Add ePBL BBL mstar and bottom mixed layer diagnostics #259

Workflow file for this run

.github/workflows/verify-linux.yml at bf90d5f

	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

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Add ePBL BBL mstar and bottom mixed layer diagnostics #259

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Add ePBL BBL mstar and bottom mixed layer diagnostics #259

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