HDF5 collective output #194
Workflow file for this run
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| # Github Actions workflow | |
| # | |
| # runs compilation tests on Linux Ubuntu and Mac platforms | |
| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| changesCheck: | |
| name: Check file changes | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check for changes | |
| id: diff | |
| run: | | |
| if [ $GITHUB_BASE_REF ]; then | |
| # Pull Request | |
| echo "Pull request:" | |
| git fetch origin $GITHUB_BASE_REF --depth=1 | |
| export DIFF=$( git diff --name-only origin/$GITHUB_BASE_REF $GITHUB_SHA ) | |
| echo " diff between origin/$GITHUB_BASE_REF and $GITHUB_SHA" | |
| else | |
| # Push | |
| echo "Push request:" | |
| git fetch origin ${{ github.event.before }} --depth=1 | |
| export DIFF=$( git diff --name-only ${{ github.event.before }} $GITHUB_SHA ) | |
| echo " diff between ${{ github.event.before }} and $GITHUB_SHA" | |
| fi | |
| echo "***"; echo "$DIFF"; echo "***" | |
| # Escape newlines (replace \n with %0A) | |
| # deprecated: | |
| #echo "::set-output name=diff::$( echo "$DIFF" | sed ':a;N;$!ba;s/\n/%0A/g' )" | |
| # new: | |
| # replace new line with %0A - will result finding only one file with a very long name... | |
| #echo "diff=$( echo "$DIFF" | sed ':a;N;$!ba;s/\n/%0A/g' )" >> $GITHUB_OUTPUT | |
| # doesn't work... | |
| #echo "diff=\"$DIFF\"" >> "$GITHUB_OUTPUT" | |
| # new multi-line format: | |
| # (https://docs.github.com/en/actions/using-workflows/workflow-commands-for-github-actions#multiline-strings) | |
| echo "diff<<EOF" >> $GITHUB_OUTPUT | |
| echo "$DIFF" >> $GITHUB_OUTPUT | |
| echo "EOF" >> $GITHUB_OUTPUT | |
| - name: Output changes | |
| run: echo "${{ steps.diff.outputs.diff }}" | |
| - name: Check files | |
| run: | | |
| RUN_CHECKS=0 | |
| DIFF="${{ steps.diff.outputs.diff }}" | |
| # Loop by lines | |
| while read path; do | |
| # Set $directory to substring before / | |
| directory="$( echo $path | cut -d'/' -f1 -s )" | |
| echo "file: $path - directory: $directory" | |
| if [ -z "$directory" ]; then | |
| # root directory | |
| RUN_CHECKS=1 | |
| elif [ "$directory" == src ]; then | |
| # src/ directory | |
| RUN_CHECKS=1 | |
| elif [ "$directory" == setup ]; then | |
| # setup/ directory | |
| RUN_CHECKS=1 | |
| elif [ "$directory" == EXAMPLES ]; then | |
| # EXAMPLES/ directory | |
| RUN_CHECKS=1 | |
| elif [ "$directory" == tests ]; then | |
| # tests/ directory | |
| RUN_CHECKS=1 | |
| elif [ "$directory" == .github ]; then | |
| # .github/ directory | |
| RUN_CHECKS=1 | |
| fi | |
| done <<< "$DIFF" | |
| echo | |
| echo "run checks: ${RUN_CHECKS}" | |
| if [[ ${RUN_CHECKS} -eq 0 ]]; then echo "nothing to check, exiting..."; exit 1; fi | |
| macosCheck: | |
| name: Test on Mac | |
| runs-on: macos-latest | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install dependencies | |
| run: | | |
| brew cleanup | |
| brew reinstall gcc # need gfortran (symlink to gfortran-10) | |
| brew install hwloc openmpi | |
| echo "" | |
| echo "compiler versions:" | |
| echo "gcc --version" | |
| gcc --version | |
| echo "gfortran --version" | |
| gfortran --version | |
| echo "mpif90 --version" | |
| mpif90 --version | |
| echo "" | |
| ## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux | |
| brew install gnu-sed | |
| echo "PATH=/opt/homebrew/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV | |
| ## OpenMP | |
| echo "OMP_NUM_THREADS=2" >> $GITHUB_ENV | |
| ## MPI | |
| echo | |
| echo "MPI environment:" | |
| echo "mpif90 on path: $(which mpif90)" | |
| echo | |
| # add OpenMPI path to have ./configure detect mpi.h | |
| echo "MPI_INC=/opt/homebrew/include" >> $GITHUB_ENV | |
| ## avoids MPI issue with number of slots | |
| echo "OMPI_MCA_rmaps_base_oversubscribe=1" >> $GITHUB_ENV | |
| echo "OMPI_MCA_rmaps_base_inherit=1" >> $GITHUB_ENV | |
| ## avoids MPI issue when running in MacOS | |
| echo "OMPI_MCA_btl=self,tcp" >> $GITHUB_ENV | |
| # newer OpenMPI version (5.x) | |
| echo "PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe" >> $GITHUB_ENV | |
| # exports for xterm output (for make tests) | |
| echo "TERM=xterm" >> $GITHUB_ENV | |
| # warning: (arm64) could not find object file symbol for symbol ___mulsc3 | |
| echo "LDFLAGS=-lgcc" >> $GITHUB_ENV | |
| echo "" | |
| echo "exports:" | |
| export | |
| echo "" | |
| - name: configure | |
| run: ./configure | |
| # skipping - compilation check done as well in make tests | |
| #- name: make | |
| # run: make -j2 all | |
| - name: make tests | |
| run: make tests | |
| linuxCheck: | |
| name: Test on ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| needs: changesCheck | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest,ubuntu-22.04] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: configure | |
| run: ./configure | |
| - name: make | |
| run: make -j2 all | |
| linuxCheck-Intel: | |
| name: Test Intel on ubuntu-22.04 | |
| runs-on: ubuntu-22.04 | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Cache Intel oneapi packages | |
| id: cache-intel-oneapi | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/intel/oneapi | |
| key: install-${{ runner.os }}-all | |
| - name: Install packages | |
| if: steps.cache-intel-oneapi.outputs.cache-hit != 'true' | |
| run: | | |
| wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| echo "" | |
| sudo echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list | |
| sudo apt-get update | |
| echo "" | |
| # info | |
| #sudo -E apt-cache pkgnames intel | grep intel-oneapi | |
| #echo "" | |
| echo "installing packages intel oneapi:" | |
| sudo apt-get install -y intel-oneapi-compiler-fortran-2023.2.2 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.2 intel-oneapi-mpi intel-oneapi-mpi-devel | |
| echo "" | |
| - name: compiler infos | |
| run: | | |
| echo "" | |
| source /opt/intel/oneapi/setvars.sh | |
| echo "" | |
| echo "compiler versions:" | |
| echo "icx --version" | |
| which icx | |
| icx --version | |
| echo "" | |
| echo "icc --version" | |
| which icc | |
| icc --version | |
| echo "" | |
| echo "ifx --version" | |
| which ifx | |
| ifx --version | |
| echo "" | |
| echo "ifort --version" | |
| which ifort | |
| ifort --version | |
| echo "" | |
| echo "mpiifort --version" | |
| which mpiifort | |
| mpiifort --version | |
| echo "" | |
| echo "mpif90 --version" | |
| which mpif90 | |
| mpif90 --version | |
| echo "" | |
| # infos | |
| which ifort | |
| which icc | |
| which mpiifort | |
| echo "mpirun:" | |
| which mpirun | |
| echo "" | |
| # intel setup for running tests | |
| echo "" | |
| echo "replacing mpif90 with mpiifort link:" | |
| sudo ln -sf $(which mpiifort) $(which mpif90) | |
| mpif90 --version | |
| echo "" | |
| # debug | |
| #export I_MPI_DEBUG=5,pid,host | |
| #export I_MPI_LIBRARY_KIND=debug | |
| # remove -ftrapuv which leads to issues for running tests | |
| sed -i "s/-ftrapuv//g" flags.guess | |
| # environment setting | |
| export TERM=xterm | |
| # export info | |
| echo "exports:" | |
| export | |
| echo "" | |
| echo "" | |
| printenv >> $GITHUB_ENV | |
| echo "CXX=icpc" >> $GITHUB_ENV | |
| echo "CC=icc" >> $GITHUB_ENV | |
| echo "FC=ifort" >> $GITHUB_ENV | |
| echo "" | |
| - name: configure debug | |
| run: | | |
| ./configure --enable-debug FC=ifort CC=icc MPIFC=mpiifort | |
| - name: make debug | |
| run: | | |
| make -j2 all | |
| make -j2 all --always-make | |
| make clean | |
| - name: configure | |
| run: | | |
| ./configure FC=ifort CC=icc MPIFC=mpiifort | |
| - name: make | |
| run: | | |
| make -j2 all | |
| make clean | |
| # note: fails with -ftrapuv flag due to MPI issue on virtual nodes | |
| - name: make tests | |
| run: | | |
| make tests | |
| linuxTest_0: | |
| name: Test run example 0 - make tests | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: configure | |
| run: ./configure | |
| - name: make tests | |
| run: make tests | |
| linuxTest_1: | |
| name: Test run example 1 - regional_Greece_small debug | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-debug | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/regional_Greece_small | |
| DEBUG: true | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_2: | |
| name: Test run example 2 - regional_Greece_small | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-vectorization | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/regional_Greece_small | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_3: | |
| name: Test run example 3 - regional_sgloberani | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: # no extra flags | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/regional_sgloberani | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_4: | |
| name: Test run example 4 - point_force | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: "FLAGS_CHECK=-O3 -mcmodel=medium -std=gnu -Wall -Wno-do-subscript -Wno-conversion -Wno-maybe-uninitialized" | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/point_force | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_5: | |
| name: Test run example 5 - moon_global | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-vectorization | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/moon_global | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_6: | |
| name: Test run example 6 - mars_regional | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-vectorization | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/mars_regional | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_7: | |
| name: Test run example 7 - global_small | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-vectorization | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/global_small | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_8: | |
| name: Test run example 8 - global_small w/ FULL_GRAVITY netCDF | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| env: | |
| NETCDF: true | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-debug | |
| NETCDF: true | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/global_small | |
| FULL_GRAVITY: true | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_9: | |
| name: Test run example 9 - global_small w/ FULL_GRAVITY PETSc | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| env: | |
| PETSC: true | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: # no extra flags | |
| PETSC: true | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/global_small | |
| FULL_GRAVITY: true | |
| PETSC: true | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_10: | |
| name: Test run example 10 - regional_Greece_small_LDDRK kernel ADIOS2 | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install packages | |
| env: | |
| ADIOS2: true | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: # no extra flags | |
| ADIOS2: true | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/regional_Greece_small_LDDRK | |
| ADIOS2: true | |
| RUN_KERNEL: true | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash |