default)
-- Disabling support for HDF5
-- Checking whether Fortran type INTEGER(KIND=MPI_OFFSET_KIND) has the same size as INTEGER(KIND=C_LONG_LONG)
-- Checking whether Fortran type INTEGER(KIND=MPI_OFFSET_KIND) has the same size as INTEGER(KIND=C_LONG)
-- Checking whether Fortran type INTEGER(KIND=MPI_OFFSET_KIND) has the same size as INTEGER(KIND=C_INT)
CMake Error at utils/externals/scorpio/cmake/SPIOTypeUtils.cmake:172 (message):
  Could not find a Fortran type for passing PIO Offsets from Fortran to C
Call Stack (most recent call first):
  utils/externals/scorpio/src/clib/CMakeLists.txt:183 (get_pio_offset_type)
  
  -- Configuring incomplete, errors occurred!

Here's the commands I used:

e3sm_root=/lcrc/group/e3sm/ac.whannah/scratch/chrys/tmp_clone

cd ${e3sm_root}/components/homme
eval $(${e3sm_root}/cime/CIME/Tools/get_case_env)

mach_file=${e3sm_root}/components/homme/cmake/machineFiles/chrysalis.cmake

cmake -C ${mach_file} \
-DBUILD_HOMME_WITHOUT_PIOLIBRARY=FALSE \
-DHOMME_ENABLE_COMPOSE=FALSE \
-DHOMME_BUILD_EXECS=FALSE \
-DBUILD_HOMME_TOOL=TRUE \
${e3sm_root}/components/homme

jayeshkrishna · 2024-05-17T17:24:50Z

@whannah1 : Do you have the right environment set for building HOMME on Chrysalis (https://acme-climate.atlassian.net/wiki/spaces/DOC/pages/2735079654/Standalone+HOMME) ? Looks like Fortran compiler issues (not available etc).

Can you also try a simple cmake with no extra config flags (cmake -C $mach_file ${e3sm_root}/components/homme)?

whannah1 · 2024-05-17T17:33:14Z

I don't have a special env set other than what I get from eval $(${e3sm_root}/cime/CIME/Tools/get_case_env)

I tried the simpler cmake -C ${mach_file} ${e3sm_root}/components/homme and got the same result

whannah1 · 2024-05-17T17:58:22Z

After retrying with a fresh clone of this branch I can't reproduce the configuration error on chrysalis, so I think it's good aside from the perlmutter linker error I made an issue about here: E3SM-Project/scorpio#586

jayeshkrishna · 2024-05-30T17:29:20Z

@oksanaguba / @mt5555 : This PR should be ready to merge to next, please go ahead and merge the changes when next is open.

…next (PR #6429) Fixes standalone HOMME build issues with SCORPIO 1.6.3 [BFB]

rljacob · 2024-05-31T16:28:44Z

homme_integration suites now has one of its test passing (HOMME_P24.f19_g16_rx1.A) but the other has a build fail:

2024-05-30 22:51:50: MODEL_BUILD FAILED for test 'HOMMEBFB_P24.f19_g16_rx1.A.chrysalis_intel'.
Command: ./case.build --model-only
Output: WARNING: Found difference in test STOP_N: case: 11 original value 5
Building test for HOMMEBFB in directory /lcrc/group/e3sm2/e3smtest/scratch/chrys/J/HOMMEBFB_P24.f19_g16_rx1.A.chrysalis_intel.C.JNextHomme_integration20240530_224749
ERROR: Command: 'gmake -j8 VERBOSE=1 test-execs' failed with error 'See /lcrc/group/e3sm2/e3smtest/scratch/chrys/HOMMEBFB_P24.f19_g16_rx1.A.chrysalis_intel.C.JNextHomme_integration20240530_224749/bld/homme.bldlog' from dir '/lcrc/group/e3sm2/e3smtest/scratch/chrys/HOMMEBFB_P24.f19_g16_rx1.A.chrysalis_intel.C.JNextHomme_integration20240530_224749/bld'

Adding path to the timing binary directory to the set of include directories. This change is required for these tests that need path to the fortran perf mod. This fixes build issues with the HOMMEBFB test suite using the latest version of the SCORPIO library (new versions of the SCORPIO library no longer export internal SCORPIO build paths with the SCORPIO library targets)

oksanaguba · 2024-06-01T01:27:40Z

why is not-cime build working without these changes?

oksanaguba · 2024-06-01T01:28:56Z

... and also how did scorpio changes affect timing lib?

…#6429) second merge of this branch. Fix build issue with timing library.

jayeshkrishna · 2024-06-01T05:07:30Z

SCORPIO used to export all of its internal build dirs with its lib targets (piof/pioc). We now only export the install paths (and dependencies). With older version of SCORPIO the HOMME builds must have been using perf/timing mods from SCORPIO (instead of the timing mods/libs in HOMME).
Also, the failing tests (builds) are only built for HOMMEBFB_* test suite (these tests are not built for the HOMME_* suite)

oksanaguba · 2024-06-02T02:46:04Z

thanks, @jayeshkrishna -- i was puzzled why of all homme ut tests in that folder only remap_ut fails to build, but it seems that the other tests do not use source files with timers.

oksanaguba · 2024-06-02T02:48:52Z

Separately, do you know if these warnings when configuring homme tests are an issue?

CMake Warning (dev) at /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/cmake-3.24.3-jii6uyz/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args` (NetCDF_C)
  does not match the name of the calling package (NetCDF).  This can lead to
  problems in calling code that expects `find_package` result variables
  (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  utils/externals/scorpio/cmake/LibFind.cmake:302 (find_package_handle_standard_args)
  utils/externals/scorpio/cmake/FindNetCDF.cmake:51 (find_package_component)
  utils/externals/scorpio/src/clib/CMakeLists.txt:64 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

and

CMake Warning (dev) at /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/cmake-3.24.3-jii6uyz/share/cmake-3.24/Modules/CheckIncludeFile.cmake:82 (message):
  Policy CMP0075 is not set: Include file check macros honor
  CMAKE_REQUIRED_LIBRARIES.  Run "cmake --help-policy CMP0075" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.

  CMAKE_REQUIRED_LIBRARIES is set to:

    /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/netcdf-c-4.4.1-qvxyzq2/lib/libnetcdf.so

  For compatibility with CMake 3.11 and below this check is ignoring it.
Call Stack (most recent call first):
  /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/cmake-3.24.3-jii6uyz/share/cmake-3.24/Modules/CheckTypeSize.cmake:256 (check_include_file)
  utils/externals/scorpio/cmake/SPIOTypeUtils.cmake:137 (check_type_size)
  utils/externals/scorpio/src/clib/CMakeLists.txt:183 (get_pio_offset_type)
This warning is for project developers.  Use -Wno-dev to suppress it.

and

CMake Warning (dev) at /gpfs/fs1/soft/chrysalis/spack/opt/spack/linux-centos8-x86_64/intel-20.0.4/cmake-3.24.3-jii6uyz/share/cmake-3.24/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
  The package name passed to `find_package_handle_standard_args`
  (NetCDF_Fortran) does not match the name of the calling package (NetCDF).
  This can lead to problems in calling code that expects `find_package`
  result variables (e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
  utils/externals/scorpio/cmake/LibFind.cmake:302 (find_package_handle_standard_args)
  utils/externals/scorpio/cmake/FindNetCDF.cmake:51 (find_package_component)
  utils/externals/scorpio/src/flib/CMakeLists.txt:228 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

jayeshkrishna · 2024-06-03T16:55:02Z

@oksanaguba : These CMake warnings should be ok for now (low priority) and will be fixed in future release of SCORPIO.

jayeshkrishna added 2 commits May 16, 2024 19:29

Rm reference to piolib_mod

4da9dcd

Removing reference to piolib_mod module since its no longer available. Using the function directly from pio module instead.

Explicitly add path to SCORPIO include directory

b06c4a3

SCORPIO no longer exports build directory with the library targets. Adding path to SCORPIO include directory for HOMME standalone builds

jayeshkrishna added BFB PR leaves answers BFB HOMME standalone issues with the standalone HOMME code that dont impact E3SM SCORPIO The E3SM I/O library (derived from PIO) labels May 17, 2024

jayeshkrishna requested a review from mt5555 May 17, 2024 14:32

jayeshkrishna assigned mt5555 May 17, 2024

mt5555 approved these changes May 18, 2024

View reviewed changes

skyler-ruiter pushed a commit to skyler-ruiter/E3SM that referenced this pull request May 29, 2024

adds changes from PR E3SM-Project#6429

c6fe5d1

jayeshkrishna assigned oksanaguba May 30, 2024

rljacob assigned rljacob and unassigned mt5555 and oksanaguba May 30, 2024

rljacob added a commit that referenced this pull request May 30, 2024

Merge branch 'origin/jayeshkrishna/homme/port_to_scorpio_1.6.2' into …

cd89388

…next (PR #6429) Fixes standalone HOMME build issues with SCORPIO 1.6.3 [BFB]

jayeshkrishna requested a review from oksanaguba June 1, 2024 00:23

oksanaguba approved these changes Jun 1, 2024

View reviewed changes

rljacob added a commit that referenced this pull request Jun 1, 2024

Merge branch 'jayeshkrishna/homme/port_to_scorpio_1.6.2' into next (PR …

4af500a

…#6429) second merge of this branch. Fix build issue with timing library.

rljacob merged commit 01e3cd9 into master Jun 3, 2024
13 checks passed

rljacob deleted the jayeshkrishna/homme/port_to_scorpio_1.6.2 branch June 3, 2024 21:54

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Fix HOMME build issues with SCORPIO 1.6.3 #6429

Fix HOMME build issues with SCORPIO 1.6.3 #6429

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Fix HOMME build issues with SCORPIO 1.6.3 #6429

Fix HOMME build issues with SCORPIO 1.6.3 #6429

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