verify-linux.yml

# This file is part of MOM6, the Modular Ocean Model version 6.
# See the LICENSE file for licensing information.
# SPDX-License-Identifier: Apache-2.0

name: Linux verification

on: [push, pull_request]

env:
  MOM_TARGET_SLUG: ${{ github.repository }}
  MOM_TARGET_LOCAL_BRANCH: ${{ github.base_ref }}

jobs:
  # Documentation

  check-style-and-docstrings:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v4
      with:
        submodules: recursive

    - name: Check white space (non-blocking)
      run: |
        ./.testing/trailer.py -e TEOS10 -l 120 src config_src 2>&1 | tee style_errors
      continue-on-error: true

    - name: Install packages used when generating documentation
      run: |
        sudo apt-get update
        sudo apt-get install python3-sphinx python3-lxml perl
        sudo apt-get install texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
        sudo apt-get install graphviz

    - name: Build doxygen HTML
      run: |
        cd docs
        perl -e 'print "perl version $^V" . "\n"'
        mkdir _build && make nortd DOXYGEN_RELEASE=Release_1_8_13 UPDATEHTMLEQS=Y
        cat _build/doxygen_warn_nortd_log.txt

    - name: Report doxygen or style errors
      run: |
        grep "warning:" docs/_build/doxygen_warn_nortd_log.txt | grep -v "as part of a" | tee doxy_errors
        cat style_errors doxy_errors > all_errors
        cat all_errors
        test ! -s  all_errors

  # Executables

  build-symmetric:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 with symmetric indexing
        run: make -C .testing -j build/symmetric/MOM6

      - name: Prepare artifact
        run: tar -cf mom6-symmetric.tar .testing/build/symmetric/MOM6

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-symmetric-artifact
          path: mom6-symmetric.tar
          retention-days: 1

  build-asymmetric:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 with asymmetric indexing
        run: make -C .testing -j build/asymmetric/MOM6

      - name: Prepare artifact
        run: tar -cf mom6-asymmetric.tar .testing/build/asymmetric/MOM6

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-asymmetric-artifact
          path: mom6-asymmetric.tar
          retention-days: 1

  build-repro:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 with bit-reproducible optimization
        run: make -C .testing -j build/repro/MOM6

      - name: Prepare artifact
        run: tar -cf mom6-repro.tar .testing/build/repro/MOM6

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-repro-artifact
          path: mom6-repro.tar
          retention-days: 1

  build-openmp:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 supporting OpenMP
        run: make -C .testing -j build/openmp/MOM6

      - name: Prepare artifact
        run: tar -cf mom6-openmp.tar .testing/build/openmp/MOM6

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-openmp-artifact
          path: mom6-openmp.tar
          retention-days: 1

  build-target:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile target FMS
        run: |
          make -C .testing \
          DO_REGRESSION_TESTS=1 \
          build/target_codebase
          make -C .testing/build/target_codebase/.testing -j \
          build/deps/lib/libFMS.a

      - name: Compile target MOM6
        run: |
          make -C .testing -j \
          DO_REGRESSION_TESTS=1 \
          build/target/MOM6

      - name: Prepare artifact
        run: tar -cf mom6-target.tar .testing/build/target/MOM6

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-target-artifact
          path: mom6-target.tar
          retention-days: 1

  build-opt:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 with aggressive optimization
        run: make -C .testing -j build/opt/MOM6

      - name: Compile timing tests
        run: make -C .testing build.timing

      - name: Prepare artifact
        run: |
          tar -cf mom6-opt.tar \
          --exclude='.testing/build/timing/time_*.o' \
          .testing/build/opt/MOM6 \
          .testing/build/timing/time_*

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-opt-artifact
          path: mom6-opt.tar
          retention-days: 1

  build-opt-target:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile target FMS
        run: |
          make -C .testing \
          DO_REGRESSION_TESTS=1 \
          build/target_codebase
          make -C .testing/build/target_codebase/.testing -j \
          build/deps/lib/libFMS.a

      - name: Compile target MOM6
        run: |
          make -C .testing -j \
          DO_REGRESSION_TESTS=1 \
          build/opt_target/MOM6

      - name: Compile target timing tests
        run: |
          make -C .testing/build/target_codebase/.testing \
          DO_REGRESSION_TESTS=1 \
          build.timing

      - name: Prepare artifact
        run: |
          tar -cf mom6-opt-target.tar \
          --exclude='.testing/build/target_codebase/.testing/build/timing/time_*.o' \
          .testing/build/opt_target/MOM6 \
          .testing/build/target_codebase/.testing/build/timing/time_*

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-opt-target-artifact
          path: mom6-opt-target.tar
          retention-days: 1

  build-coverage:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 with code coverage
        run: make -C .testing -j build/cov/MOM6

      - name: Compile MOM6 unit tests
        run: |
          make -C .testing -j build/unit/test_MOM_file_parser
          make -C .testing -j build.unit

      - name: Prepare artifact
        run: |
          tar -cf mom6-coverage.tar \
          --exclude='.testing/build/unit/test_*.o' \
          .testing/build/cov/MOM6 \
          .testing/build/cov/*.gcno \
          .testing/build/unit/test_* \
          .testing/build/unit/*.gcno

      - uses: actions/upload-artifact@v4
        with:
          name: mom6-coverage-artifact
          path: mom6-coverage.tar
          retention-days: 1

  build-coupled-api:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup/

      - name: Compile FMS
        run: make -C .testing -j build/deps/lib/libFMS.a

      - name: Compile MOM6 for the GFDL coupled driver
        run: make -C .testing -j check_mom6_api_coupled

  # Tests

  test-grid:
    runs-on: ubuntu-latest
    needs:
      - build-symmetric
      - build-asymmetric

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download symmetric MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Download asymmetric MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-asymmetric-artifact

      - name: Unpack artifacts
        run: |
          tar -xpvf mom6-symmetric.tar
          tar -xpvf mom6-asymmetric.tar

      - name: Run grid verification test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          -o build/asymmetric/MOM6 \
          test.grid

  test-layout:
    runs-on: ubuntu-latest
    needs: build-symmetric

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download Artifacts
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-symmetric.tar

      - name: Run layout test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          test.layout

  test-rotate:
    runs-on: ubuntu-latest
    needs: build-symmetric

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download Artifacts
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-symmetric.tar

      - name: Run rotation test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          test.rotate

  test-restart:
    runs-on: ubuntu-latest
    needs: build-symmetric

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download Artifacts
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-symmetric.tar

      - name: Run restart test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          test.restart

  test-nan:
    runs-on: ubuntu-latest
    needs: build-symmetric

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download Artifacts
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-symmetric.tar

      - name: Run NaN initialization test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          test.nan

  test-dim:
    runs-on: ubuntu-latest
    needs: build-symmetric

    strategy:
      matrix:
        dim:
          - {id: t, desc: "time"}
          - {id: l, desc: "horizontal length"}
          - {id: h, desc: "vertical thickness"}
          - {id: z, desc: "vertical coordinate"}
          - {id: q, desc: "enthalpy"}
          - {id: r, desc: "density"}

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download symmetric MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-symmetric.tar

      - name: Run ${{ matrix.dim.desc }} dimension test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          test.dim.${{ matrix.dim.id }}

  test-openmp:
    runs-on: ubuntu-latest
    needs:
      - build-symmetric
      - build-openmp

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download symmetric MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Download OpenMP MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-openmp-artifact

      - name: Unpack artifacts
        run: |
          tar -xpvf mom6-symmetric.tar
          tar -xpvf mom6-openmp.tar

      - name: Run OpenMP test
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          -o build/openmp/MOM6 \
          test.openmp

  test-repro:
    runs-on: ubuntu-latest
    needs:
      - build-symmetric
      - build-repro

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download DEBUG MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Download REPRO MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-repro-artifact

      - name: Unpack artifacts
        run: |
          tar -xpvf mom6-symmetric.tar
          tar -xpvf mom6-repro.tar

      - name: Verify REPRO equivalence
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          -o build/repro/MOM6 \
          test.repro

  test-regression:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    needs:
      - build-symmetric
      - build-target

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download symmetric MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-symmetric-artifact

      - name: Download target MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-target-artifact

      - name: Unpack artifacts
        run: |
          tar -xpvf mom6-symmetric.tar
          tar -xpvf mom6-target.tar

      - name: Check for regressions
        run: |
          make -C .testing -j \
          -o build/symmetric/MOM6 \
          -o build/target/MOM6 \
          DO_REGRESSION_TESTS=1 \
          test.regression

  run-coverage:
    runs-on: ubuntu-latest
    needs: build-coverage

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download unit coverage tests
        uses: actions/download-artifact@v4
        with:
          name: mom6-coverage-artifact

      - name: Unpack artifacts
        run: |
          tar -xpvf mom6-coverage.tar
          find .testing/build/cov -name "*.gcno" -exec touch {} \;
          find .testing/build/unit -name "*.gcno" -exec touch {} \;

      - name: Generate MOM6 coverage
        run: |
          make -C .testing -j \
          -o build/cov/MOM6 \
          run.cov

      - name: Generate unit test coverage
        run: |
          cd .testing && make -j \
          $(for f in build/unit/test_*; do echo "-o $f"; done) \
          run.cov.unit

      - name: Report coverage to CI
        run: |
          cd .testing && make \
          -o build/cov/MOM6 \
          $(for f in build/unit/test_*; do echo "-o $f"; done) \
          report.cov report.cov.unit
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

  # These are most likely nonsense on a GitHub node, but someday it could work.
  run-timings:
    if: github.event_name != 'pull_request'
    runs-on: ubuntu-latest
    needs:
      - build-opt

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

      - name: Download timing tests
        uses: actions/download-artifact@v4
        with:
          name: mom6-opt-artifact

      - name: Unpack artifacts
        run: tar -xpvf mom6-opt.tar

      - name: Run unit test timings
        run: |
          cd .testing && make -j \
          $(for f in build/timing/time_*; do echo "-o $f"; done) \
          run.timing

      - name: Show timing results
        run: make -C .testing show.timing

  # These are most likely nonsense on a GitHub node, but someday it could work.
  compare-timings:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    needs:
      - build-opt
      - build-opt-target

    steps:
      - uses: actions/checkout@v4
        with:
          submodules: recursive

      - uses: ./.github/actions/ubuntu-setup

        # NOTE: This needs to occur before the artifacts are unpacked, because
        #   our rule for setting up `target_codebase` depends on its presence,
        #   rather than its contents.
        # If we can improve this rule, then this can be moved after unpacking.
      - name: Re-clone target directory
        run: |
          make -C .testing \
          DO_REGRESSION_TESTS=1 \
          build/target_codebase

      - name: Download optimized MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-opt-artifact

      - name: Download optimized target MOM6
        uses: actions/download-artifact@v4
        with:
          name: mom6-opt-target-artifact

      - name: Unpack artifacts
        run: |
            tar -xpvf mom6-opt.tar
            tar -xpvf mom6-opt-target.tar

      - name: Install preprocessor dependency
        run: pip install f90nml

      - name: Profile with FMS clocks
        run: |
          make -C .testing -j \
          -o build/opt/MOM6 \
          -o build/opt_target/MOM6 \
          profile

      - name: Profile with perf
        run: |
          sudo sysctl -w kernel.perf_event_paranoid=2
          make -C .testing -j \
          -o build/opt/MOM6 \
          -o build/opt_target/MOM6 \
          perf

      - name: Run unit test timings
        run: |
          cd .testing && make -j \
          $(for f in build/timing/time_*; do echo "-o $f"; done) \
          run.timing

      - name: Show timing results
        run: make -C .testing DO_REGRESSION_TESTS=1 show.timing

      - name: Run target timing tests
        run: |
          cd .testing/build/target_codebase/.testing && make -j \
          $(for f in build/timing/time_*; do echo "-o $f"; done) \
          run.timing

      - name: Compare unit test timings
        run: |
          make -C .testing \
          DO_REGRESSION_TESTS=1 \
          compare.timing

  # Cleanup

  cleanup-common:
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    needs:
      - test-grid
      - test-openmp
      - test-repro
      - run-coverage

    steps:
      - uses: geekyeggo/delete-artifact@v5
        with:
          name: |
            mom6-asymmetric-artifact
            mom6-openmp-artifact
            mom6-repro-artifact
            mom6-coverage-artifact

  # NOTE: There is no way to conditionally define the elements in `needs`.
  #   For now, we must create separate rules for each case.

  cleanup-push:
    if: github.event_name != 'pull_request'
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    needs:
      - test-layout
      - test-rotate
      - test-restart
      - test-nan
      - test-dim
      - test-grid
      - test-openmp
      - test-repro
      - run-timings

    steps:
      - uses: geekyeggo/delete-artifact@v5
        with:
          name: |
            mom6-symmetric-artifact
            mom6-opt-artifact

  cleanup-pr:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    permissions:
      id-token: write
    needs:
      - test-layout
      - test-rotate
      - test-restart
      - test-nan
      - test-dim
      - test-grid
      - test-openmp
      - test-repro
      - test-regression
      - compare-timings

    steps:
      - uses: geekyeggo/delete-artifact@v5
        with:
          name: |
            mom6-symmetric-artifact
            mom6-target-artifact
            mom6-opt-artifact
            mom6-opt-target-artifact