(*) Merge GFDL to main (2022-10-27) #229
Merged
alperaltuntas merged 87 commits intoDec 14, 2022
Merged
Conversation
…n-20220602 update to main 20220602 commit
…n-20220603 update to main branch 20220629 commit
…ESMF-managed threading. authored-by: Gerhard Theurich <gerhard.j.theurich@noaa.gov>
…n-20220729 (1) update to MOM6 main branch 20220729 commit (GFDL-candidate-20220721) (2) cap update: supporting traditional and ESMF-managed threading
* Change dumbbell initialization * Change in Dumbbell Layer Mode * Fix sponge diagnostics * Fix ALE Sponge Diagnostics * A minor style change removing spaces around = in optional. function arguments. * Fix ALE sponge diagnostics * character declaration fix
- Ice shelf needs to be initialized prior to
ocean state initialization. This fixes any cases with
an ice shelf using the FMScap.
Added the new runtime parameter CHANNEL_DRAG_MAX_BBL_THICK, to allow the CHANNEL_DRAG parameterization to use the full dynamically determined depth of the bottom boundary layer, or to use a fixed maximum thickness, regardless of the settings of other parameters, although for now the default value is set based on the settings of USE_JACKSON_PARAM and DRAG_AS_BODY_FORCE in order to reproduce existing solutions by default. There are new entries in some MOM_parameter_doc files. All answers in the MOM6-examples test suite are bitwise identical, and this test suite has been tested and works with revised values of this parameter.
…in-20220820 update to MOM6 20220820 main branch
change t-freeze calcualtion for sppt
* Porous barrier variables, which are grouped in porous_barrier_ptrs, are changed from pointers to allocatables. * Copies (aliases) of these variables in MOM_CS are removed. * The name porous_barrier_ptrs is yet to be changed to minimize the number of files needed to be edited.
* The interface porous_widths is deleted and subroutine por_widths is renamed as porous_widths. * porous_barrier_CS is added to control input and diagnostics of the module * Diagnostics for both interface and layer averages weights are added in subroutine porous_widths. * An _init subroutine is added to facilitate reading parameters and registering diagnostics * checksum debugs are added within subroutine porous_widths.
This commit primarily fixes indexing bugs in subroutine porous_widths. * Loop range is subroutine porous_widths is changed from data domain to computation domain. * find_eta call is now with a proper halo to cover all velocity points. * Halo update for porous barrier fields is added in step_MOM_*. Other changes: * mask_depth, a component of porous_barrier_CS is now used to as the criterion for masking. This removes the limit that the cell edge depth has to be below sea surface. * Output variable eta_cor was unused and is now changed to a local. * Some unused indexing variables are removed.
parameters * subroutine set_subgrid_topo_at_vel_from_file is added to read max, min and avg depth at the edges from file. * The subroutine is only called when a new runtime parameter SUBGRID_TOPO_AT_VEL is True. Default is false.
* id_clock is added (as a private variable) to time porous barrier calculations. * Some small format fixes
* A runtime parameter PORBAR_ETA_INTERP is added to control different methods for calculating interface height at the velocity points from adjacent tracer cells. * Two small thickness variables are added and scaled the unit of eta. This is to assit the harmonic mean calculation, but eventually the if-test eta_s - eta_prev>0 should be relaced by Angstrom. * Runtime parameter POROUS_BARRIER_MASKING_DEPTH is renamed to make it a liitlle bit shorter. * log_version call is added to separate out porous_barriers module in parameter file.
The main loops in porous_widths are simpified and cleaned up. * calc_por_layer iss slightly modified to reduced the if-blocks in the main loops. * k-loops are moved out. * To assist this new structure, two 2-D arrays are added to the stack. * A new function eta_at_uv is added to treat different interpolations. This is currently done at every point within the loop, and it is probably adding too much an overhead. It is better pre-calculate eta_[uv] all together, which would increase the stack size.
The averaged weight over a layer (por_face_area[UV]) and the weight at the interface (por_layer_width[UV]) are now calculated separately, as the only two updates in step_mom are in fact using only one of them. This reduces some unnecessary calculations. * Two new subroutines replaced the original `porous_widths`. They could be combined with interface if we remove porous_barrier_ptrs type, and use variables (of different nz) as output. * There is a place holder switch do_next in the two calc_por subs. This is used to further reduce calculations for all layers above D_max. Will be tested and implemented in the next commit. * A new subroutine calc_eta_at_uv is added to calculate eta at uv. This simplifies the code, but also increases stack and some performance overhead.
* A new runtime parameter USE_POROUS_BARRIER is added to control this feature. The default is True at the moment to assist potential test. It should be changed to false in the future. * A boolean array is added to avoid unnecessary porous barrier calculations above the shallowest points. * The layer-averaged weights are bounded by 1.0 explicitly, to avoid the cases it goes beyond due to roundoff errors. * For very thin layers (Angstrom), layer-averaged weights are set to zeros for simplicity. * Perhaps it is more reasonable to use the inferace weight for these cases. * It might be useful to make the thin layer definition a runtime parameter. * A bug related the size of eta_[uv] is fixed. This commit is potentially answer-changing when the porouss barrier module is used.
* The recently introduced ANSWER_DATE functionality is used to maintain a version that should be bit-for-bit reproducible for previous porous barrier related runs. * Rename porous_barrier_ptrs to porous_barrier_type * Some small documentation edits
* Fixed a bug that eta_[uv] was not properly initialized, which caused issues with global chksums with DEBUG=True. * Documents added to comply with Doxygen tests
* Fix nudged OBCs for tracers
Failed codecov.io uploads now report the stderr output. This will allow us to start diagnosing the intermittent failures and, possibly, find a solution.
The actual calculation of SHT is stripped out of the tidal SAL subroutine to make module MOM_spherical_harmonics self-contained. * Forward and inverse spherical harmonic transform calculations are imported from MOM_tidal_forcing module, as two new subroutines are in module MOM_spherical_harmonics. This generalization allows the spherical harmonic transforms to applications other than SSH based SAL. * The main loops in the two new subroutine are also simplified. * Child variables in the control structure for SHT are now private. * The associated Legendre polynomials in the diagonal (n=m) is now precomputed and stored, rather than recalculating at every step. This does not have the memory cost as fully precomputing all the polynomials, but still reduces some repeat calculations. The performance appears to be improved with this change. * SAL calculation is simplified as forward transform, scaling and inverse transform. * A few variables names inherited from MPAS-O are changed.
* A new module is introduced with the sole purpose of storing Love numbers. This makes module MOM_tidal_forcing less chunkier and easier to read. * A new function in module MOM_spherical_harmonics is introduced to calculate the starting index of the first element for each order m, replacing a previous function of a similar purpose but a bit more complicated.
* Option to do reproducing sums for forward spherical harmonic transform is added, which is controlled by a runtime parameter. * New timers are added to monitor the performance of the more expensive global sum.
* Associated Legendre polynomials calculation is vectorized. * Some redundant variables are removed. * Fix filename suffix for module MOM_spherical_harmonics
* In MOM_tidal_forcing module, spherical harmonic coefficients (for SAL) are now parts of tidal_forcing_CS to avoid repeated allocations. The same applies to the Love number scaling factors. * Allocations for arrays used for reproducing sums are moved to subroutine spherical_harmonics_init in the MOM_spherical_harmonics module.
* Documentations are added for all modules related to SHT SAL. References from the MPAS-O group will need to be updated once they are published. * Variables names are shortened and changed to follow MOM6 style. (from camel to snake) * Change RhoE and RhoW in Love number scaling to runtime parameters * Correct a bug in a_recur size * Local arrays in SHT subroutines are properly initialized.
* Love number scaling coefficients multiplication is re-ordered to avoid ambiguity and to follow MOM6 style. * Coefficients for Pmm is simplified. Both changes introduce bit-wise level answer change to previous SHT SAL related unpublished commits. * Patches for Doxygen
Started the refactoring of code related to ALE_main, including: - Split remap_all_state_vars into remap_tracers and remap_velocities - Created the new public subroutine pre_ALE_diagnostics, and call it from step_MOM - Eliminate the unused argument conv_adjust to regridding_main - Eliminated check_grid, and moved these tests into regridding_main - Eliminate check_remapping_grid, and replace it with calls directly to check_grid_column inside of remapping_main All answers are bitwise identical, but there are new public interfaces and changes to the arguments of other public interfaces.
Continued the refactoring of code related to ALE_main, including: - Added the new public subroutine pre_ALE_adjustments - Added the new arguments h_new, dzRegrid, and PCM_cell to ALE_main - Added the new arguments h_new and dzRegrid to ALE_offline_main - Moved the code copying the new thickness to the primary thickness out of ALE_main and into step_MOM_thermo All answers are bitwise identical, but there are new public interfaces and changes to the arguments of other public interfaces.
Move the post_data call for dzRegrid to immediately follow its calculation in regridding main. All answers and diagnostics are bitwise identical, but because this commit changes the order in which some diagnostics are posted, the TC testing falsely reports a failure due to changed diagnostics.
Replaced ALE_main with ALE_regrid and calls to ALE_remap_tracers and ALE_remap_velocities from step_MOM_thermo. Also eliminated ALE_main_offline and ALE_offline_tracer_final, as they can now be replaced with a calls to ALE_regrid and a call to ALE_remap_tracers. Also added unit descriptions to a number of comments describing variables in MOM_ALE.F90. All answers are bitwise identical, but there are 3 new publicly visible subroutines (ALE_regrid, ALE_remap_tracers, and ALE_remap_velocities) and three previous interfaces (ALE_main, ALE_main_offline and ALE_offline_tracer_final) have been eliminated.
Revised or extended comments to correct or more clearly document the units of 49 internal variables in modules in the core directory. All answers are bitwise identical.
Added separate restart variables for some of the oblique OBC restart variables at north-south or east-west faces. Before this fix, some of the full 3-d arrays for restarts were being overwritten for oblique OBC segments that join at adjacent corners on the north-east side of tracer points, as is noted in github.com/NOAA-GFDL/issues/208. The discussion surrounding this issue confirms that there are cases using oblique OBCs (like some North-West Atlantic cases) that do not past the restart reproducibility tests. Some halo updates were also corrected, in accordance with the introduction of these new variables and their proper staggering locations. In a number of places, the proper case-sensitive horizontal indexing convention, as described in github.com/NOAA-GFDL/MOM6/wiki/Code-style-guide#soft-case-convention, is now being used. This commit also corrected the comments describing a number of the variables in the OBC_segment_type to make it clearer where they are discretized. This changes the names of oblique OBC-related variables in the restart files, but since the previous version did not reproduce across restarts, there does not seem to be any point in retaining those incorrect answers. All answers in the MOM6-examples test suite are bitwise identical, but this will change (fix) solutions with oblique OBCs and OBC_RAD_VEL_WT < 1.
Added two new arrays (OBCmaskCu and OBCmaskCv) to the ocean_grid_type and dyn_horgrid_type to mask out values over land or at open boundary condition points. Without open boundary conditions, these arrays are identical to mask2dCu and mask2dCv. These arrays are used in some of the lateral parameterization modules to zero out certain gradient-dependent fluxes at open boundary points. With these changes, the Bering test case solutions no longer exhibit any dependence on whether DEBUG_OBC is true or false or the value of OBC_SILLY_THICK, so this commit should help to address some of the issues discussed in github.com/NOAA-GFDL/issues/208. All answers are bitwise identical in the MOM6-examples test cases, but they change for some other tests that use open boundary conditions more extensively, and there are new arrays in some transparent types.
Eliminated OBC arguments that are no longer used by three internal routines in MOM_lateral_mixing_coeffs. All answers are bitwise identical.
This patch moves the local `use_tides` flag of the split RK2 solver, which tracks the TIDES parameter, into the RK2 control structure (CS), and uses it to conditionally call `tidal_forcing_end(). The `tidal_forcing_init()` function conditionally allocates the spherical harmonic fields, but `tidal_forcing_end()` is always called, which will in turn always attempt to deallocate the fields. In some compilers, under certain levels of debugging, this can raise a runtime error.
…ain-2022-10-27 GFDL to main 2022-10-27
Testing to see if GH actions is failing due to MPI installation
Collaborator
Author
|
Cherry-picked 3808641 to fix issue in GH actions due to MPI installation. |
Codecov ReportBase: 37.19% // Head: 37.19% // Increases project coverage by
Additional details and impacted files@@ Coverage Diff @@
## dev/ncar #229 +/- ##
==========================================
Coverage 37.19% 37.19%
==========================================
Files 261 263 +2
Lines 72392 73147 +755
Branches 13550 13625 +75
==========================================
+ Hits 26925 27206 +281
- Misses 40470 40929 +459
- Partials 4997 5012 +15
Help us with your feedback. Take ten seconds to tell us how you rate us. Have a feature suggestion? Share it here. ☔ View full report at Codecov. |
|
@gustavo-marques I am going to do an update to |
|
Actually, it looks like the macos change was unneeded here, I was confusing the regression test. Let's just go with this for now and we'll do things properly next time it happens. |
Member
|
testing... |
alperaltuntas
approved these changes
Dec 14, 2022
alperaltuntas
added a commit
that referenced
this pull request
Apr 2, 2026
* check-cleanliness CI test * Oops, forgot to update gitmodules. (DUPLICATION IS EVIL) * call git-fleximod update before git diff check * Revert: Oops, forgot to update gitmodules. (DUPLICATION IS EVIL) * switch to git-fleximod test for hash consistency checking * update MOM6 submodule but forget to update gitmodules. This should result in CI failure * revert MOM6 submodule. This should fix in CI failure
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
13 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
A full description of what's been merged is provided at mom-ocean#1586
This PR will change answers for the CESM tests because the following parameters were removed from MOM_parameter_doc.all:
In MOM_interface, these parameters were set to KVML = 1.0E-04 m2 s-1 and KDML = 0.0 m2 s-1. I've verified that setting KVML = 0.0 (which is equivalent to what's being done in this PR) does not result in significant changes in a G compset. Differences in key metrics over 10 years are documented in these notebooks.
To accommodate these changes, this PR must be evaluated in conjunction with ESCOMP/MOM_interface#128