updates readme (adds zenodo badge) #18
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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@v2 | |
| - 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 $GITHUB_SHA" | |
| fi | |
| echo "$DIFF" | |
| # Escape newlines (replace \n with %0A) | |
| echo "::set-output name=diff::$( echo "$DIFF" | sed ':a;N;$!ba;s/\n/%0A/g' )" | |
| - name: Output changes | |
| run: echo "${{ 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 [[ ${RUN_CHECKS} -eq 0 ]]; then echo "nothing to check, exiting..."; exit 1; fi | |
| macosCheck: | |
| name: Test on Mac | |
| runs-on: macos-latest | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| brew cleanup | |
| brew reinstall gcc # need gfortran (symlink to gfortran-10) | |
| brew install hwloc openmpi | |
| echo "" | |
| echo "compiler versions:" | |
| echo "gcc --version" | |
| gcc --version | |
| echo "gfortran --version" | |
| gfortran --version | |
| echo "mpif90 --version" | |
| mpif90 --version | |
| echo "" | |
| ## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux | |
| brew install gnu-sed | |
| echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$PATH" >> $GITHUB_ENV | |
| ## OpenMP | |
| echo "OMP_NUM_THREADS=2" >> $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 | |
| # exports for xterm output (for make tests) | |
| echo "TERM=xterm" >> $GITHUB_ENV | |
| echo "" | |
| echo "exports:" | |
| export | |
| echo "" | |
| - name: configure | |
| run: | | |
| ./configure | |
| echo "modifying external_libs/scotch/src/Makefile.inc" | |
| cp -v external_libs/scotch/src/Make.inc/Makefile.inc.i686_mac_darwin8 external_libs/scotch/src/Makefile.inc | |
| # 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: ${{ matrix.os }} | |
| needs: changesCheck | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest,ubuntu-18.04] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: configure | |
| run: ./configure | |
| - name: make | |
| run: make -j2 all | |
| linuxCheck-Intel: | |
| name: Test Intel on ubuntu-20.04 | |
| runs-on: ubuntu-20.04 | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Cache Intel oneapi packages | |
| id: cache-intel-oneapi | |
| uses: actions/cache@v2 | |
| with: | |
| path: /opt/intel/oneapi | |
| key: install-${{ 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 "" | |
| echo "packages intel oneapi:" | |
| sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic intel-oneapi-mpi intel-oneapi-mpi-devel | |
| - name: compiler infos | |
| run: | | |
| echo "" | |
| source /opt/intel/oneapi/setvars.sh | |
| echo "" | |
| echo "compiler versions:" | |
| echo "icc --version" | |
| icc --version | |
| echo "ifort --version" | |
| ifort --version | |
| echo "mpiifort --version" | |
| mpiifort --version | |
| echo "mpif90 --version" | |
| mpif90 --version | |
| echo "" | |
| export TERM=xterm | |
| echo "exports:" | |
| export | |
| echo "" | |
| which ifort | |
| which icc | |
| which mpiifort | |
| echo "" | |
| printenv >> $GITHUB_ENV | |
| echo "CXX=icpc" >> $GITHUB_ENV | |
| echo "CC=icc" >> $GITHUB_ENV | |
| echo "FC=ifort" >> $GITHUB_ENV | |
| echo "" | |
| - name: configure serial debug | |
| run: ./configure --enable-debug --without-mpi FC=ifort CC=icc | |
| - name: make serial debug | |
| run: | | |
| make -j2 all | |
| make -j2 all --always-make | |
| make clean | |
| - name: configure serial | |
| run: ./configure --without-mpi FC=ifort CC=icc | |
| - name: make serial | |
| run: | | |
| make -j2 all | |
| make clean | |
| - name: configure parallel debug | |
| run: ./configure --enable-debug --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include" | |
| - name: make parallel debug | |
| run: | | |
| make -j2 all | |
| make -j2 all --always-make | |
| make clean | |
| - name: configure parallel | |
| run: ./configure --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${I_MPI_ROOT}/include" | |
| - name: make parallel | |
| run: | | |
| make -j2 all | |
| make clean | |
| # check: fails due to intel MPI issue with mpif90 using gfortran as default 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@v2 | |
| - 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 - meshfem3D simple model | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi # --enable-vectorization | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/simple_model/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_2: | |
| name: Test run example 2 - fault tpv5 | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/fault_examples/tpv5/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_3: | |
| name: Test run example 3 - layered halfspace | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| TESTNGLL: 6 | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/layered_halfspace/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_4: | |
| name: Test run example 4 - small adjoint | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/small_adjoint_multiple_sources/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_5: | |
| name: Test run example 5 - socal1D | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/ | |
| TESTID: 0 | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_6: | |
| name: Test run example 6 - socal1D 1d_socal | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/ | |
| TESTID: 1 | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_7: | |
| name: Test run example 7 - socal1D 1d_prem | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/ | |
| TESTID: 2 | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_8: | |
| name: Test run example 8 - socal1D 1d_cascadia | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/socal1D/ | |
| TESTID: 3 | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_9: | |
| name: Test run example 9 - coupling FK | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/small_example_coupling_FK_specfem/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_10: | |
| name: Test run example 10 - homogeneous halfspace | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/homogeneous_halfspace_HEX8_elastic_no_absorbing/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_11: | |
| name: Test run example 11 - poroelastic | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/homogeneous_poroelastic/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_12: | |
| name: Test run example 12 - PML elastic | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_elastic_absorbing_CPML_5sides/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_13: | |
| name: Test run example 13 - PML acoustic | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/CPML_examples/homogeneous_halfspace_HEX8_acoustic_absorbing_CPML_5sides/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_14: | |
| name: Test run example 14 - waterlayered halfspace | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/waterlayered_halfspace/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_15: | |
| name: Test run example 15 - tomographic model | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/tomographic_model/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_16: | |
| name: Test run example 16 - cavity | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/cavity/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_17: | |
| name: Test run example 17 - sep bathymetry | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --with-mpi | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/meshfem3D_examples/sep_bathymetry/ | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |