Aug2024

.codecov.yml

@@ -0,0 +1,10 @@
+coverage:
+    status:
+        project:
+            default:
+                threshold: 100%
+                base: parent
+        patch:
+            default:
+                threshold: 100%
+                base: parent

.github/actions/macos-setup/action.yml

@@ -0,0 +1,33 @@
+name: 'install-macos-prerequisites'
+
+description: 'Install prerequisites for Mac OS compilation'
+
+runs:
+  using: 'composite'
+
+  steps:
+    - name: Install macOS packages
+      shell: bash
+      run: |
+        echo "::group::Install packages"
+        brew reinstall gcc
+        brew install automake
+        brew install netcdf
+        brew install netcdf-fortran
+        brew install mpich
+        echo "::endgroup::"
+
+    # NOTE: Floating point exceptions are currently disabled due to an error in
+    # HDF5 1.4.3.  They will be re-enabled when the default brew version has
+    # been updated to a working version.
+
+    - name: Set compiler flags
+      shell: bash
+      run: |
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/actions/testing-setup/action.yml

@@ -0,0 +1,45 @@
+name: 'Build-.testing-prerequisites'
+description: 'Build pre-requisites for .testing including FMS and a symmetric MOM6 executable'
+inputs:
+  build_symmetric:
+    description: 'If true, will build the symmetric MOM6 executable'
+    required: false
+    default: 'true'
+runs:
+  using: 'composite'
+  steps:
+    - name: Git info
+      shell: bash
+      run: |
+        echo "::group::Git commit info"
+        echo "git log:"
+        git log | head -60
+        echo "::endgroup::"
+
+    - name: Env
+      shell: bash
+      run: |
+        echo "::group::Environment"
+        env
+        echo "::endgroup::"
+
+    - name: Compile FMS library
+      shell: bash
+      run: |
+        echo "::group::Compile FMS library"
+        cd .testing
+        REPORT_ERROR_LOGS=true make build/deps/lib/libFMS.a -s -j
+        echo "::endgroup::"
+
+    - name: Compile MOM6 in symmetric memory mode
+      shell: bash
+      run: |
+        echo "::group::Compile MOM6 in symmetric memory mode"
+        cd .testing
+        test ${{ inputs.build_symmetric }} == true && make build/symmetric/MOM6 -j
+        echo "::endgroup::"
+
+    - name: Set flags
+      shell: bash
+      run: |
+        echo "TIMEFORMAT=... completed in %lR  (user: %lU, sys: %lS)" >> $GITHUB_ENV

.github/actions/ubuntu-setup/action.yml

@@ -0,0 +1,31 @@
+name: 'install-ubuntu-prerequisites'
+
+description: 'Install prerequisites for Ubuntu Linux compilation'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Install Ubuntu Linux packages
+      shell: bash
+      run: |
+        echo "::group::Install linux packages"
+        sudo apt-get update
+        sudo apt-get install netcdf-bin
+        sudo apt-get install libnetcdf-dev
+        sudo apt-get install libnetcdff-dev
+        sudo apt-get install openmpi-bin
+        sudo apt-get install libopenmpi-dev
+        sudo apt-get install linux-tools-common
+        echo "::endgroup::"
+
+    - name: Store compiler flags used in Makefile
+      shell: bash
+      run: |
+        echo "::group::config.mk"
+        cd .testing
+        echo "FCFLAGS_DEBUG = -g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
+        echo "FCFLAGS_REPRO = -g -O2 -fbacktrace" >> config.mk
+        echo "FCFLAGS_INIT = -finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
+        echo "FCFLAGS_FMS = -g -fbacktrace -O0" >> config.mk
+        cat config.mk
+        echo "::endgroup::"

.github/workflows/coupled-api.yml

@@ -0,0 +1,30 @@
+name: API for coupled drivers
+
+on: [push, pull_request]
+
+jobs:
+  test-top-api:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/ubuntu-setup
+
+    - uses: ./.github/actions/testing-setup
+      with:
+        build_symmetric: 'false'
+
+    - name: Compile MOM6 for the GFDL coupled driver
+      shell: bash
+      run: make check_mom6_api_coupled -j
+
+    - name: Compile MOM6 for the NUOPC driver
+      shell: bash
+      run: make check_mom6_api_nuopc -j

.github/workflows/coverage.yml

@@ -0,0 +1,48 @@
+name: Code coverage
+
+on: [push, pull_request]
+
+jobs:
+  build-coverage:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/ubuntu-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile file parser unit tests
+      run: make -j build/unit/test_MOM_file_parser
+
+    - name: Run file parser unit tests
+      run: make run.cov.unit
+
+    - name: Compile unit testing
+      run: make -j build.unit
+
+    - name: Run (single processor) unit tests
+      run: make run.unit
+
+    - name: Report unit test coverage to CI
+      run: make report.cov.unit
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+    - name: Compile ocean-only MOM6 with code coverage
+      run: make -j build/cov/MOM6
+
+    - name: Run coverage tests
+      run: make -j -k run.cov
+
+    - name: Report coverage to CI
+      run: make report.cov
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/documentation-and-style.yml

@@ -0,0 +1,39 @@
+name: Doxygen and style
+
+on: [push, pull_request]
+
+jobs:
+  doxygen:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+      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

.github/workflows/expression.yml

@@ -0,0 +1,29 @@
+name: Expression verification
+
+on: [push, pull_request]
+
+jobs:
+  test-repro-and-dims:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/ubuntu-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile MOM6 using repro optimization
+      run: make build/repro/MOM6 -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Run tests
+      run: make test.repro test.dim -k -s

.github/workflows/macos-regression.yml

@@ -0,0 +1,35 @@
+name: MacOS regression
+
+on: [pull_request]
+
+jobs:
+  test-macos-regression:
+
+    runs-on: macOS-latest
+
+    env:
+      CC: gcc
+      FC: gfortran
+      FMS_COMMIT: 2019.01.03
+
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/macos-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile reference model
+      run: make build.regressions MOM_TARGET_SLUG=$GITHUB_REPOSITORY MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF DO_REGRESSION_TESTS=true -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Regression test
+      run: make test.regression DO_REGRESSION_TESTS=true -k -s

.github/workflows/macos-stencil.yml

@@ -0,0 +1,35 @@
+name: MacOS stencil tests
+
+on: [push, pull_request]
+
+jobs:
+  test-macos-stencil:
+
+    runs-on: macOS-latest
+
+    env:
+      CC: gcc
+      FC: gfortran
+      FMS_COMMIT: 2019.01.03
+
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/macos-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile MOM6 in asymmetric memory mode
+      run: make build/asymmetric/MOM6 -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Run tests
+      run: make test.grid test.layout test.rotate -k -s

.github/workflows/other.yml

@@ -0,0 +1,29 @@
+name: OpenMP and Restart verification
+
+on: [push, pull_request]
+
+jobs:
+  test-openmp-nan-restarts:
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: .testing
+
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+    - uses: ./.github/actions/ubuntu-setup
+
+    - uses: ./.github/actions/testing-setup
+
+    - name: Compile with openMP
+      run: make build/openmp/MOM6 -j
+
+    - name: Create validation data
+      run: make run.symmetric -k -s
+
+    - name: Run tests
+      run: make test.openmp test.nan test.restart -k -s