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GFDL to main 2024-05-16 #1627

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d8579d2
Use a class to deliver elemental procedures for EOS
adcroft Oct 2, 2023
7cc191a
Add rule and workflow to compare results of micro-timing tests
adcroft Nov 15, 2023
34b880f
Add units to comments in MOM_neutral_diffusion
Hallberg-NOAA Nov 16, 2023
11759d6
Fix unpaired parentheses in a formatting string
Hallberg-NOAA Nov 19, 2023
b898297
+(*)Add continuity_fluxes & continuity_adjust_vel
Hallberg-NOAA Nov 7, 2023
fc0bef1
+Pass-through from continuity_PPM via continuity
Hallberg-NOAA Nov 14, 2023
6b86ab8
+Create zonal_edge_thickness in MOM_continuity_PPM
Hallberg-NOAA Nov 15, 2023
d3496fe
+Call zonal_edge_thickness outside of zonal_mass_flux
Hallberg-NOAA Nov 16, 2023
bbda30f
+Add zonal_BT_mass_flux & meridional_BT_mass_flux
Hallberg-NOAA Nov 16, 2023
a70482c
+Add continuity_zonal_convergence
Hallberg-NOAA Nov 18, 2023
6b6f8dc
Move continuity_fluxes to MOM_continuity_PPM.F90
Hallberg-NOAA Nov 19, 2023
7877292
+Add optional argument du_cor to continuity_PPM
Hallberg-NOAA Dec 12, 2023
7d334f8
Makedep: Include support for CPP condition blocks
marshallward Dec 13, 2023
4e8fbe1
+Standardize input salinity units as "ppt"
Hallberg-NOAA Aug 16, 2023
8395404
Merge branch 'main' into dev/gfdl
marshallward Dec 18, 2023
a28443b
Fix for an OBC issue with mask_tables
kshedstrom Dec 6, 2023
5c14668
+FIX_USTAR_GUSTLESS_BUG is now USTAR_GUSTLESS_BUG
Hallberg-NOAA Dec 15, 2023
7ddc727
This commit guarantees consistency of the ice sheet code under rotate…
alex-huth Nov 27, 2023
b0ff6bd
fixed documentation of inputs to subroutine sum_square_matrix
alex-huth Nov 27, 2023
f7233e0
Optimized sub-cell grounding subroutines, increasing computational ef…
alex-huth Nov 30, 2023
d7096bd
fixed documented units of fN and fN_scale for ice shelf coulomb frict…
alex-huth Dec 19, 2023
90de5de
Rename u arg to step_MOM_dyn_split_RK2 as u_inst
Hallberg-NOAA Dec 15, 2023
eac3bb3
+FIX_UNSPLIT_DT_VISC_BUG is now UNSPLIT_DT_VISC_BUG
Hallberg-NOAA Dec 15, 2023
2ea0ac3
+Add MOM_dynamics_split_RK2b enabled by SPLIT_RK2B
Hallberg-NOAA Nov 12, 2023
8b98bd0
*+Revise algorithm in step_MOM_dyn_split_RK2b
Hallberg-NOAA Dec 12, 2023
9d57c15
Regroup MOM_dynamics_split_RK2b halo updates
Hallberg-NOAA Dec 17, 2023
5137442
+Correct description of SPLIT_RK2B
Hallberg-NOAA Dec 20, 2023
a03bb95
+Add cuberoot function
Hallberg-NOAA Dec 20, 2023
d7d126a
Update Gaea F5 datasets path
marshallward Jan 18, 2024
4813b17
*Use Halley method iterations in cuberoot function
Hallberg-NOAA Jan 19, 2024
17f1c40
Cuberoot: Apply first iteration explicitly (#11)
marshallward Jan 26, 2024
435ccaa
Data table documentation (#551)
ashjbarnes Jan 29, 2024
f1e0f01
Params: Add do_not_log to param block open/close
marshallward Jan 28, 2024
5ca70ba
Open parameter block before querying BODNER23
kshedstrom Jan 9, 2024
541c2f4
(*)Oil_tracer_column_physics unit conversion fix
Hallberg-NOAA Jan 19, 2024
76f0668
(*)Avoid using RHO_0 in non-Boussinesq averaging
Hallberg-NOAA Jan 20, 2024
60cb551
Intrinsics: Faster cuberoot scaling functions
marshallward Jan 28, 2024
5edba9b
Cuberoot: Refactor (re|de)scale functions
marshallward Jan 30, 2024
736ef16
Cuberoot: Break **3 into explicit integer cubes
marshallward Jan 30, 2024
671c85d
(*)Use cuberoot in ePBL_column
Hallberg-NOAA Jan 10, 2024
07bace6
*Fix two bugs in convert_temp_salt_for_TEOS10
Hallberg-NOAA Jan 30, 2024
915cfe2
+ALE_remap_scalar with arbitrary thickness units
Hallberg-NOAA Jan 26, 2024
e7a7a82
(*)MOM_temp_salt_init_from_Z Z-unit tracer remap
Hallberg-NOAA Jan 27, 2024
9a6ddee
*+non-Boussinesq revisions to MOM_generic_tracer
Hallberg-NOAA Jan 28, 2024
ea12532
Fix issue with restart filenames when using ensembles.
wfcooke Feb 1, 2024
9282cd1
+(*)Bodner param with cuberoot and non-Boussinesq
Hallberg-NOAA Jan 19, 2024
4757bcb
Remove some unused calculations if non-Boussinesq
Hallberg-NOAA Jan 21, 2024
de7e5b7
Document MOM_regridding and coord variable units
Hallberg-NOAA Feb 1, 2024
c37a2f0
Document core and linear EOS variable units
Hallberg-NOAA Jan 29, 2024
0fb905f
+(*)non-Boussinesq ALE_sponges work in Z units
Hallberg-NOAA Jan 23, 2024
f14a681
(*)Use thickness_to_dz with BRYAN_LEWIS_DIFFUSIVITY
Hallberg-NOAA Jan 24, 2024
3f7465a
+tracer_Z_init can rescale tracers
Hallberg-NOAA Jan 28, 2024
f92e4ac
Update MOM_mixed_layer_restrat.F90 (#568)
marshallward Feb 25, 2024
e69d771
Merge branch 'main' into dev/gfdl
marshallward Feb 28, 2024
f2e7abf
MLE: Use default answer date outside of block (#570)
marshallward Feb 28, 2024
86c5ed9
(*)Fix bug in h_neglect used to remap diags to rho
Hallberg-NOAA Feb 27, 2024
8f7df08
(*)non-Boussinesq Z unit update_OBC_segment_data
Hallberg-NOAA Jan 24, 2024
d0e9c25
*Corrected CFC diagnostics and non-Bous CFC fluxes
Hallberg-NOAA Jan 24, 2024
fd5696b
Pinning package requirements for readthedocs
adcroft Feb 29, 2024
f9da673
Create BUILD and WORK directory macros
marshallward Jan 16, 2024
2ae6385
Refactor set_viscous_BBL channel drag calculations
Hallberg-NOAA Dec 22, 2023
da02ffc
+Add find_L_open_concave_iterative
Hallberg-NOAA Dec 30, 2023
e1ea758
Add the debugging routine test_L_open_concave
Hallberg-NOAA Jan 15, 2024
714d2da
Minor refactoring in set_viscous_BBL
Hallberg-NOAA Mar 5, 2024
6153d97
Compute dz in the halo for OBC segments
kshedstrom Mar 9, 2024
0ff03ae
+Fix myStats global indexing segmentation faults
Hallberg-NOAA Feb 6, 2024
0bd4c16
(*)Fix apply_topography_edits_from_file indexing
Hallberg-NOAA Feb 8, 2024
9e78615
Earlier initialization thickness halo updates
Hallberg-NOAA Feb 4, 2024
1ae2a3a
+(*)Refactor MOM_diag_remap for global indices
Hallberg-NOAA Feb 5, 2024
d311b1d
+(*)Use z-space remapping for some diagnostics
Hallberg-NOAA Feb 5, 2024
611f575
+(*)Fix downsample_mask indexing bugs
Hallberg-NOAA Feb 6, 2024
2bc04bd
(*)Eliminate IIm1 and JJm1 in Update_Stokes_Drift
Hallberg-NOAA Feb 29, 2024
744dbcc
Document remapping function variable units
Hallberg-NOAA Feb 14, 2024
a23c7d8
fix gtracer restart repro issue with OBC
yichengt900 Mar 12, 2024
4fd0162
Rotation bugfixes
marshallward Mar 14, 2024
32f6316
+Rotationally symmetric neutral diffusion option
Hallberg-NOAA Feb 29, 2024
812510b
Add an option in hor_visc to use cont thickness
herrwang0 Mar 4, 2024
37ff301
fix opemmp parallel
herrwang0 Mar 4, 2024
2b59089
Set up auxiliary domain for unrotated grid
Hallberg-NOAA Mar 5, 2024
5e34f48
Set flags properly for rotated tripolar grids
Hallberg-NOAA Mar 6, 2024
f9372f3
+Add get_netcdf_filename for a get_field_nc error
Hallberg-NOAA Mar 11, 2024
a3fd1f3
+Rotationally symmetric epipycnal diffusion option
Hallberg-NOAA Mar 18, 2024
a71fbce
Merge branch 'main' into main_to_dev_20240405
marshallward Apr 5, 2024
2d121dc
(*)Pass dz to user initialize_ALE_sponge calls
Hallberg-NOAA Jan 24, 2024
c86358b
(*)Avoiding using RHO_0 in non-Boussinesq debugging
Hallberg-NOAA Jan 20, 2024
43b2a43
Add units to the descriptions of 141 variables
Hallberg-NOAA Apr 1, 2024
b98acd8
Add units to the descriptions of 115 variables
Hallberg-NOAA Mar 19, 2024
5b9ae52
Disable codecov upload requirement
marshallward Apr 12, 2024
6f1c79e
CPP expression parser for makedep
marshallward Apr 2, 2024
3a3baf1
(*)Fix Stokes drift spectrum rescaling
Hallberg-NOAA Apr 2, 2024
6c44c5f
Fix for using tidal amplitude in determining the BBL thickness
adcroft Apr 4, 2024
f7a4491
Perf: Better error report for failed parsing
marshallward Apr 5, 2024
1c4d0dc
Better document variable units in 3 user modules
Hallberg-NOAA Apr 5, 2024
0efe83d
Proto-type cricital latitude modification of Henyey
adcroft Jul 14, 2023
01b2ea9
Document units of 34 real variables in vertFPmix
Hallberg-NOAA Oct 26, 2023
4058462
Refactoring density integrals for efficiency
Hallberg-NOAA Mar 31, 2024
25989ad
Allow ALE boundary extrapolation behaviour to differ at initialisatio…
claireyung May 2, 2024
46fd6e6
+Rotationally symmetric KPP_smooth_BLD option
Hallberg-NOAA Apr 20, 2024
a3e9e1c
(*)Revise 13 diagnostics for rotational symmetry
Hallberg-NOAA Apr 20, 2024
efe1b4a
+Fix multiple bugs when MEKE_GM_SRC_ALT is True
Hallberg-NOAA May 5, 2024
a200f5f
Added missing values for vector u2_bg(:) within set_viscous_ML
alex-huth May 3, 2024
1829b7f
Makedep: Better handling of parentheses
marshallward May 7, 2024
93d9bb8
+(*)Fix USE_QG_LEITH_VISC = True reproducibility
Hallberg-NOAA Jan 28, 2023
bb8a653
Add diags for east, north velocity components.
kshedstrom Apr 29, 2024
0c790f2
SAL: Explicitly allocate sht variable in SAL_CS
marshallward May 10, 2024
e253883
Merge branch 'main' into dev/gfdl
marshallward May 14, 2024
6272bbc
Testing: Correct perf parsing of C++ output
marshallward May 14, 2024
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2 changes: 1 addition & 1 deletion .github/actions/testing-setup/action.yml
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ runs:
run: |
echo "::group::Compile FMS library"
cd .testing
REPORT_ERROR_LOGS=true make deps/lib/libFMS.a -s -j
REPORT_ERROR_LOGS=true make build/deps/lib/libFMS.a -s -j
echo "::endgroup::"

- name: Compile MOM6 in symmetric memory mode
Expand Down
18 changes: 2 additions & 16 deletions .github/workflows/coverage.yml
Original file line number Diff line number Diff line change
Expand Up @@ -31,14 +31,7 @@ jobs:
- name: Run (single processor) unit tests
run: make run.unit

- name: Report unit test coverage to CI (PR)
if: github.event_name == 'pull_request'
run: make report.cov.unit REQUIRE_COVERAGE_UPLOAD=true
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

- name: Report unit test coverage to CI (Push)
if: github.event_name != 'pull_request'
- name: Report unit test coverage to CI
run: make report.cov.unit
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
Expand All @@ -49,14 +42,7 @@ jobs:
- name: Run coverage tests
run: make -j -k run.cov

- name: Report coverage to CI (PR)
if: github.event_name == 'pull_request'
run: make report.cov REQUIRE_COVERAGE_UPLOAD=true
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

- name: Report coverage to CI (Push)
if: github.event_name != 'pull_request'
- name: Report coverage to CI
run: make report.cov
env:
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
22 changes: 22 additions & 0 deletions .github/workflows/perfmon.yml
Original file line number Diff line number Diff line change
Expand Up @@ -40,14 +40,36 @@ jobs:
sudo sysctl -w kernel.perf_event_paranoid=2
make perf DO_REGRESSION_TESTS=true

# This job assumes that build/target_codebase was cloned above
- name: Compile timing tests for reference code
if: ${{ github.event_name == 'pull_request' }}
run: >-
make -j build.timing_target
MOM_TARGET_SLUG=$GITHUB_REPOSITORY
MOM_TARGET_LOCAL_BRANCH=$GITHUB_BASE_REF
DO_REGRESSION_TESTS=true

- name: Compile timing tests
run: |
make -j build.timing

# DO_REGERESSION_TESTS=true is needed here to set the internal macro TARGET_CODEBASE
- name: Run timing tests for reference code
if: ${{ github.event_name == 'pull_request' }}
run: >-
make -j run.timing_target
DO_REGRESSION_TESTS=true

- name: Run timing tests
run: |
make -j run.timing

- name: Display timing results
run: |
make -j show.timing

- name: Display comparison of timing results
if: ${{ github.event_name == 'pull_request' }}
run: >-
make -j compare.timing
DO_REGRESSION_TESTS=true
2 changes: 1 addition & 1 deletion .gitlab-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ stages:
# that is unique to this pipeline.
# We use the "fetch" strategy to speed up the startup of stages
variables:
JOB_DIR: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/builds/$CI_PIPELINE_ID"
JOB_DIR: "/gpfs/f5/gfdl_o/scratch/oar.gfdl.ogrp-account/runner/builds/$CI_PIPELINE_ID"
GIT_STRATEGY: fetch

# Always eport value of $JOB_DIR
Expand Down
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