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update to dev/emc
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‎.github/actions/testing-setup/action.yml

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@@ -0,0 +1,77 @@
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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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inputs:
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build_symmetric:
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description: 'If true, will build the symmetric MOM6 executable'
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required: false
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default: 'true'
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install_python:
9+
description: 'If true, will install the local python env needed for .testing'
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required: false
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default: 'true'
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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
21+
echo "::endgroup::"
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- name: Env
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shell: bash
25+
run: |
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echo "::group::Environment"
27+
env
28+
echo "::endgroup::"
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30+
- name: Install needed packages for compiling
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shell: bash
32+
run: |
33+
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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38+
- 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::"
45+
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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"
50+
cd .testing
51+
echo "FCFLAGS_DEBUG=-g -O0 -Wextra -Wno-compare-reals -fbacktrace -ffpe-trap=invalid,zero,overflow -fcheck=bounds" >> config.mk
52+
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
56+
echo "::endgroup::"
57+
58+
- 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
63+
test ${{ inputs.build_symmetric }} == true && 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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test ${{ inputs.install_python }} == true && 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/coupled-api.yml

+33
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name: API for coupled drivers
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on: [push, pull_request]
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jobs:
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test-top-api:
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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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with:
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build_symmetric: 'false'
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install_python: 'false'
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- name: Compile MOM6 for the GFDL coupled driver
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shell: bash
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run: make check_mom6_api_coupled -j
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- name: Compile MOM6 for the NUOPC driver
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shell: bash
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run: make check_mom6_api_nuopc -j
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- name: Compile MOM6 for the MCT driver
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shell: bash
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run: make check_mom6_api_mct -j

‎.github/workflows/coverage.yml

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name: Code coverage
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3+
on: [push, pull_request]
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5+
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
15+
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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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21+
- 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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3+
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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10+
steps:
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- uses: actions/checkout@v2
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with:
13+
submodules: recursive
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15+
- name: Check white space (non-blocking)
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run: |
17+
./.testing/trailer.py -e TEOS10 -l 120 src config_src 2>&1 | tee style_errors
18+
continue-on-error: true
19+
20+
- name: Install packages used when generating documentation
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run: |
22+
sudo apt-get update
23+
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
32+
cat _build/doxygen_warn_nortd_log.txt
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34+
- 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
37+
cat style_errors doxy_errors > all_errors
38+
cat 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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18+
- 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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html
55

66

7-
# Build output
8-
*.o
9-
*.mod
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MOM6
11-
12-
13-
# Autoconf
7+
# Autoconf output
148
aclocal.m4
159
autom4te.cache/
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config.log

‎.gitlab-ci.yml

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@@ -31,7 +31,7 @@ setup:
3131
# Clone regressions directory
3232
- git clone --recursive http://gitlab.gfdl.noaa.gov/ogrp/Gaea-stats-MOM6-examples.git tests && cd tests
3333
# Install / update testing scripts
34-
- git clone https://github.com/adcroft/MRS.git MRS
34+
- git clone -b new-code-struct https://github.com/adcroft/MRS.git MRS
3535
# Update MOM6-examples and submodules
3636
- (cd MOM6-examples && git checkout . && git checkout dev/gfdl && git pull && git submodule init && git submodule update)
3737
- (cd MOM6-examples/src/MOM6 && git submodule update)
@@ -60,7 +60,7 @@ gnu:ocean-only-nolibs:
6060
- time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
6161
- make -f MRS/Makefile.build build/gnu/env && cd build/gnu
6262
# mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
63-
- ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{solo_driver,dynamic_symmetric,ext*} ../../../src ../../MOM6-examples/src/FMS
63+
- ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{drivers/solo_driver,memory/dynamic_symmetric,infra/FMS1,ext*} ../../../src ../../MOM6-examples/src/FMS
6464
- sed -i '/FMS\/.*\/test_/d' path_names
6565
- ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF" path_names
6666
- time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
@@ -73,7 +73,7 @@ gnu:ice-ocean-nolibs:
7373
- time tar zxf $CACHE_DIR/tests_$CI_PIPELINE_ID.tgz && cd tests
7474
- make -f MRS/Makefile.build build/gnu/env && cd build/gnu
7575
# mkdir -p build/gnu/repro/symmetric_dynamic/ocean_only && cd build/gnu/repro/symmetric_dynamic/ocean_only
76-
- ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{coupled_driver,dynamic,ext*} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
76+
- ../../MOM6-examples/src/mkmf/bin/list_paths -l ../../../config_src/{drivers/FMS_cap,memory/dynamic_nonsymmetric,infra/FMS1,ext*} ../../../src ../../MOM6-examples/src/{FMS,coupler,SIS2,icebergs,ice_param,land_null,atmos_null}
7777
- sed -i '/FMS\/.*\/test_/d' path_names
7878
- ../../MOM6-examples/src/mkmf/bin/mkmf -t ../../MOM6-examples/src/mkmf/templates/ncrc-gnu.mk -p MOM6 -c"-Duse_libMPI -Duse_netCDF -D_USE_LEGACY_LAND_ -Duse_AM3_physics" path_names
7979
- time (source ./env ; make NETCDF=3 REPRO=1 MOM6 -s -j)
@@ -117,11 +117,36 @@ run:
117117
- time tar zxf $CACHE_DIR/build-pgi-repro-$CI_PIPELINE_ID.tgz
118118
# time tar zxf $CACHE_DIR/build-gnu-debug-$CI_PIPELINE_ID.tgz
119119
- (echo '#!/bin/tcsh';echo 'make -f MRS/Makefile.tests all') > job.sh
120-
- sbatch --clusters=c3,c4 --nodes=29 --time=0:34:00 --account=gfdl_o --qos=debug --job-name=mom6_regressions --output=log.$CI_PIPELINE_ID --wait job.sh
120+
- sbatch --clusters=c3,c4 --nodes=29 --time=0:34:00 --account=gfdl_o --qos=debug --job-name=mom6_regressions --output=log.$CI_PIPELINE_ID --wait job.sh || MJOB_RETURN_STATE=Fail
121121
- cat log.$CI_PIPELINE_ID
122+
- test -z "$MJOB_RETURN_STATE"
122123
- test -f restart_results_gnu.tar.gz
123124
- time tar zvcf $CACHE_DIR/results-$CI_PIPELINE_ID.tgz *.tar.gz
124125

126+
gnu.testing:
127+
stage: run
128+
tags:
129+
- ncrc4
130+
script:
131+
- cd .testing
132+
- 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
133+
- make work/local-env
134+
- make -s -j
135+
- (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
136+
- 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
137+
138+
intel.testing:
139+
stage: run
140+
tags:
141+
- ncrc4
142+
script:
143+
- cd .testing
144+
- 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
145+
- make work/local-env
146+
- make -s -j
147+
- (echo '#!/bin/bash';echo '. ./work/local-env/bin/activate';echo 'make MPIRUN="srun -mblock --exclusive" test -s -j') > job.sh
148+
- 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
149+
125150
# Tests
126151
gnu:non-symmetric:
127152
stage: tests

‎.readthedocs.yml

+12-7
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@@ -1,11 +1,16 @@
1-
# don't build extra formats (like HTML zip)
2-
formats:
3-
- none
1+
version: 2
42

5-
# path to pip requirements file to bring in
6-
# doxygen extensions
7-
requirements_file: docs/requirements.txt
3+
# Extra formats
4+
# PDF generation is failing for now; disabled on 2020-12-02
5+
#formats:
6+
# - pdf
7+
8+
# Build documentation
9+
sphinx:
10+
configuration: docs/conf.py
811

912
python:
1013
# make sure we're using Python 3
11-
version: 3.5
14+
version: 3
15+
install:
16+
- requirements: docs/requirements.txt

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