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Main to NCAR (30 July 2024) #291

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Aug 9, 2024
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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
10521a9
Merge pull request #127 from jiandewang/feature/update-to-main-20240228
jiandewang Mar 4, 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
dc24883
Error cleanup (Intel Fortran)
marshallward Mar 10, 2024
de59adf
Make the US argument to MOM_domains_init optional
Hallberg-NOAA Mar 20, 2024
e75d1da
Merge pull request #272 from Hallberg-NOAA/fix_dev_ncar_20240319
alperaltuntas Mar 20, 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
ab7bd14
Merge pull request #130 from marshallward/emc_fix_warn
jiandewang Mar 27, 2024
5e34f48
Set flags properly for rotated tripolar grids
Hallberg-NOAA Mar 6, 2024
87913b5
Merge pull request #1621 from NCAR/dev/ncar-candidate-240319
alperaltuntas Apr 1, 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
6d0150d
Merge remote-tracking branch 'MAIN/main' into feature/update-to-main-…
jiandewang Apr 16, 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
0730606
Merge pull request #132 from jiandewang/feature/update-to-main-20240401
jiandewang Apr 25, 2024
aac5bb8
Replace db array default values with real literals
marshallward Apr 26, 2024
a89d085
Merge pull request #12 from marshallward/db_type_fix
jiandewang Apr 26, 2024
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
129e1bd
Merge pull request #1623 from jiandewang/DEV-EMC-candidate-20240425
jiandewang May 8, 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
3bcfbbe
Merge pull request #134 from jiandewang/feature/update-to-main-20240508
jiandewang May 13, 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
7a2a33b
Use FMS1 for MacOS builds
adcroft May 18, 2024
b32aea7
Add end of run restart functionality to MOM6 (#133)
dpsarmie May 21, 2024
83bc4a6
GitLab CI: Direct build directory to $HOME
marshallward May 20, 2024
758b5a3
Add maximum number of iterations in find_depth_of_pressure_in_cell
claireyung Apr 24, 2024
9f3da0b
Fix minor issues
claireyung May 16, 2024
93f2aee
Fix error in diagnostic axis registration for grid space axes
MJHarrison-GFDL May 6, 2024
c1c32d2
Replace USE_GRID_SPACE_DIAGNOSTIC_AXES with USE_INDEX_DIAGNOSTIC_AXES
MJHarrison-GFDL May 20, 2024
1cf20b3
Better variables for updated masks in fill_miss_2d
Hallberg-NOAA Mar 5, 2024
bfe3e4f
fix line length too long issue in mom_cap.F90
jiandewang May 22, 2024
83fb3f0
Merge pull request #1630 from jiandewang/DEV-EMC-endofrun-restart-can…
jiandewang May 22, 2024
2b69f1e
Bugfix for tracer advection diagnostic in symmetric memory mode
breichl May 23, 2024
7384dba
Autoconf: Detect FMS IO implementation
marshallward May 23, 2024
c7d3268
.testing: Target build uses its own Makefile
marshallward May 24, 2024
8ecb260
CI: Fix FMS_COMMIT, remove FRAMEWORK
marshallward May 28, 2024
59e3a8f
Merge branch 'main' into dev/gfdl
marshallward May 29, 2024
f21ec03
*Fix ALE_remap_scalar call with h_in_Z_units
Hallberg-NOAA May 24, 2024
705a384
Add diag send complete calls to MOM
Apr 1, 2024
7305528
Add diag_manager_set_time_end calls to the solo drivers
May 14, 2024
d90ff6b
(*)Refactor and document soliton_initialization
Hallberg-NOAA Apr 19, 2024
3c87d98
(*)Correct rescaling of KPP pseudo-salt flux
Hallberg-NOAA May 11, 2024
506d186
+Eliminate fluxes%KPP_salt_flux
Hallberg-NOAA May 11, 2024
c121215
Fix TEOS10 argument descriptions
Hallberg-NOAA May 24, 2024
836e696
+Add convert_MLD_to_ML_thickness
Hallberg-NOAA Apr 23, 2024
2035af3
+*Use thickness in ideal_age_tracer_column_physics
Hallberg-NOAA Apr 23, 2024
912c568
+Pass h_MLD to mixedlayer_restrat
Hallberg-NOAA Apr 23, 2024
c300208
+*Convert MLD to ML_thickness in diabatic
Hallberg-NOAA Apr 24, 2024
d3cb7ee
+*Use visc%h_ML in tracer diffusion routines
Hallberg-NOAA Apr 24, 2024
d66adff
+*Pass visc%h_ML to call_tracer_column_fns
Hallberg-NOAA Apr 25, 2024
0578393
Remove diag_send_complete from disable_averaging
marshallward Jun 8, 2024
b4ae2b7
Disable nonrepro FMAs in convex BBL solver
marshallward Jun 17, 2024
ac2b642
Re-initialize fields within KPP
marshallward Jul 2, 2024
3fac1c5
Allow incorrect PPM:H3 tracer advection stencil
marshallward Jul 3, 2024
00f7d23
(*)+Restore USE_WRIGHT_2ND_DERIV_BUG functionality
Hallberg-NOAA Jul 14, 2024
40f4721
*Possibly initialize h_ML from MLD in restart file
Hallberg-NOAA Jul 19, 2024
ee686c8
Improve MOM_surface_chksum
Hallberg-NOAA Jul 18, 2024
aacb909
Merge pull request #1631 from NOAA-GFDL/gfdl-to-main-2024-05-31
marshallward Jul 29, 2024
df7b580
Merge branch 'main' into merge_main_073024
gustavo-marques Jul 30, 2024
69b0454
Merge branch 'dev/ncar' into merge_main_073024
gustavo-marques Aug 5, 2024
7afbb6d
Add missing missing_scale argument to read_Z_edges calls
gustavo-marques Aug 5, 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
1 change: 1 addition & 0 deletions .github/workflows/macos-regression.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ jobs:
env:
CC: gcc
FC: gfortran
FMS_COMMIT: 2019.01.03

defaults:
run:
Expand Down
1 change: 1 addition & 0 deletions .github/workflows/macos-stencil.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ jobs:
env:
CC: gcc
FC: gfortran
FMS_COMMIT: 2019.01.03

defaults:
run:
Expand Down
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: ${{ github.event_name == 'pull_request' }}
run: >-
make -j compare.timing
DO_REGRESSION_TESTS=true
5 changes: 4 additions & 1 deletion .gitlab-ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ stages:
# that is unique to this pipeline.
# We use the "fetch" strategy to speed up the startup of stages
variables:
JOB_DIR: "/lustre/f2/scratch/oar.gfdl.ogrp-account/runner/builds/$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 All @@ -32,6 +32,8 @@ p:clone:
tags:
- ncrc5
script:
# NOTE: We could sweep any builds older than 3 days here if needed
#- find $HOME/ci/[0-9]* -mtime +3 -delete 2> /dev/null || true
- .gitlab/pipeline-ci-tool.sh create-job-dir
#.gitlab/pipeline-ci-tool.sh clean-job-dir

Expand Down Expand Up @@ -353,4 +355,5 @@ cleanup:
before_script:
- echo Skipping usual preamble
script:
- rm -rf $HOME/ci/$CI_PIPELINE_ID
- rm -rf $JOB_DIR
7 changes: 7 additions & 0 deletions .gitlab/pipeline-ci-tool.sh
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,13 @@ create-job-dir () {
make -f tools/MRS/Makefile.clone clone_gfdl -j # Extras and link to datasets
bash tools/MRS/generate_manifest.sh . tools/MRS/excluded-expts.txt > manifest.mk
mkdir -p results
# Temporarily move build directory to $HOME to circumvent poor F5 performance
mkdir -p $HOME/ci/$CI_PIPELINE_ID/build
ln -s $HOME/ci/$CI_PIPELINE_ID/build build
# Builds need non-mangled access to src/.
ln -s "$(pwd)"/src $HOME/ci/$CI_PIPELINE_ID/src
# Static builds need access to ocean_only/
ln -s "$(pwd)"/ocean_only $HOME/ci/$CI_PIPELINE_ID/ocean_only
fi
section-end create-job-dir
}
Expand Down
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