Feature/update to gfdl 20200515 2bug fix #29
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Moving FMS and mkmf to the `build` directory led to conflicts in the `build/%/Makefile` and `build/%/path_names` rules, which were causing redundant builds. This patch moves these repositories back into a local `deps` directory, now kept inside of `.testing`.
The Travis environment was updated in order to get a newer GCC compiler version. This was done to enable more aggressive initialization.
The FMS version has been updated in order to permit more aggressive initialization settings in MOM6. This requires a few bugfixes in the newer FMS release.
Flags for initializing reals on stack as signaling NaNs (SNaN) and integers as 2**31 - 1 have been added in this build.
Travis bionic test
This resolves several new issues raised by the current version of
Doxygen (1.8.17). Primarily it addresses the stricter enforcement of
grouping syntax, e.g.
!>@{
...
!>@}
The current code is somewhat inconsistent in its use of !!@{ vs !>@{ ,
and moreso in the closing token. This patch updates these to always
lead with starting Doxygen comment tokens !> .
Exposing these groups also revealed a few undocumented variables, which
have been updated with minimal descriptions for now.
Finally, one subroutine in MOM_horizontal_regridding was causing a
segfault, so it had to be reworked to remove its grouping, so that
individual indices now have descriptions.
- The new FMS has test_ programs that are found by list_paths which do not build properly unless using the FMS Makefile.am method. - The "no libs" test was added to detect namespace collisions that are hidden when building with libraries. For now we'll retain this test but to do so requires a one-line hack to edit the pathnames file.
Fix "no lib" builds
Doxygen 1.8.17 documentation fixes
The target grid for the diagnostic grid update is now based on a assigning a differrent pointer based on the boolean input argument 'intensive'. This is done so that this update is done in a more 'object-oriented' way
This reverts commit 9abcb10.
The model thicknesses
Corrected the units reported for 9 diagnostics, and altered the code so that the diagnostics N2_u and N2_v are only offered if the can be calculated and the proper diagnostics are written if these diagnostics are requested (previously arrays of zeros were always output). All solutions are bitwise identical, but some diagostics in output files change and the available_diags files have altered entries.
Rewrote the subroutine doc_param_time to work like the other doc_param routines, including making the units argument optional, removing the argument layout_param, and adding the new internally visible routine time_string. Because time variables are currently logged as real values using the timeunit argument to log_param_time, these changes do not have a widespread impact. All answers are bitwise identical, but there are some limited interface changes.
- Rename `h_dest` to `h_target` in routine and in signature - Remove extraneous logic
Added or corrected comments describing the units of many of the variables in the ALE code. All solutions are bitwise identical, although there are some unit changes in arguments to unused subroutines.
Originally, the diagnostic arrays were being allocated on the first call generating the diagnostic grid. This seems overly clunky because the size of the grids are known before that. This was also causing a segfault in updates to the new routine. The allocate statements for these arrays are now done right after the number of levels is known
Corrected documented units in comments, corrected spelling errors in comments and removed unused variables. All answers are bitwise identical.
Rescaled the calculations of diagnostics of the integrated mass transports, column integrated temperature and salinity, cell thicknesses and column mass for dimensional consistency testing. All answers are bitwise identical.
Rescaled the density derivatives used in full_convection, smoothed_dRdT_dRdS and user_change_diff. This change requires that new unit_scale_type arguments be passed to these three subroutines. All answers are bitwise identical.
Converted find_interfaces from a function to a subroutine and revised determine_temperature to rescale arguments and internal variables. Also made the declaration of array sizes consistent with other MOM6 code. All answers are bitwise identical, but there are changes to public interfaces.
Removed an unneeded halo update in iceberg_forces. All answers are bitwise identical.
+Corrected diagnostics and diagnostic units
+Corrected doc_param_time
Added grid type arguments to calls to update_ALE_sponge_field so that the internal array pointers set by this routine will use the same indexing conventions as the rest of the MOM6 code. Also added comments describing some arguments and other variables and got rid of some unneeded line continuations in MOM.F90. All answers are bitwise identical, but there are two new arguments to update_ALE_sponge_field.
Added array-syntax notation for a full-array copy in ISOMIP_Tracer.F90. All answers are bitwise identical.
Initialized dMLD_min and dMLD_max in ePBL_column, and corrected a comment in response to helpful reviews from Brandon Reichl and Andrew Shao. Because these two arrays are not used until after the 3rd iteration, this may not matter to the solution, although it should help make the code clearer and avoids unused variables. All answers in the MOM6-examples test cases are bitwise identical.
…anup MOM6: +Corrected the use of array syntax calculations
Corrected the negative CFL branch of PPM_angular_advect in MOM_internal_tides. Simultaneously there was some revision to match other equivalent PPM advection schemes in the MOM6 code and to replace some divisions by a multiplication by a reciprocal. The previous version was sufficiently wrong that it could not ever have been used in any scientifically meaningful solutions, including anything in MOM6-examples. Accordingly, the PPM_angular_advect code was changed without a flag to retain the previous answers. All answers in the MOM6-examples test cases are bitwise identical, and output files are unchanged.
The Makefile has been modified to reduce the amount of output during testing. Output is generally omitted on a successful test. When a test fails, we only display a small portion of the total output. We also now run all tests, even if they fail, in order to give a complete profile of the test failures. Regression testing rules have been integrated into the general rules. Finally, Travis config has been modified to further reduce output, and to run all of tests (make -k).
Test logging is now much shorter, so folding is less important.
CodeCov reporting log is now saved to results/ rather than piped to stdout, further reducing test logging output.
We were saving codecov output to results, but this was breaking the `test.summary` test, which only returns true if `results` is empty. This change should resolve this issue.
…into Hallberg-NOAA-units_cleanup
…g-NOAA/MOM6 into Hallberg-NOAA-improved_ePBL_iterations
…/MOM6 into Hallberg-NOAA-fix_angular_advect
Reduced output during testing
…cean#1113) - gcc/8.3.0 issued `Error: Integer too big for its kind` reported in feedback on PR mom-ocean#1111. The intent was to assume kind=4 in these calculations but apparently our compilers were promoting `mod(dy + 32*(mo + 13*yr), 2147483648)` to kind=8. There were two mistakes in the expression: - the use of `2147483648` in the `mod` is not representable with kind=4; - the `mod` produces negative values and should have been a `modulo`. - This commit reduces the range of the results by one number on the positive side and removes all the negatives.
…er to dev-master-candidate-2020-05-15 solve conflict in: (1) config_src/coupled_driver/MOM_surface_forcing_gfdl.F90 (2) src/core/MOM_forcing_type.F90
(1) add missing halo in MOM_full_convection.F90 (2) remove wrong logic "not" in MOM.F90 at line 2669
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MOM6 update RP.pdf |
DeniseWorthen
approved these changes
Jul 14, 2020
JessicaMeixner-NOAA
approved these changes
Jul 14, 2020
jiandewang
pushed a commit
to jiandewang/MOM6
that referenced
this pull request
Feb 1, 2022
+(*)Make unit_scale_type arguments non-optional
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require to update MOM6 to GFDL latest dev/master (#28)
It turned out that there are two bugs in the original code, see detail discussion at
https://docs.google.com/document/d/1soIwV56zFK8-ISvXFN_fNTdFn2VzynJZ_XoIdvI97j0/edit