Merge remote-tracking branch 'origin/next' into fci-auto-with-debug-h…

…igher-order
boutproject · Jan 31, 2025 · e052c26 · e052c26
2 parents b3841fb + 1a002d2
commit e052c26
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diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -47,9 +47,10 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_USE_ADIOS2=ON
                             -DBOUT_ENABLE_PYTHON=ON
-                            -DADIOS2_ROOT=/home/runner/local/adios2
+                            -DADIOS2_ROOT=/home/runner/local
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
@@ -74,6 +75,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
@@ -86,6 +88,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             on_cron: false
 
@@ -97,6 +100,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=ON
                             -DBOUT_BUILD_DOCS=OFF
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -110,6 +114,7 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
@@ -123,32 +128,15 @@ jobs:
                             -DBOUT_USE_PETSC=ON
                             -DBOUT_USE_SLEPC=ON
                             -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_USE_HYPRE=OFF
                             -DBOUT_ENABLE_PYTHON=ON
                             -DSUNDIALS_ROOT=/home/runner/local
                             -DPETSC_DIR=/home/runner/local/petsc
                             -DSLEPC_DIR=/home/runner/local/slepc"
             build_petsc: -petsc
             on_cron: false
 
-          - name: "Coverage"
-            os: ubuntu-latest
-            cmake_options: "-DBUILD_SHARED_LIBS=ON
-                            -DCMAKE_BUILD_TYPE=Debug
-                            -DCHECK=3
-                            -DENABLE_COVERAGE=ON
-                            -DBOUT_USE_PETSC=ON
-                            -DBOUT_USE_SLEPC=ON
-                            -DBOUT_USE_HDF5=ON
-                            -DBOUT_USE_SUNDIALS=ON
-                            -DBOUT_ENABLE_PYTHON=ON
-                            -DSUNDIALS_ROOT=/home/runner/local"
-            unit_only: YES
-            on_cron: false
         exclude:
-          # Don't run the coverage tests if the branch isn't master or next
-          - is_master_or_next: false
-            config:
-              name: "Coverage"
           - is_cron: true
             config:
               on_cron: false
@@ -178,6 +166,7 @@ jobs:
                  slepc-dev
                  liblapack-dev
                  libparpack2-dev
+                 libhypre-dev
 
       - uses: actions/checkout@v4
         with:
@@ -210,22 +199,6 @@ jobs:
       - name: Build BOUT++
         run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
-      - name: Capture coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        # Explicitly run the coverage capture target, because
-        # ci_script.sh also does the upload, and we're going to do
-        # that ourselves in the next step
-        run: |
-          # Ensure that there is a corresponding .gcda file for every .gcno file
-          # This is to try and make the coverage report slightly more accurate
-          # It still won't include, e.g. any solvers we don't build with though
-          find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
-          make -C build code-coverage-capture
-
-      - name: Upload coverage
-        if: ${{ matrix.config.name == 'Coverage' }}
-        uses: codecov/codecov-action@v4
-
   Fedora:
     # This is its own job as it doesn't use most of the steps of the
     # standard_tests

diff --git a/bout++Config.cmake.in b/bout++Config.cmake.in
@@ -91,7 +91,7 @@ elseif(EXISTS "@NCXX4_CONFIG@")
   set(NCXX4_CONFIG "@NCXX4_CONFIG@")
 elseif(EXISTS "@NCXX_BINARY_DIR@")
   # If we downloaded netCDF-cxx4, then we need to add its build directory to our search paths
-  list(APPEND CMAKE_PREFIX_PATH "@NCXX_BINARY_DIR@")  
+  list(APPEND CMAKE_PREFIX_PATH "@NCXX_BINARY_DIR@")
 endif()
 if(EXISTS "@PVODE_ROOT@")
   set(PVODE_ROOT "@PVODE_ROOT@")
@@ -103,6 +103,12 @@ endif()
 if(EXISTS "@Libuuid_ROOT@")
   set(Libuuid_ROOT "@Libuuid_ROOT@")
 endif()
+if(EXISTS "@ADIOS2_ROOT@")
+  set(ADIOS2_ROOT "@ADIOS2_ROOT@")
+elseif(EXISTS "@ADIOS2_BINARY_DIR@")
+  # If we downloaded ADIOS2, then we need to add its build directory to our search paths
+  list(APPEND CMAKE_PREFIX_PATH "@ADIOS2_BINARY_DIR@")
+endif()
 
 if(@BOUT_USE_SYSTEM_MPARK_VARIANT@)
   set(mpark_variant_ROOT "@mpark_variant_ROOT@")
@@ -117,6 +123,11 @@ endif()
 
 set(MPIEXEC_EXECUTABLE @MPIEXEC_EXECUTABLE@)
 find_dependency(MPI @MPI_CXX_VERSION@ EXACT)
+if (BOUT_HAS_ADIOS2 OR BOUT_HAS_HYPRE OR BOUT_HAS_SUNDIALS)
+  # These libraries may also require MPI_C
+  enable_language(C)
+  find_dependency(MPI COMPONENTS C)
+endif()
 
 if (BOUT_USE_OPENMP)
   find_dependency(OpenMP)
@@ -158,5 +169,8 @@ endif()
 if (BOUT_USE_UUID_SYSTEM_GENERATOR)
  find_dependency(Libuuid)
 endif()
+if (BOUT_HAS_ADIOS2)
+  find_dependency(ADIOS2 @ADIOS2_VERSION@ EXACT)
+endif()
 
 include("${CMAKE_CURRENT_LIST_DIR}/bout++Targets.cmake")
diff --git a/cmake/FindHYPRE.cmake b/cmake/FindHYPRE.cmake
@@ -7,14 +7,15 @@ include(FindPackageHandleStandardArgs)
 
 find_package(HYPRE CONFIG QUIET)
 if (HYPRE_FOUND)
+  message(STATUS "Found HYPRE: ${HYPRE_VERSION}")
   return()
 endif()
 
 find_path(HYPRE_INCLUDE_DIR
   NAMES HYPRE.h
   DOC "HYPRE include directories"
   REQUIRED
-  PATH_SUFFIXES include
+  PATH_SUFFIXES include include/hypre
 )
 
 find_library(HYPRE_LIBRARY

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
@@ -190,9 +190,12 @@ endif()
 message(STATUS "NetCDF support: ${BOUT_USE_NETCDF}")
 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})
 
-option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" ON)
+option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" OFF)
 option(BOUT_DOWNLOAD_ADIOS2 "Download and build ADIOS2" OFF)
 if (BOUT_USE_ADIOS2)
+  enable_language(C)
+  find_package(MPI REQUIRED COMPONENTS C)
+
   if (BOUT_DOWNLOAD_ADIOS2)
     message(STATUS "Downloading and configuring ADIOS2")
     include(FetchContent)
@@ -211,18 +214,11 @@ if (BOUT_USE_ADIOS2)
     # Note: SST requires <rdma/fabric.h> but doesn't check at configure time
     set(ADIOS2_USE_SST OFF CACHE BOOL "" FORCE)
     FetchContent_MakeAvailable(adios2)
-    target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi)
     message(STATUS "ADIOS2 done configuring")
   else()
-    find_package(ADIOS2)
-    if (ADIOS2_FOUND)
-      ENABLE_LANGUAGE(C)
-      find_package(MPI REQUIRED COMPONENTS C)
-      target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
-    else()
-      set(BOUT_USE_ADIOS2 OFF)
-    endif()
+    find_package(ADIOS2 REQUIRED)
   endif()
+  target_link_libraries(bout++ PUBLIC adios2::cxx11_mpi MPI::MPI_C)
 endif()
 message(STATUS "ADIOS2 support: ${BOUT_USE_ADIOS2}")
 set(BOUT_HAS_ADIOS2 ${BOUT_USE_ADIOS2})
@@ -282,7 +278,7 @@ if (BOUT_USE_SUNDIALS)
     FetchContent_Declare(
       sundials
       GIT_REPOSITORY https://github.com/LLNL/sundials
-      GIT_TAG        v7.0.0
+      GIT_TAG        v7.2.1
       )
     # Note: These are settings for building SUNDIALS
     set(EXAMPLES_ENABLE_C OFF CACHE BOOL "" FORCE)

diff --git a/examples/6field-simple/data/BOUT.inp b/examples/6field-simple/data/BOUT.inp
@@ -1,11 +1,3 @@
-# settings file for BOUT++
-# High-Beta reduced MHD case
-
-##################################################
-# Global settings used by the core code
-
-nout = 100          # number of time-steps
-timestep = 1.0       # time between outputs
 wall_limit = 0.45  # wall time limit (in hours)
 
 twistshift = true   # use twist-shift condition?
@@ -17,7 +9,9 @@ zperiod = 15        # Fraction of a torus to simulate
 MXG = 2
 MYG = 2
 
-grid = "cbm18_dens8.grid_nx68ny64.nc"
+[mesh]
+
+file = "cbm18_dens8.grid_nx68ny64.nc"
 
 [mesh:paralleltransform]
 type = shifted # Use shifted metric method
@@ -70,6 +64,14 @@ rtol = 1e-05  # relative tolerance
 use_precon = false    # Use preconditioner: User-supplied or BBD
 
 mxstep = 10000   # Number of internal steps between outputs
+output_step = 1.0       # time between outputs
+# settings file for BOUT++
+# High-Beta reduced MHD case
+
+##################################################
+# Global settings used by the core code
+
+nout = 100          # number of time-steps
 
 ##################################################
 # settings for high-beta reduced MHD

diff --git a/examples/IMEX/advection-diffusion/data/BOUT.inp b/examples/IMEX/advection-diffusion/data/BOUT.inp
@@ -1,10 +1,3 @@
-# Settings for ImEx example case
-
-##################################################
-# settings used by the core code
-
-nout = 50     # number of time-steps
-timestep = 0.01  # time between outputs
 
 periodicX = true   # Make domain periodic in X
 
@@ -52,6 +45,13 @@ type = splitrk
 timestep = 0.0001   # Internal timestep
 nstages = 9       # Stages in RKL steps for diffusive component
 adapt_period = 5  # Internal steps between accuracy checks
+output_step = 0.01  # time between outputs
+# Settings for ImEx example case
+
+##################################################
+# settings used by the core code
+
+nout = 50     # number of time-steps
 
 ##################################################
 # settings for split operator model

diff --git a/examples/IMEX/advection-reaction/data/BOUT.inp b/examples/IMEX/advection-reaction/data/BOUT.inp
@@ -1,19 +1,14 @@
-# Settings for split operator test case
-
-##################################################
-# settings used by the core code
-
-nout = 100     # number of time-steps
-timestep = 0.01   # time between outputs
 
 MZ = 64     # number of points in z direction (2^n)
 
-grid = "simple_xz.nc"
-
 NXPE = 1
 
 periodicX = true   # Make domain periodic in X
 
+[mesh]
+
+file = "simple_xz.nc"
+
 ##################################################
 # derivative methods
 
@@ -45,6 +40,13 @@ flux = U1
 
 type = splitrk
 timestep = 0.0001
+output_step = 0.01   # time between outputs
+# Settings for split operator test case
+
+##################################################
+# settings used by the core code
+
+nout = 100     # number of time-steps
 
 ##################################################
 # settings for split operator model

diff --git a/examples/IMEX/diffusion-nl/data/BOUT.inp b/examples/IMEX/diffusion-nl/data/BOUT.inp
@@ -1,7 +1,4 @@
 
-nout = 10
-timestep = 1
-
 alpha = 2.5  # Diffusion exponent: D = f ^ alpha
 
 MXG = 0
@@ -22,3 +19,8 @@ ixseps2 = ny
 
 scale = 1
 function = 1 + 0.5*sin(y)
+
+[solver]
+output_step = 1
+
+nout = 10
diff --git a/examples/IMEX/drift-wave-constraint/data/BOUT.inp b/examples/IMEX/drift-wave-constraint/data/BOUT.inp
@@ -1,8 +1,3 @@
-# Drift wave test
-# All variables in normalised units
-
-timestep = 100
-nout = 100
 
 [mesh]
 
@@ -22,6 +17,11 @@ Ne0 = 1 + 0.1*(0.5 - x)
 
 [solver]
 type = imexbdf2
+# Drift wave test
+# All variables in normalised units
+
+output_step = 100
+nout = 100
 
 [drift]
 nu = 0.1

diff --git a/examples/IMEX/drift-wave/data/BOUT.inp b/examples/IMEX/drift-wave/data/BOUT.inp
@@ -1,8 +1,3 @@
-# Drift wave test
-# All variables in normalised units
-
-timestep = 100
-nout = 100
 
 [mesh]
 
@@ -31,3 +26,10 @@ function = sin(y-z)
 [Ne]
 scale = 0
 function = 0
+
+[solver]
+# Drift wave test
+# All variables in normalised units
+
+output_step = 100
+nout = 100