CI.yml

# 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
        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-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 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

    # 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 - meshfem3D simple 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: --with-mpi  # --enable-vectorization
      run: ./.github/scripts/run_build.sh
      shell: bash

    - name: Run test
      env:
        TESTDIR: EXAMPLES/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/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@v3

    - 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/applications/meshfem3D_examples/sep_bathymetry/
      run: ./.github/scripts/run_tests.sh
      shell: bash

  linuxTest_18:
    name: Test run example 18 - socal1D hdf5 i/o
    runs-on: ubuntu-latest
    needs: [linuxCheck]

    steps:
    - uses: actions/checkout@v3

    - name: Install packages
      env:
        TEST: with-hdf5
      run: ./.github/scripts/run_install.sh
      shell: bash

    - name: Run build
      env:
        TESTFLAGS: --with-mpi --with-hdf5 HDF5_INC=/usr/include/hdf5/openmpi/ HDF5_LIBS=-L/usr/lib/x86_64-linux-gnu/hdf5/openmpi
      run: ./.github/scripts/run_build.sh
      shell: bash

    - name: Run test
      env:
        TEST: with-hdf5
        TESTDIR: EXAMPLES/applications/meshfem3D_examples/socal1D/
        TESTID: 0
      run: ./.github/scripts/run_tests.sh
      shell: bash