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Added a comment in USER_initialize_thickness and removed a constant that is being multiplied by 0. All answers are bitwise identical.
…OAA/MOM6 into Hallberg-NOAA-use_unit_scaling_type
…e-2018-10-15 Merge dev/master candidate 2018 10 15
Corrected an openMP directives that omitted a recently added unit_scale_type variable. All answers are bitwise identical, and the code once again compiles with openMP enabled.
Recast the internal calculations in the MOM6 ice shelf code and several persistent ice shelf state variables to use vertical height units of Z in place of m for dimensional consistency testing. This includes adding new unit_scale_type arguments to several routines and new elements to the ice shelf control structure. All answers are bitwise identical in the MOM6 test cases, including rescaling Z over a large range.
Changed the units of fluxes%ustar and forces%ustar from m/s to Z/s for dimensional consistency testing. This includes adding new unit_scale_type arguments to several routines and new elements to the top-level ocean model control structures. All answers are bitwise identical in the MOM6 test cases, including rescaling Z over a large range.
Split two lines that had become longer than 120 characters with the recent addtion of new subroutine arguments and scaling factors. All answers are bitwise identical.
so as to include topographic beta effect in computing Rhines scale
Changed the units of fluxes%ustar_shelf and fluxes%ustar_berg from m/s to Z/s for dimensional consistency testing. All answers are bitwise identical in the MOM6 test cases, including rescaling Z over a large range.
to remove the redundant copy of G%bathyT, lat, and lon
Corrected the grid staggering locations indicated in 6 comments, the text of a seventh and added units in an eighth. All answers are bitwise identical.
Use US%m_to_Z in place of G%Zd_to_m to convert units from m to Z in set_up_ALE_sponge_vel_field_varying, whic required adding a unit_scale_type argument. All answers are bitwise identical.
Recast internal depth and height variables in MOM_internal_tides to use units of Z instead of m. This required adding a unit_scale_type arguments to internal_tides_init and itidal_lowmode_loss, and a modified call from diabatic_driver_init. All answers are bitwise identical.
Recast internal depth and height variables in MOM_tidal_mixing to use units of Z instead of m. This required adding a unit_scale_type arguments to the internal subroutines read_tidal_energy and read_tidal_constituents. Also eliminated the use of where statements and array syntax, which are strongly discouraged because they can operate on uninitialized points in the halo regions. All answers are bitwise identical.
Use US%m_to_Z in place of 1/G%Zd_to_m to convert units from m to Z in tracer_Z_init. This required adding a unit_scale_type argument to tracer_Z_init and 4 subroutines that used the previous interface to tracer_Z_init. All answers are bitwise identical.
This is necessary to allow for instabilities and turbulence to develop in a zonally symmetric channel configuration..
Added a unit_scale_type argument to diag_remap_update and a pointer to a unit_scale_type structure to diag_mediator_init and store a this pointer in the diag_ctrl type, all to accomodate rescaling of depths via US%Z_to_m instead of G%Zd_to_m. All answers are bitwise identical.
Added a unit_scale_type argument to MOM_initialize_fixed and moved the call to rescale_dyn_horgrid_bathymetry into MOM_initialize_fixed immediately after the call to MOM_initialize_topography. Also added a unit_scale_type argument to mask_outside_OBCs and open_boundary_config to accomodate rescaling of depths via US%Z_to_m instead of G%Zd_to_m. All answers are bitwise identical.
- Cosmetic clean up of comments - added adjustl() to string comparison - for some reason a leading whitespace was present with Intel compiler but not GNU.
Feature to flag and trap cases where obsolete restart fields are attempted to be used
- Uses stages to parallelize testing process - Adds a doxygen job that tests for doxygen errors - Reduces dependency on other repositories - No longer uses scripst from MOM6-examples/tools/tests/Travis-MOM6/ - Still uses configurations from MOM6-examples/ocean_only/ - Adds test building/using a debug executable - Adds a .testing/ directory - Uses the latest xenial image on Travis (with openmpi) Todo: - Add code coverage (needs more experiments) - Break dependence on MOM6-examples (long term project) - Add other portable tests (e.g. parameter scaling, rotation, etc)
- Like the original cased tracer, the ca13csed tracer used in generic_BLING.F90 needs to be initialized to zero at all subsurface layers (when do_13c = .true.)
Set ca13csed to zero at k>1
Re-factor of Travis-CI usage
With the xanadu release of FMS, the coupler_types module within FMS has finally been properly scoped without adding unnecssary dependencies. The coupler_types.F90 files in the MOM6 config_src/solo_driver directories are no longer needed. In addition, the routines inside coupler_util.F90 files have not been used anywhere in MOM6 for some time, their functionality being provided via interfaces inside the coupler_types_mod. These 5 files have now been removed. All answers are bitwise identical.
Added unit_scale_type arguments to several subroutines in the nuopc_driver directory, added a unit_scale_type element to the nuopc_driver versoin of ocean_state_type, and use this argument to appropriately rescale forces%ustar for dimensional consistency testing. These changes are required to go with the dev-master-candidate-2018-04-22 updates to MOM6. With these changes, the code in origin/dev-master-candidate-2018-04-22 compiles up through the nuopc_driver version of MOM_ocean_model.o.
This patch appends a checksum for the dependencies of the depth and area
lists stored in the Depth_list.nc file, which are used to compute
diagnostics based on APE.
The data in Depth_list.nc depends on the grid fields, and may not be
reproducible when such grids are constructed internally using compiled
code within the executable. This issue was observed in the
'double_gyre' experiment when a PGI-compiled executable was tested using
a Depth_list.nc file generated by a GNU-compiled executable.
By appending a checksum for the grid fields used to compute
Depth_list.nc, we can ensure that the data is consistent with the
experiment grid data. Grid data which is read from external files, such
as mosaic or topography fields, are unaffected by this issue.
This patch improves the reproducibilty of standard diagnostics, such as
total energy, but has no impact on the reproducibility of the internal
model dynamics, which does not depend on Depth_list.nc.
Checksums are computed for the G%bathyT and masked G%areaT grid fields
using the FMS mpp_checksum subroutine, which require collective
operations, and are stored as hex strings in global attributes of the
netCDF file. Strings are used to remain consistent with FMS restart
checksums, and to avoid an observed re-casting of 8-byte integers to
4-bytes by the netCDF library. Attribute names are based on the grid
variable names.
Two flags have been introduced to control this behavior:
REQUIRE_DEPTH_LIST_CHECKSUMS (default: True)
This flag will abort the run if the Depth_list.nc file is present
and checksums are absent from the file. Although this could impose
greater restrictions on existing runs, few runs are configured to
save the depth list file (READ_DEPTH_LIST) and the default behavior
is to reconstruct these lists on every run.
UPDATE_DEPTH_LIST_CHECKSUMS (default: False)
When REQUIRE_DEPTH_LIST_CHECKSUMS is set to false, this flag will
automatically update the checksums of the Depth_list.nc file. While
this can affect the reproducibility of APE diagnostics, it will
ensure the reproducibility of such diagnostics in subsequent runs.
Additional documentation of the parameters used to store Depth_list.nc attribute names was added.
The depth checksum is now replaced with masked depth, mask2dT * bathyT, and the calculation of the depth list has also been updated to use the masked depth. Various style conformance changes, such as contraction of do and if terminations (enddo, endif) and reduction of whitespace in various multiline function call, has also been applied. Finally, the attribute name docstrings were updated for clarity.
- There is no source code change in this commit. - The switch to the xanadu version of FMS and coupler moves source code between repositories, and therefore requires new build paths which are wired into the testing scripts. This commit checks out a specific version of the gitlab testing scripts along with a xanadu commit of MOM6-examples (which is on branch xanadu-fms). - Once the dev/gfdl branch of MOM6-examples has been rolled forward to xanadu we will return the commit used for gitlab testing to the HEAD of dev/gfdl.
Using the masked depth (mask2dT * bathyT) was observed to change energy values within floating point precision, so the changes have been reverted. This may be revised at a later time, when we are prepared to update the energy stats to the new values in the regression tests. The depth checksum attribute has also been renamed to reflect this change. This will allow us to re-define the variable as masked at some later date, and can distinguish between the masked and unmasked checksums during testing.
gitlab: specify MOM6-examples and script commits
Depth list repro
The calculation of beta in the MEKE module had an explicit division by zero when computing the lateral topography derivatives, which were raising floating point exceptions in the debug builds. This occurs in the MEKE_equilibrium and MEKE_lengthScales functions. This issue was not observed in the production tests due to MEKE_TOPOGRAPHIC_BETA always being set to zero. When FPEs are disabled, the 0 * (1./0.) operation produces a NaN which is passed to a max() function, which ignores the NaN and always returns the other value. We resolve this by explicitly checking for zero values in bathyT and setting the topographic beta to zero when this term is zero. While this could potentially change the value of the Rhines scale, these values only occur over land, which are in general masked, and should not affect the calculation. The unoptimized expressions were retained, but recommended changes which reduce the number of divisions were included in comments. No value changes were observed in our test suite, and the patch should be bitwise reproducible. Minor changes: - We do not calculate the topographic beta term if the scaling factor, MEKE_TOPOGRAPHIC_BETA is zero - the default value of beta was unset in MEKE_lengthScales was unset when CS%use_old_lscale is True, so we set this to zero. - Minor whitespace and index syntax changes
…OAA/MOM6 into Hallberg-NOAA-unified_coupler_types
feiyulu
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Latest changes from MOM dev/gfdl
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Sep 13, 2019
…_salt_coeffs Optional use of differing restoring piston velocities for temp and salt
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