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Merge pull request #4 from ocean-eddy-cpt/update-mom6-nov-2020
Update CPT fork of MOM6 to latest (12/10/2020) from NOAA-GFDL
2 parents adf6046 + 788aeb0 commit 2507f7a

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

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name: 'Build-.testing-prerequisites'
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description: 'Build pre-requisites for .testing including FMS and a symmetric MOM6 executable'
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runs:
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using: 'composite'
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steps:
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- name: Git info
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shell: bash
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run: |
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echo "::group::Git commit info"
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echo "git log:"
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git log | head -60
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echo "::endgroup::"
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- name: Env
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shell: bash
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run: |
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echo "::group::Environment"
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env
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echo "::endgroup::"
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- name: Install needed packages for compiling
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shell: bash
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run: |
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echo "::group::Install linux packages"
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sudo apt-get update
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sudo apt-get install netcdf-bin libnetcdf-dev libnetcdff-dev mpich libmpich-dev
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echo "::endgroup::"
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- name: Compile FMS library
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shell: bash
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run: |
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echo "::group::Compile FMS library"
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cd .testing
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make deps/lib/libFMS.a -s -j
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echo "::endgroup::"
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- name: Store compiler flags used in Makefile
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shell: bash
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run: |
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echo "::group::config.mk"
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cd .testing
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echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
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echo "FCFLAGS_REPRO=-g -O2 -fbacktrace" >> config.mk
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echo "FCFLAGS_INIT=-finit-real=snan -finit-integer=2147483647 -finit-derived" >> config.mk
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echo "FCFLAGS_COVERAGE=--coverage" >> config.mk
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cat config.mk
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echo "::endgroup::"
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- name: Compile MOM6 in symmetric memory mode
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shell: bash
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run: |
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echo "::group::Compile MOM6 in symmetric memory mode"
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cd .testing
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make build/symmetric/MOM6 -j
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echo "::endgroup::"
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- name: Install local python venv for generating input data
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shell: bash
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run: |
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echo "::group::Create local python env for input data generation"
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cd .testing
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make work/local-env
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echo "::endgroup::"
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- name: Set flags
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shell: bash
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run: |
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echo "TIMEFORMAT=... completed in %lR (user: %lU, sys: %lS)" >> $GITHUB_ENV

‎.github/workflows/coverage.yml‎

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name: Code coverage
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on: [push, pull_request]
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jobs:
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build-test-nans:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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env:
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REPORT_COVERAGE: true
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/testing-setup
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- name: Run and post coverage
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run: make run.symmetric -k -s

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

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name: Doxygen and style
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on: [push, pull_request]
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jobs:
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doxygen:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- name: Check white space (non-blocking)
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run: |
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./.testing/trailer.py -e TEOS10 -l 120 src config_src | tee style_errors
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continue-on-error: true
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- name: Install packages used when generating documentation
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run: |
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sudo apt-get update
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sudo apt-get install python3-sphinx python3-lxml perl
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sudo apt-get install texlive-binaries texlive-base bibtool tex-common texlive-bibtex-extra
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sudo apt-get install graphviz
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- name: Build doxygen HTML
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run: |
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cd docs
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perl -e 'print "perl version $^V" . "\n"'
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mkdir _build && make nortd DOXYGEN_RELEASE=Release_1_8_13 UPDATEHTMLEQS=Y
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cat _build/doxygen_warn_nortd_log.txt
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- name: Report doxygen or style errors
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run: |
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grep "warning:" docs/_build/doxygen_warn_nortd_log.txt | grep -v "as part of a" | tee doxy_errors
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cat style_errors doxy_errors > all_errors
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test ! -s all_errors

‎.github/workflows/expression.yml‎

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name: Expression verification
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on: [push, pull_request]
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jobs:
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test-repro-and-dims:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/testing-setup
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- name: Compile MOM6 using repro optimization
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run: make build/repro/MOM6 -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Run tests
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run: make test.repros test.dims -k -s

‎.github/workflows/other.yml‎

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name: OpenMP and Restart verification
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on: [push, pull_request]
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jobs:
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test-openmp-nan-restarts:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/testing-setup
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- name: Compile with openMP
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run: make build/openmp/MOM6 -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Run tests
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run: make test.openmps test.nans test.restarts -k -s

‎.github/workflows/regression.yml‎

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name: Regression
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on: [pull_request]
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jobs:
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build-test-regression:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/testing-setup
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- name: Compile reference model
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run: make build.regressions MOM_TARGET_SLUG=$GITHUB_REPOSITORY MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF DO_REGRESSION_TESTS=true -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Regression test
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run: make test.regressions DO_REGRESSION_TESTS=true -k -s

‎.github/workflows/stencil.yml‎

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name: Stencil related verification
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on: [push, pull_request]
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jobs:
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test-symmetric-layout-rotation:
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runs-on: ubuntu-latest
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defaults:
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run:
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working-directory: .testing
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steps:
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- uses: actions/checkout@v2
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with:
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submodules: recursive
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- uses: ./.github/actions/testing-setup
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- name: Compile MOM6 in asymmetric memory mode
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run: make build/asymmetric/MOM6 -j
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- name: Create validation data
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run: make run.symmetric -k -s
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- name: Run tests
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run: make test.grids test.layouts test.rotations -k -s

‎.gitignore‎

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*.swp
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*~
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html
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*.log
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# Build output
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*.o
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*.mod
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MOM6
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build/
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_build/
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deps/
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MOM6.tags
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bib*.aux
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citelist.doc*
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# Autoconf
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aclocal.m4
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autom4te.cache/
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config.log
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config.status
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configure
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/Makefile
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Makefile.mkmf

‎.gitlab-ci.yml‎

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- test -f restart_results_gnu.tar.gz
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- time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz
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gnu.testing:
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stage: run
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tags:
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- ncrc4
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script:
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- cd .testing
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- module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan ; module load PrgEnv-gnu ; module unload netcdf gcc ; module load gcc/7.3.0 cray-hdf5 cray-netcdf
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- make work/local-env
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- make -s -j
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- (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
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- sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_PIPELINE_ID --wait job.sh || cat log.$CI_PIPELINE_ID && make test
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intel.testing:
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stage: run
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tags:
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- ncrc4
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script:
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- cd .testing
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- module unload PrgEnv-pgi PrgEnv-intel PrgEnv-gnu darshan; module load PrgEnv-intel; module unload netcdf intel; module load intel/18.0.6.288 cray-hdf5 cray-netcdf
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- make work/local-env
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- make -s -j
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- (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
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- sbatch --clusters=c3,c4 --nodes=5 --time=0:05:00 --account=gfdl_o --qos=debug --job-name=MOM6.gnu.testing --output=log.$CI_PIPELINE_ID --wait job.sh || cat log.$CI_PIPELINE_ID && make test
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# Tests
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gnu:non-symmetric:
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stage: tests

‎.readthedocs.yml‎

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# don't build extra formats (like HTML zip)
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formats:
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- none
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version: 2
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# path to pip requirements file to bring in
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# doxygen extensions
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requirements_file: docs/requirements.txt
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# Extra formats
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# PDF generation is failing for now; disabled on 2020-12-02
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#formats:
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# - pdf
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# Build documentation
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sphinx:
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configuration: docs/conf.py
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python:
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# make sure we're using Python 3
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version: 3.5
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version: 3
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install:
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- requirements: docs/requirements.txt

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