Merge Pull Request #12664 from trilinos/Trilinos/master_merge_2024011…

…2_175838

Automatically Merged using Trilinos Master Merge AutoTester
PR Title: b'Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20240112_175838 branch to master'
PR Author: trilinos-autotester

.github/workflows/muelu_clang_format.yml → .github/workflows/clang_format.yml

@@ -1,4 +1,4 @@
-name: Check MueLu clang-format
+name: Check packages with clang-format
 
 on: [pull_request]
 
@@ -10,8 +10,8 @@ jobs:
     - uses: actions/checkout@v3
     - uses: DoozyX/[email protected]
       with:
-        source: './packages/muelu'
-        exclude: ''
+        source: './packages/muelu ./packages/tempus'
+        exclude: './packages/tempus/examples'
         extensions: 'cpp,hpp'
         clangFormatVersion: 14
         inplace: true
@@ -35,7 +35,7 @@ jobs:
       if: ${{ hashFiles('format_patch.txt') != '' }}          
       with:
         message: |
-          Your PR updated files in MueLu, but did not respect the clang formatting settings.  Please apply the patch found [here](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}/artifacts/${{ steps.upload-artf.outputs.artifact-id }})
+          Your PR updated files that did not respect package clang formatting settings.  Please apply the patch found [here](https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }}/artifacts/${{ steps.upload-artf.outputs.artifact-id }})
         
     - uses: actions/github-script@v3
       if: ${{ hashFiles('format_patch.txt') != '' }}

cmake/std/atdm/van1-tx2/all_supported_builds.sh

@@ -5,4 +5,6 @@ export ATDM_CONFIG_CTEST_S_BUILD_NAME_PREFIX=Trilinos-atdm-
 export ATDM_CONFIG_ALL_SUPPORTED_BUILDS=(
   van1-tx2_arm-20.1_openmpi-4.0.5_openmp_static_opt
   van1-tx2_arm-20.1_openmpi-4.0.5_openmp_static_dbg
+  van1-tx2_arm-22.1_openmpi-4.0.5_openmp_static_opt
+  van1-tx2_arm-22.1_openmpi-4.0.5_openmp_static_dbg
   )

cmake/std/atdm/van1-tx2/custom_builds.sh

@@ -7,18 +7,27 @@ if atdm_match_any_buildname_keyword \
      arm-20.1_openmpi-4.0.5 \
      arm-20.1 \
      arm-20 \
+  ; then
+  export ATDM_CONFIG_COMPILER=ARM-20.1_OPENMPI-4.0.5
+elif atdm_match_any_buildname_keyword \
+     arm-22.1-openmpi-4.0.5 \
+     arm-22.1_openmpi-4.0.5 \
+     arm-22.1 \
+     arm-22 \
      arm \
      default \
   ; then
-  export ATDM_CONFIG_COMPILER=ARM-20.1_OPENMPI-4.0.5
+  export ATDM_CONFIG_COMPILER=ARM-22.1_OPENMPI-4.0.5
+
 else
   echo
   echo "***"
   echo "*** ERROR: A supported compiler was not selected for 'van1-tx2' (stria) env in buildname '${ATDM_CONFIG_BUILD_NAME}'"
   echo "***"
   echo "*** Supported compilers include:"
   echo "***"
-  echo "****  arm-20.1-openmpi-4.0.5    (arm, arm-20, arm-20.1, default)"
+  echo "****  arm-22.1-openmpi-4.0.5    (arm, arm-22, arm-22.1, default)"
+  echo "****  arm-20.1-openmpi-4.0.5    (arm-20, arm-20.1)"
   echo "***"
   return
 

cmake/std/atdm/van1-tx2/custom_builds_unit_tests.sh

@@ -20,21 +20,29 @@ testAll() {
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
   ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
+  ATDM_CONFIG_BUILD_NAME=before-arm-22.1-openmpi-4.0.5_after
+  . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
+
+  ATDM_CONFIG_BUILD_NAME=before-arm-22.1_openmpi-4.0.5-after
+  . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
+
   ATDM_CONFIG_BUILD_NAME=default
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
-  ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
   ATDM_CONFIG_BUILD_NAME=before_arm-20-afert
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
   ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
   ATDM_CONFIG_BUILD_NAME=before-arm-after
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
-  ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
   ATDM_CONFIG_BUILD_NAME=BEFORE-ARM-AFTER
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
-  ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
   # Make sure 'arms' does not match 'arm'
   ATDM_CONFIG_BUILD_NAME=anything-arms
@@ -45,6 +53,9 @@ testAll() {
   . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
   ${_ASSERT_EQUALS_} ARM-20.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 
+  ATDM_CONFIG_BUILD_NAME=before_arm-22.1-after
+  . ${ATDM_CONFIG_SCRIPT_DIR}/utils/set_build_options.sh
+  ${_ASSERT_EQUALS_} ARM-22.1_OPENMPI-4.0.5 ${ATDM_CONFIG_COMPILER}
 }
 
 

cmake/std/atdm/van1-tx2/environment.sh

@@ -48,12 +48,6 @@ fi
 if [[ "$ATDM_CONFIG_COMPILER" == "ARM-20.1_OPENMPI-4.0.5" ]]; then
   module load sparc-dev/arm-20.1_openmpi-4.0.5
   module unload yaml-cpp
-
-  if [ "$ATDM_CONFIG_NODE_TYPE" == "OPENMP" ] ; then
-    unset OMP_PLACES
-    unset OMP_PROC_BIND
-  fi
-
   # We'll use TPL_ROOT for consistency across ATDM environments
   export MPI_ROOT=${MPI_DIR}
   export BLAS_ROOT=${ARMPL_DIR}
@@ -66,6 +60,24 @@ if [[ "$ATDM_CONFIG_COMPILER" == "ARM-20.1_OPENMPI-4.0.5" ]]; then
   export PARMETIS_ROOT=${PARMETIS_DIR}
   export SUPERLUDIST_ROOT=${SUPERLU_DIST_DIR}
   export BINUTILS_ROOT=${BINUTILS_DIR}
+  # SUPERLU_DIST and NETCDF libraries live in $ROOT/lib in this version
+  export ATDM_CONFIG_SUPERLUDIST_LIBS="-L${SUPERLUDIST_ROOT}/lib;-lsuperlu_dist"
+  export ATDM_CONFIG_NETCDF_LIBS="-L${NETCDF_ROOT}/lib;${NETCDF_ROOT}/lib/libnetcdf.a;${PNETCDF_ROOT}/lib/libpnetcdf.a;${ATDM_CONFIG_HDF5_LIBS}"
+elif [[ "$ATDM_CONFIG_COMPILER" == "ARM-22.1_OPENMPI-4.0.5" ]]; then
+  export BLAS_ROOT=${ARMPL_DIR}
+  module load sparc-dev/arm-22.1_openmpi-4.0.5
+  module unload yaml-cpp
+  # superlu and binutils are not included in the devpack:
+  module load superlu/5.2.1
+  module load binutils/2.33.1
+  # This version of sparc-dev sets most of the $TPL_ROOT style variables,
+  # except these:
+  export MPI_ROOT=${MPI_DIR}
+  export SUPERLU_ROOT=${SUPERLU_DIR}
+  export BINUTILS_ROOT=${BINUTILS_DIR}
+  # SUPERLU_DIST and NETCDF libraries live in $ROOT/lib64 in this version
+  export ATDM_CONFIG_SUPERLUDIST_LIBS="-L${SUPERLUDIST_ROOT}/lib64;-lsuperlu_dist"
+  export ATDM_CONFIG_NETCDF_LIBS="-L${NETCDF_ROOT}/lib64;${NETCDF_ROOT}/lib64/libnetcdf.a;${PNETCDF_ROOT}/lib/libpnetcdf.a;${ATDM_CONFIG_HDF5_LIBS}"
 else
   echo
   echo "***"
@@ -74,6 +86,11 @@ else
   return
 fi
 
+if [ "$ATDM_CONFIG_NODE_TYPE" == "OPENMP" ] ; then
+  unset OMP_PLACES
+  unset OMP_PROC_BIND
+fi
+
 if [[ "$ATDM_CONFIG_NODE_TYPE" == "OPENMP" ]] ; then
   export ATDM_CONFIG_CTEST_PARALLEL_LEVEL=16
   export OMP_NUM_THREADS=2
@@ -83,9 +100,14 @@ else
   export OMP_NUM_THREADS=1
 fi
 
+# Also unload this cmake module as 3.17 is too old to configure Trilinos.
+# sparc-cmake/3.23.2 is the version we want to use
+# (and both devpacks load it), but because it has a
+# different name it won't unload this older version.
+module unload cmake/3.17.1
+
 # Common modules for all builds
 module load ninja
-module load cmake/3.17.1
 
 export ATDM_CONFIG_USE_HWLOC=OFF
 export HWLOC_LIBS=
@@ -99,18 +121,14 @@ export ATDM_CONFIG_CGNS_LIBRARY_NAMES="cgns"
 # HDF5 settings
 export ATDM_CONFIG_HDF5_LIBS="-L${HDF5_ROOT}/lib;${HDF5_ROOT}/lib/libhdf5_hl.a;${HDF5_ROOT}/lib/libhdf5.a;-lz;-ldl"
 
-# NETCDF settings
-export ATDM_CONFIG_NETCDF_LIBS="-L${NETCDF_ROOT}/lib;${NETCDF_ROOT}/lib/libnetcdf.a;${PNETCDF_ROOT}/lib/libpnetcdf.a;${ATDM_CONFIG_HDF5_LIBS}"
-
 # BLAS settings
 export ATDM_CONFIG_BLAS_LIBS="-L${BLAS_ROOT}/lib;-larmpl_lp64_mp;-larmflang;-lomp"
 
 # LAPACK settings
 export ATDM_CONFIG_LAPACK_LIBS="-L${LAPACK_ROOT}/lib;-larmpl_lp64_mp;-larmflang;-lomp"
 
-# SuperLUDist settings
+# Common SuperLUDist settings
 export ATDM_CONFIG_SUPERLUDIST_INCLUDE_DIRS="${SUPERLUDIST_ROOT}/include"
-export ATDM_CONFIG_SUPERLUDIST_LIBS="-L${SUPERLUDIST_ROOT}/lib;-lsuperlu_dist"
 
 # METIS settings - force linker order!
 export ATDM_CONFIG_PARMETIS_LIBS="${PARMETIS_ROOT}/lib/libparmetis.a;${METIS_ROOT}/lib/libmetis.a"

packages/framework/get_dependencies.sh

@@ -96,25 +96,27 @@ fi
 # Set up symlinks to the desired *.ini files
 echo
 cd ${script_dir}/GenConfig/deps/LoadEnv/ini_files
+relative_path_to_script_dir="../../../.."
 if [[ -d ${script_dir}/srn-ini-files ]] && [[ "$ini_file_option" == "--srn" ]]; then
     echo "STATUS: Link files from srn-ini-files"
-    ln -sf ${script_dir}/srn-ini-files/trilinos/framework/environment-specs.ini
-    ln -sf ${script_dir}/srn-ini-files/trilinos/framework/supported-systems.ini
+    ln -sf ${relative_path_to_script_dir}/srn-ini-files/trilinos/framework/environment-specs.ini
+    ln -sf ${relative_path_to_script_dir}/srn-ini-files/trilinos/framework/supported-systems.ini
 elif [[ -d ${script_dir}/son-ini-files ]] && [[ "$ini_file_option" == "--son" ]]; then
     echo "STATUS: Link files from son-ini-files"
-    ln -sf ${script_dir}/son-ini-files/trilinos/framework/environment-specs.ini
-    ln -sf ${script_dir}/son-ini-files/trilinos/framework/supported-systems.ini
+    ln -sf ${relative_path_to_script_dir}/son-ini-files/trilinos/framework/environment-specs.ini
+    ln -sf ${relative_path_to_script_dir}/son-ini-files/trilinos/framework/supported-systems.ini
 else
     echo "STATUS: Link files from ini-files"
-    [ -e ${script_dir}/ini-files/environment-specs.ini ] && ln -sf ${script_dir}/ini-files/environment-specs.ini
-    [ -e ${script_dir}/ini-files/supported-systems.ini ] && ln -sf ${script_dir}/ini-files/supported-systems.ini
+    [ -e ${relative_path_to_script_dir}/ini-files/environment-specs.ini ] && ln -sf ${relative_path_to_script_dir}/ini-files/environment-specs.ini
+    [ -e ${relative_path_to_script_dir}/ini-files/supported-systems.ini ] && ln -sf ${relative_path_to_script_dir}/ini-files/supported-systems.ini
 fi
-ln -sf ${script_dir}/ini-files/supported-envs.ini
+ln -sf ${relative_path_to_script_dir}/ini-files/supported-envs.ini
 cd - > /dev/null
 
 cd ${script_dir}/GenConfig/ini_files
-ln -sf ${script_dir}/ini-files/config-specs.ini
-ln -sf ${script_dir}/ini-files/supported-config-flags.ini
+relative_path_to_script_dir="../.."
+ln -sf ${relative_path_to_script_dir}/ini-files/config-specs.ini
+ln -sf ${relative_path_to_script_dir}/ini-files/supported-config-flags.ini
 
 # Print summary of ini file settings
 cd ${script_dir}

packages/framework/pr_tools/PullRequestLinuxDriverMerge.py

@@ -171,9 +171,9 @@ def merge_branch(source_url, target_branch, sourceSHA):
 
     if sha_exists_as_branch_on_remote:
         print_wrapper("REMARK: Detected ref as a remote branch, will merge as such")
-        check_call_wrapper(['git', 'merge', '--no-edit', "source_remote/" + sourceSHA])
+        check_call_wrapper(['git', 'merge', '--no-ff', '--no-edit', "source_remote/" + sourceSHA])
     else:
-        check_call_wrapper(['git', 'merge', '--no-edit', sourceSHA])
+        check_call_wrapper(['git', 'merge', '--no-ff', '--no-edit', sourceSHA])
 
     return 0
 

packages/framework/pr_tools/unittests/test_PullRequestLinuxDriverMerge.py

@@ -169,7 +169,7 @@ def test_mergeBranch_without_source_remote(self):
                                        mock.call(['git', 'fetch', 'origin', 'fake_develop']),
                                        mock.call(['git', 'reset', '--hard', 'HEAD']),
                                        mock.call(['git', 'checkout', '-B', 'fake_develop', 'origin/fake_develop']),
-                                       mock.call(['git', 'merge', '--no-edit', 'df324ae']),
+                                       mock.call(['git', 'merge', '--no-ff', '--no-edit', 'df324ae']),
                                        ])
         return
 
@@ -199,7 +199,7 @@ def test_mergeBranch_with_source_remote(self, m_check_call):
                                        mock.call(['git', 'fetch', 'origin', 'fake_develop']),
                                        mock.call(['git', 'reset', '--hard', 'HEAD']),
                                        mock.call(['git', 'checkout', '-B', 'fake_develop', 'origin/fake_develop']),
-                                       mock.call(['git', 'merge', '--no-edit', 'df324ae']),
+                                       mock.call(['git', 'merge', '--no-ff', '--no-edit', 'df324ae']),
                                        ])
         self.assertIn("git remote exists, removing it", m_stdout.getvalue())
         return
@@ -229,7 +229,7 @@ def test_mergeBranch_ref_is_remote_branch(self, m_check_call):
                                        mock.call(['git', 'fetch', 'origin', 'fake_develop']),
                                        mock.call(['git', 'reset', '--hard', 'HEAD']),
                                        mock.call(['git', 'checkout', '-B', 'fake_develop', 'origin/fake_develop']),
-                                       mock.call(['git', 'merge', '--no-edit', 'source_remote/some_ref']),
+                                       mock.call(['git', 'merge', '--no-ff', '--no-edit', 'source_remote/some_ref']),
                                        ])
         self.assertIn("git remote exists, removing it", m_stdout.getvalue())
         return

packages/ifpack2/src/Ifpack2_BlockTriDiContainer_impl.hpp

@@ -3209,6 +3209,7 @@ namespace Ifpack2 {
         printf("Start ExtractBCDTag\n");
 #endif
             Kokkos::deep_copy(e_scalar_values, Kokkos::ArithTraits<btdm_magnitude_type>::zero());
+            Kokkos::deep_copy(scalar_values_schur, Kokkos::ArithTraits<btdm_magnitude_type>::zero());
 
             write5DMultiVectorValuesToFile(part2packrowidx0_sub.extent(0), e_scalar_values, "e_scalar_values_before_extract.mm");