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Merge pull request #210 from Sichao25/yus/ci
Switch from MPICH to OpenMPI in CI
2 parents 0711fbf + 861a29e commit cb10fb7

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‎.github/workflows/clang-tidy.yml‎

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# Now it is separated to avoid affecting MPICH is not compatible with Ubuntu-latest and bear is not compatible with OPENMPI. This workflow should be merged after either compatibility issue is resolved.
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name: Clang-Tidy Check
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on:
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push:
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branches:
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- main
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- develop
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pull_request:
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branches:
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- main
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- develop
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jobs:
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clang-tidy-check:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash
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strategy:
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matrix:
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build_type: [Release]
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memory_test: [ON, OFF]
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compiler: [g++]
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language: ['cpp']
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exclude:
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- build_type: Release
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memory_test: ON
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- build_type: RelWithDebInfo
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memory_test: OFF
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steps:
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- name: Update packages
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run: sudo apt-get update
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- name: Install mpich
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run: sudo apt-get install -yq libmpich-dev mpich
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- name: Install cmake
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run: sudo apt-get install -yq cmake
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- uses: actions/checkout@v4
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- name: build Catch2
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'Catch2-openmpi'
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repo-path: 'catchorg/Catch2'
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repo-ref: ''
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cache: true
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- name: build kokkos
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'kokkos-openmpi'
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repo-path: 'kokkos/kokkos'
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repo-ref: '4.6.01'
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cache: true
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options: '-DCMAKE_CXX_STANDARD=17
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-DBUILD_SHARED_LIBS=OFF
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-DKokkos_ENABLE_SERIAL=ON
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-DKokkos_ENABLE_OPENMP=OFF
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-DKokkos_ENABLE_CUDA=OFF
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-DKokkos_ENABLE_CUDA_LAMBDA=OFF
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-DKokkos_ENABLE_CUDA_CONSTEXPR=OFF'
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- name: build kokkos-kernels
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'kokkos-kernels-openmpi'
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repo-path: 'kokkos/kokkos-kernels'
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repo-ref: '4.6.01'
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cache: true
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options: '-DCMAKE_CXX_STANDARD=17
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-DBUILD_SHARED_LIBS=OFF
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos-openmpi/install/lib/cmake/Kokkos'
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- name: build omega_h
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'omega_h-openmpi'
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repo-path: 'SCOREC/omega_h'
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repo-ref: ''
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cache: true
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options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
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-DCMAKE_C_COMPILER=`which mpicc`
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-DBUILD_SHARED_LIBS=OFF
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-DOmega_h_USE_MPI=ON
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-DOmega_h_USE_Kokkos=ON
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-DBUILD_TESTING=OFF
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-DMPIEXEC_EXECUTABLE=`which mpirun`
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos-openmpi/install/lib/cmake/Kokkos'
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- name: build meshFields
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'meshFields-openmpi'
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repo-path: 'SCOREC/meshFields'
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repo-ref: ''
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cache: true
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options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
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-DCMAKE_C_COMPILER=`which mpicc`
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-DMPIEXEC_EXECUTABLE=`which mpirun`
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos-openmpi/install/lib/cmake/Kokkos
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-DOmega_h_DIR=${{ runner.temp }}/build-omega_h-openmpi/install/lib/cmake/Omega_h'
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- name: build perfstubs
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'perfstubs-openmpi'
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repo-path: 'UO-OACISS/perfstubs'
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repo-ref: ''
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cache: true
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options: '-DCMAKE_CXX_COMPILER=mpicxx'
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- name: build kokkos-fortran-interop
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'kokkos-fortran-interop-openmpi'
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repo-path: 'kokkos/kokkos-fortran-interop'
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repo-ref: ''
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cache: true
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options: '-DCMAKE_BUILD_TYPE=Release
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-DCMAKE_CXX_COMPILER=`which mpicxx`
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-DCMAKE_C_COMPILER=`which mpicc`
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-DCMAKE_Fortran_COMPILER=`which mpifort`
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-DBUILD_TESTING=OFF
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-DFLCL_BUILD_TESTS=OFF
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-DFLCL_BUILD_EXAMPLE=OFF
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos-openmpi/install/lib/cmake/Kokkos'
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- name: build ADIOS2
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'ADIOS2-openmpi'
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repo-path: 'ornladios/ADIOS2'
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repo-ref: ''
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cache: true
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options: '-DADIOS2_USE_CUDA=OFF'
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- name: build redev
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'redev-openmpi'
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repo-path: 'SCOREC/redev'
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repo-ref: ''
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cache: true
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options: '-DCMAKE_CXX_COMPILER=`which mpicxx`
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-DMPIEXEC_EXECUTABLE=`which mpirun`
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-DCMAKE_BUILD_TYPE=Release
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-DBUILD_SHARED_LIBS=OFF
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-DADIOS2_DIR=${{ runner.temp }}/build-ADIOS2-openmpi/install/lib/cmake/adios2
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-Dperfstubs_DIR=${{ runner.temp }}/build-perfstubs-openmpi/install/lib/cmake'
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- name: checkout pcms_testcases
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uses: actions/checkout@v3
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with:
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repository: jacobmerson/pcms_testcases
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path: pcms_testcases
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- name: Install fftw3
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run: sudo apt-get install -yq libfftw3-dev pkg-config
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- name: Install Bear
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run: sudo apt-get install -yq bear
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- name: configure pcms
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run : |
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mkdir ${{ runner.temp }}/build-pcms
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cmake -S . -B ${{ runner.temp }}/build-pcms -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
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-DCMAKE_C_COMPILER=mpicc \
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-DCMAKE_CXX_COMPILER=mpicxx \
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-DCMAKE_Fortran_COMPILER=mpifort \
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-DPCMS_TIMEOUT=10 \
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-DCatch2_DIR=${{ runner.temp }}/build-Catch2-openmpi/install/lib/cmake/Catch2 \
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-DOmega_h_DIR=${{ runner.temp }}/build-omega_h-openmpi/install/lib/cmake/Omega_h \
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-Dmeshfields_DIR=${{ runner.temp }}/build-meshFields-openmpi/install/lib/cmake/meshfields \
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-Dredev_DIR=${{ runner.temp }}/build-redev-openmpi/install/lib/cmake/redev \
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-Dflcl_DIR=${{ runner.temp }}/build-kokkos-fortran-interop-openmpi/install/lib/cmake/flcl \
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-DMPIEXEC_EXECUTABLE=mpirun \
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-DADIOS2_DIR=${{ runner.temp }}/build-ADIOS2-openmpi/install/lib/cmake/adios2 \
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-Dperfstubs_DIR=${{ runner.temp }}/build-perfstubs-openmpi/install/lib/cmake \
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos-openmpi/install/lib/cmake/Kokkos \
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-DKokkosKernels_DIR=${{ runner.temp }}/build-kokkos-kernels-openmpi/install/lib/cmake/KokkosKernels/ \
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-DPCMS_TEST_DATA_DIR=$PWD/pcms_testcases
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- name: Configure pcms with Bear
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run: |
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cd ${{ runner.temp }}/build-pcms
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bear -- make
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- name: Install clang-tidy
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run: |
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sudo apt-get update
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sudo apt-get install -yq clang-tidy-18
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- name: Run clang-tidy
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run: |
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EXIT_CODE=0
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while read file; do
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if ! clang-tidy -p ${{ runner.temp }}/build-pcms "$file" --quiet; then
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echo "$file has clang-tidy issues"
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EXIT_CODE=1
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fi
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done < <(find src -name "*.cpp" -o -name "*.hpp" -o -name "*.c" -o -name "*.h" -o -name "*.cc" -o -name "*.cxx" | grep -v 'src/pcms/capi/' | grep -v 'src/pcms/fortranapi/')
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if [ $EXIT_CODE -eq 1 ]; then
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echo "Some C/C++ files have clang-tidy issues. Please fix them with clang-tidy-18."
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exit 1
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fi
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echo "All C/C++ files pass clang-tidy checks"

‎.github/workflows/cmake-test.yml‎

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@@ -21,7 +21,6 @@ jobs:
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strategy:
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matrix:
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build_type: [Release]
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clang_tidy: [ON, OFF]
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memory_test: [ON, OFF]
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compiler: [g++]
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language: ['cpp']
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- name: Update packages
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run: sudo apt-get update
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- name: Install mpi
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run: sudo apt-get install -yq mpich
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- name: Install openmpi
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run: sudo apt-get install -yq libopenmpi-dev openmpi-bin
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- name: Install cmake
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run: sudo apt-get install -yq cmake
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run: sudo apt-get install -yq libfftw3-dev pkg-config
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- name: build pcms
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if: matrix.clang_tidy == 'OFF'
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uses: ./.github/actions/install-repo
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with:
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repo-name: 'pcms'
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-DCMAKE_C_COMPILER=`which mpicc`
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-DCMAKE_CXX_COMPILER=`which mpicxx`
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-DCMAKE_Fortran_COMPILER=`which mpifort`
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-DPCMS_TIMEOUT=5
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-DMPIEXEC_PREFLAGS="--oversubscribe"
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-DPCMS_TIMEOUT=10
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-DCatch2_DIR=${{ runner.temp }}/build-Catch2/install/lib/cmake/Catch2
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-DOmega_h_DIR=${{ runner.temp }}/build-omega_h/install/lib/cmake/Omega_h
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-Dmeshfields_DIR=${{ runner.temp }}/build-meshFields/install/lib/cmake/meshfields
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-DPCMS_TEST_DATA_DIR=$PWD/pcms_testcases'
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# - name: Install Valgrind
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# if: matrix.clang_tidy == 'OFF'
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# run: sudo apt-get install -yq valgrind
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# - name: Run CTest
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# if: matrix.clang_tidy == 'OFF'
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# run: ctest --test-dir ${{ runner.temp }}/build-pcms
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- name: Run CTest
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run: ctest --test-dir ${{ runner.temp }}/build-pcms
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# - name: Print Test
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# if: matrix.clang_tidy == 'OFF'
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# run: cat ${{ runner.temp }}/build-pcms/Testing/Temporary/LastTest.log
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- name: Install Bear
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if: matrix.clang_tidy == 'ON'
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run: sudo apt-get install -yq bear
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- name: configure pcms
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if: matrix.clang_tidy == 'ON'
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run : |
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mkdir ${{ runner.temp }}/build-pcms
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cmake -S . -B ${{ runner.temp }}/build-pcms -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
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-DCMAKE_C_COMPILER=mpicc \
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-DCMAKE_CXX_COMPILER=mpicxx \
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-DCMAKE_Fortran_COMPILER=mpifort \
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-DPCMS_TIMEOUT=5 \
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-DCatch2_DIR=${{ runner.temp }}/build-Catch2/install/lib/cmake/Catch2 \
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-DOmega_h_DIR=${{ runner.temp }}/build-omega_h/install/lib/cmake/Omega_h \
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-Dmeshfields_DIR=${{ runner.temp }}/build-meshFields/install/lib/cmake/meshfields \
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-Dredev_DIR=${{ runner.temp }}/build-redev/install/lib/cmake/redev \
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-Dflcl_DIR=${{ runner.temp }}/build-kokkos-fortran-interop/install/lib/cmake/flcl \
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-DMPIEXEC_EXECUTABLE=mpirun \
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-DADIOS2_DIR=${{ runner.temp }}/build-ADIOS2/install/lib/cmake/adios2 \
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-Dperfstubs_DIR=${{ runner.temp }}/build-perfstubs/install/lib/cmake \
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-DKokkos_DIR=${{ runner.temp }}/build-kokkos/install/lib/cmake/Kokkos \
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-DKokkosKernels_DIR=${{ runner.temp }}/build-kokkos-kernels/install/lib/cmake/KokkosKernels/ \
227-
-DPCMS_TEST_DATA_DIR=$PWD/pcms_testcases
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- name: Configure pcms with Bear
230-
if: matrix.clang_tidy == 'ON'
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run: |
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cd ${{ runner.temp }}/build-pcms
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bear -- make -j 4
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- name: Install clang-tidy
236-
if: matrix.clang_tidy == 'ON'
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run: |
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sudo apt-get update
239-
sudo apt-get install -yq clang-tidy-18
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- name: Run clang-tidy
242-
if: matrix.clang_tidy == 'ON'
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run: |
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EXIT_CODE=0
245-
while read file; do
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if ! clang-tidy -p ${{ runner.temp }}/build-pcms "$file" --quiet; then
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echo "$file has clang-tidy issues"
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EXIT_CODE=1
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fi
250-
done < <(find src -name "*.cpp" -o -name "*.hpp" -o -name "*.c" -o -name "*.h" -o -name "*.cc" -o -name "*.cxx" | grep -v 'src/pcms/capi/' | grep -v 'src/pcms/fortranapi/')
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if [ $EXIT_CODE -eq 1 ]; then
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echo "Some C/C++ files have clang-tidy issues. Please fix them with clang-tidy-18."
253-
exit 1
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fi
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echo "All C/C++ files pass clang-tidy checks"

‎ctest/runMultipleMpiJobs.sh‎

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Original file line numberDiff line numberDiff line change
@@ -5,10 +5,14 @@ if [[ ($# == 0) || ("${1}" == "-h" || ${1} == "--help") ]]; then
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exit 1
66
fi
77
runCmd=${1}
8-
numProcsFlag=${2}
9-
valgrindCmd=${3}
10-
valgrindOptions=${4}
8+
preFlags=${2}
9+
numProcsFlag=${3}
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valgrindCmd=${4}
11+
valgrindOptions=${5}
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valgrindLogging="--log-file=%p"
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if [[ ${preFlags} == "none" ]]; then
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preFlags=""
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fi
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#clear the valgrind args if they are 'none'
1317
if [[ ${valgrindCmd} == "none" ]]; then
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valgrindCmd=""
@@ -18,7 +22,7 @@ fi
1822
if [[ (${valgrindOptions} == "none" && ${valgrindCmd} != "none") ]]; then
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valgrindOptions=""
2024
fi
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shift 4
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shift 5
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2428
declare -a PIDS
@@ -33,7 +37,7 @@ run() {
3337
if [[ -z ${valgrindLogging} ]]; then
3438
vgLog=""
3539
fi
36-
${runCmd} ${numProcsFlag} ${procs} ${valgrindCmd} ${vgLog} ${valgrindOptions} ${exe} ${argsArray[@]} &> ${name}.log &
40+
${runCmd} ${preFlags} ${numProcsFlag} ${procs} ${valgrindCmd} ${vgLog} ${valgrindOptions} ${exe} ${argsArray[@]} &> ${name}.log &
3741
PIDS+=($!)
3842
LOGS+=(${name}.log)
3943
}

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