(*) Merge main as of 01 Nov 2021#16
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This commit adds a new module (MOM_CFC_cap) that can used to simulate chlorofluorocarbons (CFCs) tracers. It also includes the modifications needed to 1) allocate arrays in the fluxes and surface types, and 2) activate the MOM_CFC_cap module via NUOPC cap.
The MOM_control_struct is declared and passed as a pointer to a CS (usually allocated anonymously) and treated as if it were a pointer, even though there is currently no real advantage to doing so. After the FMS update, the deallocation of this CS was causing a segmentation fault in the PGI compilers. While the underlying cause was never determined, it is likely due to some automated deallocation of the CS contents, whose addressing became scrambled. This problem can be resolved by moving all of the CS contents to stack, so that the contents are automatically removed upon exiting whatever function it was instantiated. Subsequent calls can reference the local (or parent) stack contents.
This patch introduces two new testing targets to the verification suite based on a small configuration based on the `benchmark` regression test. The profile test is saved a `p0` in `.testing`. Future tests can be included if appropriate. The new targets: * `make profile`: Run the model and record the FMS timings. * `make perf`: Run the model through the `perf` tool and record timings for the resolvable functions (as symbols). In both cases, the timings are converted to JSON output files and the top results are reported to stdout, and readable in GitHub actions output. It can also be run locally. Support Python scripts have been included to do this work. This will require a functional Python environment. Some system and configuration data is logged alongside the timings, but this is still rather incomplete and needs some further planning. Times are compared to the target build (usually dev/gfdl). ANSI terminal highlighting (i.e. color) is to used to highlight excessive differences. Current issues: - Model configuration - GitHub timings are still rather unreliable, and should currently only be treated as crude estimates. This should be considered a work in progress. - The GitHub profiling rule still builds the standard configuration, evem though it is unused. - Additional tools are required to push the timings to some database, either a local sqlite3 or an external one.
…ility - remove the u,v,tv pointers from the set_up_oda_incupd subroutines - explicitly put tv,u,v in arguments of apply_oda_incupd - change name get_oda_increments to calc_oda_increments - explicitly put tv,u,v in arguments of calc_oda_increments - use loops to calculate sum of h’s - remove the 2018_answers options - added option to output increments when using full fields - added subroutine output_oda_incupd_inc to write a separate double-precision file for the increments. - add if (mask==1 ) condition to apply/calculate the increments -add pass_var,pass_vector on increments and u,v,tv at the end of calc_oda_increments and apply_oda_incupd respectively - added CS%ncount to restart file to have reproducibility on restart. - Added option ODA_INCUPD_RESET_NCOUNT (! default= True, If True, reinitialize number of updates already done.)
- Without this change, the edges don't reproduce on restart due to the h values outside being nonsense.
…mentation * Implements a module to simulate CFCs via NUOPC cap
Fix NUOPC import of fields required for the new CFC module
The export of ice fraction was previously added for the newly added CFC module.
- This addresses the FMS issue $761 NOAA-GFDL/FMS#761 - There is a mpp_broadcast in the FMS2 subroutine get_unlimited_dimension_name() and this subroutine has to be called by all pes, so it cannot be inside a if(is_root_pe()) block
Fix to sponge verbosity, also some documentation.
`make all` (the default rule) builds the executables specified by
`BUILDS`. This was hard-coded, but can be promoted to a user-defined
configuration for user-defined builds.
This should be seen as a simple alias to `make build/${b}/MOM6`.
The `repro` build was also incorrectly in the list, even though it was
also conditionally added. It has been removed from the default list.
A similar modification was made to CONFIGS, which select the "tc"
experiments. The default is still to do a `tc*` glob.
Documentation was also added.
Macros for generating individual rules for the tc's were added. This was generalized to support the contents of CONFIGS, which is now a user-defined parameter. The wildcard rules have now been replaced with more explicit rules, in preparation for the merge of TESTS and TEST_TYPES. A method for excluding tests has been added for tc3 support, and could be extended to future tests.
The Makefile rules were extended to support multiple iterations of dimension testing. Examples shown below: * test.dim Run all dimension tests * test.dim.l Run all L dimension tests * tc2.dim Run all tc2 dimension tests * tc2.dim.l Run the tc2 L dimension test Also, TESTS and TEST_TYPES were merged into a single variable, and the old plural test names (e.g. test.grids) were removed and are now handled as singular tests => test.grid. The GitHub actions testing was updated to reflect these new non-plural names. It will take some iteration to confirm that they are working.
…direction +(*)Add ALTERNATE_FIRST_DIRECTION
Testing: Generalized testing rules
The `N2_floor` buoyancy frequency was left unset when `KHTH_USE_FGNV_STREAMFUNCTION` was disabled. This could potentially cause errors, such as floating point exceptions. Ideally we would restrict the calculations of `hN2_[uv]` to when the streamfunction is enabled. But due to propagation to these values to `hN2_[xy]_PE` fields, which may be used outside of the streamfunction, it is perhaps best to just initialize `N2_floor` to zero. Although this would mostly likely be initialized to zero in production, there is a chance that this could modify answers derived from random initialization. Thanks to @wfcooke for reporting this. It was also independently (and inexplicably) detected during removal of MEKE pointers, suggesting some memory volatility.
…e_reflection Refactoring internal tide reflection
(*) N2_floor init fix when FGNV streamfn disabled
…date-2021-10-04 correct long_name for tracer_dfy for passive tracers when diag_form == 1
PRs mom-ocean#1428 and mom-ocean#1457 extended the topography clipping to allow flooding but missed the use case for positive-only depths where the MASKING_DEPTH parameter alone was in use. There were two bugs: 1. The new code assumed that MINIMUM_DEPTH would be deeper than MASKING_DEPTH (which is intuitive). However, the point of MASKING_DEPTH was only to specify the determination of the land mask. The new code assigned depths the value of MASKING_DEPTH which broke cases that were using MASKING_DEPTH as documented and were leaving MINIMUM_DEPTH=0. 2. The values of variable masking_depth were altered and subsequently not consistent with the logged parameters. A warning was issued but the behavior was nevertheless not as intended. Changes: 1. Removed the test that masking_depth > min_depth, and warning 2. Adjusted the condition and assigned value when clipping depths. This now uses the shallower of min_depth and masking_depth to decide when to clip and for the value to use otherwise. The expression for the land mask is unaltered. 3. Corrected documentation to retain original purpose of MASKING_DEPTH 4. Added some comments for declaration with units 5. Added some clarifying comments in code Todo: - resolve the need for the alternative negative depth pathway associated with the 0.5*min_depth expression.
- @klindsay28 spotted two issues for the NW2 tracers 1. Use of the wrong logical variable 2. Incorrect comment - Using the wrong logical meant that the ideal age pacakge was being called in addition to the NW2 package, but did not affect the NW2 tracers themselves.
- Following feedback from @herrwang0, we have removed the possibility for a user to try using negative depths without the MASKING_DEPTH parameter being set appropriately. This avoids the asymmetric use of MINIMUM_DEPTH that was proposed. A FATAL is now issued. - Corrected a spelling error in a comment. - Removed an unused "use" that should have been done in previous commit.
Recover topography clipping when not specifying MINIMUM_DEPTH
Correct logical associated with NW2 tracers
…ate-2021-10-04 Dev gfdl main candidate 2021 10 04
Codecov Report
@@ Coverage Diff @@
## dev/cpt #16 +/- ##
===========================================
- Coverage 29.29% 29.06% -0.24%
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Files 235 237 +2
Lines 70799 71637 +838
===========================================
+ Hits 20742 20822 +80
- Misses 50057 50815 +758
Continue to review full report at Codecov.
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I will create a new PR from dev/gfdl to include new wind stress acceleration diagnostics from Nora. |
gustavo-marques
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+(*)Pseudo_salt_tracer and forcing%netSalt
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Merging the main candidate described in https://github.com/NOAA-GFDL/MOM6/pull/1507
This PR changes answers for NW2.