feat(pak_cc): add support for parallel package convergence (#1309) #582
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| name: MODFLOW 6 continuous integration | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - develop | |
| - ci-diagnose* | |
| paths-ignore: | |
| - '**.md' | |
| - 'doc/**' | |
| pull_request: | |
| branches: | |
| - master | |
| - develop | |
| paths-ignore: | |
| - '**.md' | |
| - 'doc/**' | |
| jobs: | |
| lint: | |
| name: Lint (fprettify) | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Check Fortran source formatting | |
| run: python .github/common/fortran_format_check.py | |
| build: | |
| name: Build (gfortran 12) | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| - name: Setup gfortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Meson setup | |
| run: meson setup builddir -Ddebug=false -Dwerror=true | |
| - name: Meson compile | |
| run: meson compile -C builddir | |
| - name: Meson test | |
| run: meson test --verbose --no-rebuild -C builddir | |
| smoke_test: | |
| name: Smoke test (gfortran 12) | |
| runs-on: ubuntu-22.04 | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Setup GNU Fortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| working-directory: modflow6/autotest | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not slow and not regression and not developmode" | |
| else | |
| pytest -v -n auto --durations 0 -S | |
| fi | |
| test_gfortran_latest: | |
| name: Test (gfortran 12) | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Checkout modflow6-examples | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-examples | |
| path: modflow6-examples | |
| - name: Setup GNU Fortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: | | |
| pytest -v --durations 0 get_exes.py | |
| - name: Test modflow6 | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" | |
| fi | |
| # steps below run only on Linux to test distribution procedures, e.g. | |
| # compiling binaries, building documentation | |
| - name: Checkout usgslatex | |
| if: runner.os == 'Linux' | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: MODFLOW-USGS/usgslatex | |
| path: usgslatex | |
| - name: Install TeX Live | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt install texlive-science \ | |
| texlive-latex-extra \ | |
| texlive-font-utils \ | |
| texlive-fonts-recommended \ | |
| texlive-fonts-extra | |
| - name: Install USGS LaTeX style files and Univers font | |
| if: runner.os == 'Linux' | |
| working-directory: usgslatex/usgsLaTeX | |
| run: sudo ./install.sh --all-users | |
| - name: Test distribution scripts | |
| working-directory: modflow6/distribution | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 | |
| test_gfortran_previous: | |
| name: Test gfortran (${{ matrix.GCC_V }}, ${{ matrix.os }}) | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-20.04 ] | |
| GCC_V: [ 7, 8, 9, 10, 11 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Setup GNU Fortran ${{ matrix.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ matrix.GCC_V }} | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| cache-downloads: true | |
| cache-environment: true | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test modflow6 | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" | |
| fi | |
| test_ifort: | |
| name: Test (ifort) | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-latest, macos-latest, windows-latest ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Checkout modflow6-testmodels | |
| uses: actions/checkout@v3 | |
| with: | |
| repository: MODFLOW-USGS/modflow6-testmodels | |
| path: modflow6-testmodels | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Setup Intel Fortran | |
| uses: modflowpy/install-intelfortran-action@v1 | |
| - name: Update version files | |
| working-directory: modflow6/distribution | |
| run: python update_version.py | |
| - name: Build modflow6 | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Build modflow6 (Windows) | |
| if: runner.os == 'Windows' | |
| working-directory: modflow6 | |
| shell: pwsh | |
| run: | | |
| meson setup builddir -Ddebug=false --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Get executables (Windows) | |
| if: runner.os == 'Windows' | |
| working-directory: modflow6/autotest | |
| shell: pwsh | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if [ "${{ github.ref_name }}" == "master" ]; then | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" | |
| else | |
| pytest -v -n auto --durations 0 -m "not large" | |
| fi | |
| - name: Test programs (Windows) | |
| if: runner.os == 'Windows' | |
| working-directory: modflow6/autotest | |
| shell: pwsh | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| if ( "${{ github.ref_name }}" -eq "master" ) { | |
| pytest -v -n auto --durations 0 -m "not large and not developmode" | |
| } else { | |
| pytest -v -n auto --durations 0 -m "not large" | |
| } | |
| - name: Test scripts | |
| if: runner.os != 'Windows' | |
| working-directory: modflow6/distribution | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 | |
| - name: Test scripts (Windows) | |
| if: runner.os == 'Windows' | |
| working-directory: modflow6/distribution | |
| shell: pwsh | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 | |
| parallel_test: | |
| name: Parallel testing | |
| needs: | |
| - lint | |
| - build | |
| - smoke_test | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ ubuntu-22.04, macos-12 ] #, windows-2022 ] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| env: | |
| FC: gfortran | |
| GCC_V: 12 | |
| steps: | |
| - name: Checkout modflow6 | |
| uses: actions/checkout@v3 | |
| with: | |
| path: modflow6 | |
| - name: Setup MSYS2 | |
| if: runner.os == 'Windows' | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| update: true | |
| install: | | |
| git | |
| make | |
| mingw-w64-x86_64-gcc | |
| mingw-w64-x86_64-python | |
| mingw-w64-x86_64-python-pip | |
| mingw-w64-x86_64-python-pytest | |
| - name: Setup MPI | |
| if: runner.os == 'Windows' | |
| uses: mpi4py/setup-mpi@v1 | |
| with: | |
| mpi: msmpi | |
| - name: Setup GNU Fortran ${{ env.GCC_V }} | |
| uses: awvwgk/setup-fortran@main | |
| with: | |
| compiler: gcc | |
| version: ${{ env.GCC_V }} | |
| - name: Cache PETSc | |
| id: cache-petsc | |
| uses: actions/cache@v3 | |
| with: | |
| path: petsc | |
| key: ${{ runner.os }}-petsc | |
| - name: Clone PETSc | |
| if: runner.os != 'Windows' && steps.cache-petsc.outputs.cache-hit != 'true' | |
| run: git clone -b release https://gitlab.com/petsc/petsc.git petsc | |
| - name: Download PETSc | |
| if: runner.os == 'Windows' | |
| run: | | |
| curl https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.18.4.tar.gz -O -J | |
| mkdir petsc | |
| tar -xzf petsc-3.18.4.tar.gz -C petsc --strip-components=1 | |
| - name: Configure environment | |
| if: runner.os == 'Linux' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/linux-gnu/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/linux-gnu/bin" >> $GITHUB_PATH | |
| - name: Configure environment | |
| if: runner.os == 'macOS' | |
| run: | | |
| echo "PKG_CONFIG_PATH=$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "$GITHUB_WORKSPACE/petsc/arch-darwin-gcc-debug/bin" >> $GITHUB_PATH | |
| - name: Configure PETSc | |
| if: runner.os == 'Linux' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_ARCH=linux-gnu --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'macOS' | |
| working-directory: petsc | |
| run: | | |
| sudo ./configure PETSC_DIR="$GITHUB_WORKSPACE/petsc" PETSC_ARCH=arch-darwin-gcc-debug --download-fblaslapack --download-openmpi | |
| sudo make all | |
| - name: Configure PETSc | |
| if: runner.os == 'Windows' | |
| shell: msys2 {0} | |
| working-directory: petsc | |
| run: | | |
| pacman -Syu | |
| pacman -Sy --noconfirm autoconf automake-wrapper bison bsdcpio make git \ | |
| mingw-w64-x86_64-toolchain patch python flex \ | |
| pkg-config pkgfile tar unzip mingw-w64-x86_64-cmake \ | |
| mingw-w64-x86_64-msmpi mingw-w64-x86_64-openblas mingw-w64-x86_64-jq | |
| /usr/bin/python ./configure --with-mpiexec='/C/Program\ Files/Microsoft\ MPI/Bin/mpiexec' --with-shared-libraries=0 | |
| make all | |
| - name: Setup Micromamba | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: modflow6/environment.yml | |
| init-shell: >- | |
| bash | |
| powershell | |
| cache-environment: true | |
| cache-downloads: true | |
| - name: Build modflow6 | |
| working-directory: modflow6 | |
| run: | | |
| meson setup builddir -Ddebug=false -Dparallel=true --prefix=$(pwd) --libdir=bin | |
| meson install -C builddir | |
| meson test --verbose --no-rebuild -C builddir | |
| - name: Show Meson logs | |
| if: failure() | |
| working-directory: modflow6 | |
| run: cat builddir/meson-logs/meson-log.txt | |
| - name: Update flopy | |
| working-directory: modflow6/autotest | |
| run: python update_flopy.py | |
| - name: Get executables | |
| working-directory: modflow6/autotest | |
| env: | |
| GITHUB_TOKEN: ${{ github.token }} | |
| run: pytest -v --durations 0 get_exes.py | |
| - name: Test programs (parallel) | |
| working-directory: modflow6/autotest | |
| env: | |
| REPOS_PATH: ${{ github.workspace }} | |
| run: | | |
| branch="${{ github.ref_name }}" | |
| marker="not large" | |
| markers=$([ "$branch" == "master" ] && echo "$marker and not developmode" || echo "$marker") | |
| pytest -v -n auto --parallel --durations 0 -m "$markers" | |