updates examples and utils folder; adds support for nummaterial_velocity_file for external meshes; updates config files #107
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@v3 | |
| - 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 [[ ${RUN_CHECKS} -eq 0 ]]; then echo "nothing to check, exiting..."; exit 1; fi | |
| macosCheck: | |
| name: Test on Mac | |
| runs-on: macos-latest | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install dependencies | |
| run: | | |
| brew cleanup | |
| brew reinstall gcc # need gfortran (symlink to gfortran-10) | |
| brew install hwloc openmpi | |
| echo "" | |
| echo "compiler versions:" | |
| echo "gcc --version" | |
| gcc --version | |
| echo "gfortran --version" | |
| gfortran --version | |
| echo "mpif90 --version" | |
| mpif90 --version | |
| echo "" | |
| ## avoids sed -i '' issue on MacOS, using gnu sed to have the same sed command lines as in linux | |
| brew install gnu-sed | |
| echo "PATH=/usr/local/opt/gnu-sed/libexec/gnubin:$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 | |
| # 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: ${{ matrix.os }} | |
| needs: changesCheck | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest,ubuntu-20.04] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: configure | |
| run: ./configure | |
| - name: make | |
| run: make -j2 all | |
| linuxCheck-Intel: | |
| name: Test Intel on ubuntu-20.04 | |
| runs-on: ubuntu-20.04 | |
| needs: changesCheck | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Cache Intel oneapi packages | |
| id: cache-intel-oneapi | |
| uses: actions/cache@v3 | |
| with: | |
| path: /opt/intel/oneapi | |
| key: install-${{ 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" >> $GITHUB_ENV | |
| echo "" | |
| - name: configure debug | |
| run: | | |
| ./configure --enable-debug FC=ifort CC=icc | |
| - name: make debug | |
| run: | | |
| make -j2 all | |
| make -j2 all --always-make | |
| make clean | |
| - name: configure | |
| run: | | |
| ./configure FC=ifort CC=icc | |
| - name: make | |
| run: | | |
| make -j2 all | |
| make clean | |
| - name: configure parallel debug | |
| run: | | |
| ./configure --enable-debug --with-mpi FC=ifort CC=icc MPIFC=mpiifort MPI_INC="${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 | |
| # 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@v3 | |
| - 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 - benchmark claerbout kernel acoustic | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_2: | |
| name: Test run example 2 - benchmark claerbout kernel elastic P-SV | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC | |
| TESTCASE: P-SV | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_3: | |
| name: Test run example 3 - benchmark claerbout kernel elastic SH | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC | |
| TESTCASE: SH | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_4: | |
| name: Test run example 4 - benchmark claerbout kernel acoustic-elastic | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC_ELASTIC | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_5: | |
| name: Test run example 5 - moving sources | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/moving_sources_acoustic | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_6: | |
| name: Test run example 6 - anisotropy | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/anisotropic_isotropic_model | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_7: | |
| name: Test run example 7 - Industrial_Format_SEP | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/Industrial_Format_SEP | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_8: | |
| name: Test run example 8 - axisymmetric_case_AXISYM_option | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/axisymmetric_case_AXISYM_option | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_9: | |
| name: Test run example 9 - simple_topography_and_also_a_simple_fluid_layer debug | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - 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/simple_topography_and_also_a_simple_fluid_layer | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_10: | |
| name: Test run example 10 - simple_topography_and_also_a_simple_fluid_layer debug double_precision | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: --enable-double-precision --enable-debug | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/simple_topography_and_also_a_simple_fluid_layer | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |
| linuxTest_11: | |
| name: Test run example 11 - tomographic_ocean_model | |
| runs-on: ubuntu-latest | |
| needs: [linuxCheck] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install packages | |
| run: ./.github/scripts/run_install.sh | |
| shell: bash | |
| - name: Run build | |
| env: | |
| TESTFLAGS: # default w/out MPI | |
| run: ./.github/scripts/run_build.sh | |
| shell: bash | |
| - name: Run test | |
| env: | |
| TESTDIR: EXAMPLES/tomographic_ocean_model | |
| run: ./.github/scripts/run_tests.sh | |
| shell: bash | |