+Enable FMS2 interface reads (includes merge of PR #1165) #1352
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merge in latest MOM updates * GFDL_MOM6/dev/gfdl: (220 commits) Update cache dir for /lustre/f2 Update cache dir for /lustre/f2 Calculate height-related diagnostics in Z Set coord_adapt and coord_slight parameters in H Corrected comments in build_zlike_column +Pass max_depth to initialize_regridding in Z Corrected comments in build_sigma_column Combined scaling factors in build_adapt_column Clarified comments in Idealized_Hurricane +Recast MOM_diag_to_Z to work in units of Z +Recast MOM_ALE_sponge to work in units of Z +Added m_to_Z arg to horiz_interp_and_extrap_tracer Find energetic_PBL column height changes in Z +Find diapyc_energy_req column height changes in Z Use local variables to rescale in MOM_Point_Accel Recast MOM_sum_output to work in units of Z Simplify MOM_diagnostics code +Rescale depth inside of MEKE_lengthScales_0d +Add conversion argument to register_static_field Rescale values reported by PointAccel ...
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* TC4 integration into test suite This patch renames the tc4 test to activate it in the test suite. It also modifies the Makefile to build the input field test scripts. It also modifies the Python build scripts to be PEP8-conformant. We temporarily disable tc4 in the restart tests, since they currently fail. This needs to be addressed before we can merge this into the main branch. The patch does not enable the necessary Python modules for running on Travis, that will also be addressed later. * Travis python support; tc4 Makefile The custom TC4 Makefile has been added (oops), and the presumed Python Ubuntu packages have been added for Travis. * Verify ENABLE_THERMODYNAMICS is True before posting C_p diagnostic * Make tc4 faster * remove trailing whitespace * add unit scaling * fix restart fail for tc4 and some cleanup * remove trailiny ws * Enable tc4.restart test * +Pass timeesteps to tracer diagnostics in [T] Pass timeesteps to the tracer diagnistics routines post_tracer_diagnostics and postALE_tracer_diagnostics and to adiabatic in units of [T}. All answers are bitwise identical. * +Rescaled tracer advective flux diagnostics Rescaled the internal units of the tracer advective flux diagnostics to units of [conc H L2 T-1] for code simplicity and dimensional consistency testing. Also corrected the units of some tracer fluxes as documented in comments and commented out unused elements of the tracer_type. All answers are bitwise identical. * +Pass timesteps to ALE_main in [T] Pass the timesteps to ALE_main, ALE_main_offline, and ALE_main_accelerated in units of [T] for code simplicity and dimensional consistency testing. This also includes the rescaling of remapping-driven tracer tendencies. All answers and diagnostics are bitwise identical. * +Pass timesteps to tracer column_physics in [T] Pass timesteps to the various tracer column_physics routines in [T] for dimensional consistency testing. Also added a new unit_scale_type argument to these routines. All answers are bitwise identical, but there are minor interface changes to 13 subroutines. * +Pass timesteps to applyTracerBoundaryFluxesInOut in [T] Pass timesteps to applyTracerBoundaryFluxesInOut in [T], and use units of [T-1] for internal source and decay rates for the oil tracer and in fluxes of CFCs. Also modified extract_offline_main to return timesteps as real values with units of [T]. Also there is a new unit_scale_type argument to register_oil_tracer. All answers in the MOM6_examples test cases and regression tests are bitwise identical. * Simplified expressions in MOM_PointAccel Simplified expressions inside of MOM_PointAccel, taking into account that all velocities use the same units of [L T-1]. All answers are bitwise identical. * Corrected dimensional epsilons in downscaling Added distinct negligible volumes, face areas, horizonal areas and lengths with proper dimensional rescaling in the downsample field routines. With these changes, downscaled diagnostics should now pass the dimensional rescaling tests, whereas previously there would have been a problem when the numbers used to represent lengths are smaller than about 1e-8 times their MKS values. All answers are bitwise identical without dimensional rescaling. * Simplified expressions in MOM_offline_aux Simplified expressions in distribute_residual_uh_barotropic. All answers are bitwise identical. * Revised wave_speed to return speed in [L T-1] Revised wave_speed to return the internal wave speed in units of [L T-1] and to use mono_N2_depth in units of [Z] for code simplification and expanded dimensional consistency testing. Also revised the internal units of some related diagnostics in calculate_diagnostic_fields. All answers and diagnostics are bitwise identical. * Rescaled internal variables in wave_speed Rescale internal calculations in wave_speed and wave_speeds for greater robustness and dimensional consistency testing. All answers are bitwise identical and pass dimensional scaling tests. * +Changed the units of minimum_forcing_depth to [H] Changed the units of minimum_forcing_depth passed to applyBoundaryFluxesInOut and applyTracerBoundaryFluxesInOut to [H]. All answers are bitwise identical. * Correction of documented units in comments Corrected some units in comments and eliminated some unused variables. All answers are bitwise identical. * Adiabatic clock ID bugfix This patch fixes an initialization bug of the diabatic timer, which was being used to measure adiabatic time but was never initialized if the experiment was configured as adiabatic. We fix this by introducing a separate timer for the adiabatic solver. Although we could have reused the diabatic timer, the addition of a new variable should not add any overhead on modern compilers. * Corrected an OMP declaration Added a variable to an OMP declaration. All answers are bitwise identical, and a recently added compile-time error with openMP was fixed. * Update MOM.F90 Fixed Alistair's embarrassing error. * Dimensional rescaling in MOM_open_boundary.F90 Added rescaling for dimensional consistency testing in MOM_open_boundary.F90, including splitting variables with different units that had previously shared the same variable and adding more extensive documentation of variables. Also changed the dimensions of the timesteps passed to radiation_open_bdry_conds and update_segment_tracer_reservoirs to [T] and added vertical_grid_type and unit_scale_type arguments to open_boundary_init and open_boundary_test_extern_h. All answers are bitwise identical, although some probably bugs have been noted in comments and there are new or altered arguments to several routines. * (*)Fixed invariance bugs in MOM_open_boundary.F90 Corrected dimensional consistency bugs in update_segment_tracer_reservoirs and horizontal indexing and related bugs in gradient_at_q_points with oblique_grad OBCs. These will both change answers in test cases that use some open boundary condition options, but not in any of the MOM6-examples test cases.
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…ons of the routines with the fms-io or fms2-io interfaces added module use statments for fms2_io and MOM_io helper routines to MOM_restart added use_fms2=.true. arguments to save_restart and restore_state calls added write_ic=.true. to the save_restart call in MOM.F90 added module MOM_axis with routines to define and register axes and their metadata added module MOM_read_data_fms2.F90 with wrappers for fms2_io read_data interfaces and required routines added module MOM_write_field_fms2.F90 with wrappers for fms2_io write_data interfaces updated module use statments in MOM_io and MOM_restart to reference routines in MOM_read_data_fms2, MOM_write_field_fms2, and MOM_axis made write_field and create_file interfaces in MOM_io added create_file routines to MOM_io that accept file names or file objects to create/overwrite netcdf files that will be written to via write_field calls fixed compile-time errors added new MOM_read_data routines to MOM_read_data interface in MOM_io added placeholder call for new write_field routines to MOM_io changed use_fms2 to a required first argument in save_restart_fms2 and restore_state_fms2 changed write_ic to a required argument in write_initial_conditions fixed the layer and interface checks in MOM_get_diagnostic_axis_data commented out manual checksum registration in save_restart_fms2 so that internal fms2-io checksum computation is used added checks for time units to restore_state and save_restart added logic to make the restart time 1 to save_restart_fms2 if there is an abnormally large value passed to the routine added interface routine file_exists_FMS2 that uses the fms2_io file_exists call added subroutine get_num_restart_files to MOM_restart that searches for known variants of the input file names and returns then number of restart files available for querying, and the optional list of filepaths added loop to search the files for all mandatory variables in the list of file paths returned to by cal to get_num_restart_files added calls to get the variable dimension names and pass them as arguments to register_restart_field in restore_state_fms2 removed exit from inner variable loop in restore_state_fms2 code cleanup moved missing_fields=0 outside of the CS loop in restore_state_fms2 moved missing_fields=0 outside of the CS loop in restore_state_fms2 converted save_restart and restore_state to interface that call versions of the routines with the fms-io or fms2-io interfaces added module use statments for fms2_io and MOM_io helper routines to MOM_restart added use_fms2=.true. arguments to save_restart and restore_state calls added write_ic=.true. to the save_restart call in MOM.F90 added module MOM_axis with routines to define and register axes and their metadata added module MOM_read_data_fms2.F90 with wrappers for fms2_io read_data interfaces and required routines added module MOM_write_field_fms2.F90 with wrappers for fms2_io write_data interfaces updated module use statments in MOM_io and MOM_restart to reference routines in MOM_read_data_fms2, MOM_write_field_fms2, and MOM_axis made write_field and create_file interfaces in MOM_io added create_file routines to MOM_io that accept file names or file objects to create/overwrite netcdf files that will be written to via write_field calls fixed compile-time errors added new MOM_read_data routines to MOM_read_data interface in MOM_io added placeholder call for new write_field routines to MOM_io changed use_fms2 to a required first argument in save_restart_fms2 and restore_state_fms2 changed write_ic to a required argument in write_initial_conditions fixed the layer and interface checks in MOM_get_diagnostic_axis_data commented out manual checksum registration in save_restart_fms2 so that internal fms2-io checksum computation is used added checks for time units to restore_state and save_restart added logic to make the restart time 1 to save_restart_fms2 if there is an abnormally large value passed to the routine added interface routine file_exists_FMS2 that uses the fms2_io file_exists call added subroutine get_num_restart_files to MOM_restart that searches for known variants of the input file names and returns then number of restart files available for querying, and the optional list of filepaths added loop to search the files for all mandatory variables in the list of file paths returned to by cal to get_num_restart_files added calls to get the variable dimension names and pass them as arguments to register_restart_field in restore_state_fms2 removed exit from inner variable loop in restore_state_fms2 code cleanup removed test workflow directory moved missing_fields=0 outside of the CS loop in restore_state_fms2 converted save_restart and restore_state to interface that call versions of the routines with the fms-io or fms2-io interfaces added module use statments for fms2_io and MOM_io helper routines to MOM_restart added use_fms2=.true. arguments to save_restart and restore_state calls added write_ic=.true. to the save_restart call in MOM.F90 added module MOM_axis with routines to define and register axes and their metadata added module MOM_read_data_fms2.F90 with wrappers for fms2_io read_data interfaces and required routines added module MOM_write_field_fms2.F90 with wrappers for fms2_io write_data interfaces updated module use statments in MOM_io and MOM_restart to reference routines in MOM_read_data_fms2, MOM_write_field_fms2, and MOM_axis made write_field and create_file interfaces in MOM_io added create_file routines to MOM_io that accept file names or file objects to create/overwrite netcdf files that will be written to via write_field calls fixed compile-time errors added new MOM_read_data routines to MOM_read_data interface in MOM_io added placeholder call for new write_field routines to MOM_io changed use_fms2 to a required first argument in save_restart_fms2 and restore_state_fms2 changed write_ic to a required argument in write_initial_conditions fixed the layer and interface checks in MOM_get_diagnostic_axis_data commented out manual checksum registration in save_restart_fms2 so that internal fms2-io checksum computation is used added checks for time units to restore_state and save_restart added logic to make the restart time 1 to save_restart_fms2 if there is an abnormally large value passed to the routine added interface routine file_exists_FMS2 that uses the fms2_io file_exists call added subroutine get_num_restart_files to MOM_restart that searches for known variants of the input file names and returns then number of restart files available for querying, and the optional list of filepaths added loop to search the files for all mandatory variables in the list of file paths returned to by cal to get_num_restart_files added calls to get the variable dimension names and pass them as arguments to register_restart_field in restore_state_fms2 removed exit from inner variable loop in restore_state_fms2 code cleanup removed test workflow directory removed white space updated FMS tag in .testing Makefile fixed argument comments to use doxygen style in MOM_write_field_fms2 code cleanup removed \TODO from MOM_restart fixed documentation for module variables in MOM_read_data_fms2 and MOM_write_field_fms2 removed doxygenized TODO statements removed new MOM_read_data routines from interface, and commented out calls in MOM_io fixed doxygen definitions more doxygen fixes changed save_restart and restore_state to wrapper routines with opitional use_fms2 and write_ic arguments added use_fms2=.true. and write_ic=.true. to save_restart and restore_state calls removed the error messages from append_substring tried reordering the write_ic and use_fms2 checks in save_restart to fix error with invalid memory reference in the MOM.F90 call to save_restart-write_initial_conditions
…ing the use_fms2 and write_ic flags if present to avoid invalid memory reference error added str_len argument to register_variable_attribute calls added support to for rotated fields to write_initial_conditions and save_restart_fms2 removed whitespace
removed use_fms2 optional arguments in save_restart, restore_state, and create_file made use_fms2 a MOM_restart module variable Update MOM_state_initialization.F90 Remove space. Update MOM_ice_shelf.F90 Add space. Update MOM_driver.F90 Add space Update mom_surface_forcing_mct.F90 remove whitespace Update ocean_model_MOM.F90 Add space Update mom_ocean_model_nuopc.F90 Add space Update MOM_surface_forcing.F90 Add space Changes needed work ESM4 to run with new io
Corrected three module use statements in infra/FMS1 to eliminate any dependencies of code in config_src/infra/FMS1 on code in src/framework. These use statements eventually point to the same place as before, but with less indirection. This change should facilitate later steps to compile everything in and under the config_src/infra directories as libraries. All answers are bitwise identical.
Duplicated all of the modules in infra/FMS1 into new copies in infra/FMS2, in preparation for merging in the FMS2 i/o changes to the new infra/FMS2 directory. All answers are bitwise identical, regardless of which config_src/infra directory is used.
Added code to explicitly set a (1x1) io_domain when no other io_layout is specified, complying with changing requirements for 2020 and later versions of FMS, and following the default behavior of previous versions. All answers are bitwise identical.
…om/wrongkindofdoctor/MOM6 into FMS2_io Merged in PR mom-ocean#1165, "Add fms2-io to MOM restart interfaces", but with modifications to move the new files to config_src/infra/FMS2, where they belong, and to avoid inappropriate changes to code in the src/framework directory. All existing tests are passing with config_src/infra/FMS1, but the new changes require that the version of FMS used with config_src/infra/FMS2 to at least 2020.03, and this disables all of our AM2-based coupled test cases (due to the deliberate decision from the GFDL Modeling Systems group to drop support for this older atmospheric model). Although the new code reproduces the previous answers in ocean_only and ice_ocean_SIS2 test cases with the intel and gnu compilers, with the pgi (19.10.0) compiler there are fatal errors in all ice_ocean_SIS2 cases and in ocean_only cases driven by data override. The last version of FMS where the pgi compiler works in all cases is 2019.01. The problem in some ocean_only cases appears to be related to the use of FMS2 i/o calls in the data_override routines. With the ice_ocean_SIS2 cases, the error message in with the pgi compiler is "mpp_broadcast_text: broadcasting from invalid PE.". (Note that with the newer versions of FMS (2020.03 and later), OM_1deg requires that the namelist file for data_override_nml has the added line {reproduce_null_char_bug = .true.} to reproduce the previous answers, but it is a fatal error to add this setting with FMS versions before 2020.03.)
Eliminated scale_data from MOM_read_data_fms2, as it was duplicative of rescale_comp_data from MOM_domain_infra.F90. Also eliminated the optional scale argument from the fms2 write_field routines, because this scaling is already handled in the framework/MOM_io.F90 routines, and because the way the scaling was implemented with a pointer to defeat the intent(in) of the data array to the write routines was a deviously terrible idea that would cause endless problems. Because the mpp_domain in the MOM_domain_types have been modified to always have an io_domain set, the test and calls setting an io_domain in all of the fms2 read_data and fms2 write_data routines. In addition, there is no longer a need for a routine to read specifically from the supergrid, so the fms2 MOM_read_data_2d_supergrid routine was eliminated. The code compiles with these changes, but none of this fms2 I/O code is exercised yet in MOM6, so of course all answers are bitwise identical.
Replaced the two optional arguments xPosition and yPosition to the two routines wrapped by the interface MOM_register_variable_axes in MOM_axis.F90 with a single optional argument, position. Also dramatically refactored the code in read_data_fms2.F90 to eliminate unused variants and adding more granular subroutines to dramatically reduce duplicative code, eliminating several (unexercised) bugs in the process; that file went from 1441 lines long to 924. The code compiles with these changes, but none of this fms2 I/O code is exercised yet in MOM6, so of course all answers are bitwise identical.
Cleaned up MOM_restart.F90 in the wake of the recent merge of FMS2 I/O related changes into MOM6. The changes include calling the recently added functions get_variable_byte_size and get_num_restart_files, and revising the names of several variables in open_restart_units and the order in which the count of files is incremented for greater clarity. There are also a number of duplicative comments that were removed while others were reformatted. All answers and output are bitwise identical.
Added the option to use FMS2 interfaces to read variables in the FMS2 version of MOM_io_infra.F90. For now, this is controlled by a hard-coded module variable, FMS2_reads, in MOM_io.F90. Also extensively revised MOM_read_fms2.F90 to add the new public subroutine prepare_to_read_var that is used from MOM_io_infra.F90, to systematically determine the directions that axes in files using the cartesian_axis attribute before resorting to using the axis names or units. All of the subroutines from MOM_read_fms2.F90 whose functionality has been merged into MOM_io_infra.F90 have now been removed. All answers are bitwise identical and reproduce the FMS1 test cases, but there is a new publicly visible routine.
Codecov Report
@@ Coverage Diff @@
## dev/gfdl #1352 +/- ##
============================================
- Coverage 45.84% 45.81% -0.04%
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Files 229 234 +5
Lines 71704 72693 +989
============================================
+ Hits 32876 33306 +430
- Misses 38828 39387 +559
Continue to review full report at Codecov.
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Hallberg-NOAA
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Hallberg-NOAA
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adcroft
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Mar 23, 2021
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This PR reconciles MOM6 #1165 with the latest version of the MOM6 code and
modifies it to work with the new MOM6 software structure. The changes within the
/config_src/infra/FMS2 directory include code that uses the new FMS2 interfaces
to read files, but exactly match the publicly visible interfaces that are also
offered from /config_src/infra/FMS1. There are minor restructuring changes in
the end to code in MOM_restart.F90 for greater clarity, and there are some new
optional arguments, but it is functionally equivalent to what is already on the
main branch of MOM6. The commits (apart from merges) in this PR include:
https://github.com/wrongkindofdoctor/MOM6 into FMS2_io
(The following commits were inherited from NOAA-GFDL/MOM6 PR#1165, along with 59 merges.)