User/jml/operation fms2 the reckoning #1033
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…al_condition, added a default case that throws a fatal error if the 't_grid_str' is empty in write_initial_conditions and save_restart
Merge in latest dev/gfdl updates
* dev/gfdl: Bugfix: diabatic_salt_tendency diagnostics in ALE
… facilitate use of new open_file, which requires that these values be associated
…nitialize_ocean_public_type to set the io_domain value in Ocean_sfc%domain, which is required by the new fms-io read_data calls for domain-decomposed netcdf files in xgrid.F90/
Merge in latest dev/gfdl updates
…the domains argument
… routines MOM_open_file, MOM_close_file, and references to file_exists, FmsNetcdfFomainFile_t, read_data, defined in MOM_io to preserve encapsulation.
…e public routine references read_data from new fms_io, made FMSNetCDFDomainFile_t public
…o mpp_open_file and mpp_close_file, all open_file and close_file calls reference the new fms-io interfaces, added a routine to MOM_read_data to deal with the supergrid domain, removed unused open_file and close_file calls, replaced the fms read_data reference and calls with old_fms_read_data. MOM_read_data calls new fms read_data directly without fms2 prepended to the name, replaced old fms reads of netcdf files with new open, read, and close interface calls referenced from MOM_io
…and replaced calls with direct calls to register_variable_attribute
…blic, removed the fms2_ from the routine names
…pp_domain attribute to the new fms MOM_open_file wrapper call, replaced the create_file call with new MOM_open_file, register_field, axis registration routines, write_data, register_variable_attribute, and close_file calls
…and routines, made new fms write_data public
…ariable descriptions are already in a struct, added the field varaiable and attribute registration calls to the i-loop
…nters, put the new io public routines in abc order
…s for axis_data_CS%axis and axis_data_CS%data
…open_file interface
…h the new fms io open, register, write, and close routines
…rface. This accomodates the writing of the vertical coordinate file in MOM_ALE and MOM_coord_initialization.
…ile routines, and call to MOM_open_file. This file is not domain-decomposed, and does not need the mpp_domains from G
…ity with fms_cpu_affinity_set
…OM_io. Added use statements for fms_affinity_set,get to MOM_driver and mom_domains
merge in latest dev/gfdl updates
* dev/gfdl: Segment index added for several OBC segment flags Replaced intent(out) with intent(inout) in EOS Added option to trailer.py for line length excluding comments Adds MOM_random module Adds global extents to hor_index type Correct spelling in HI doxumentation
changed get_affinity and set_affinity to point to new wrappers in fms_affinity.F90 changed file_exist to file_exists in MOM_domains
…inity.F90, and fixed arguments in set_affinity
…ongkindofdoctor/MOM6 into user/jml/operation_fms2_the_reckoning * 'user/jml/operation_fms2_the_reckoning' of github.com:wrongkindofdoctor/MOM6: redirected get_affinity and set_affinity calls to routines in fms_affinity.F90, and fixed arguments in set_affinity added procedure to set the io_layout for 1-pe jobs to restore_state changed get_affinity and set_affinity to point to new wrappers in fms_affinity.F90 changed file_exist to file_exists in MOM_domains
… added pelist definition and argument to open_file call in write_scalar
…ity with fms_cpu_affinity_set added module use fms_affinity fms_affinity_set, fms_affinity_get to MOM_io. Added use statements for fms_affinity_set,get to MOM_driver and mom_domains
- Option -s now specifies the maximum length of lines after stripping out comments. The defaults are for the Fortran standard, not MOM6. MOM6 standard are specified in the Travis-CI invocation of trailer.py.
- niglobal,njglobal are available from the Domain type and usually accessed via a ocean_grid_type function. Modules that do not need the Domain but do use the hor_index type are obliged to use the ocean_grid_type to get the global extent, even though it's just integer information most closely related to the indices. - This commit adds niglobal,njglobal to the hor_index type so that modules that use HI, and only need indices, do not need to the full ocean_grid_type.
- MOM_random provides a wrapper to the Mersenne twister pseudo-random number generator in FMS. In particular it allows for reproducible 2d fields of numbers using the MOM6 domain decomposition. - Commit includes unit tests that check specific values as well as the statistics (the latter are not unit tests but there's no harm in doing them).
In setup_[uv]_point_obc, a number of flags for each segment were assigned without index (OBC%segment%flag), which was causing all segments to be assigned the same value. This could problems with, say, `[uv]_value_needed` flags, which have different values depending on if they are E-W or N-S oriented. This patch adds the index to the assignments.
- For arrays using intent(inout) avoids potential copies and also allows aliasing of arguments which can reduce the overhead of multiple spare arrays in the calling code.
changed get_affinity and set_affinity to point to new wrappers in fms_affinity.F90 changed file_exist to file_exists in MOM_domains redirected get_affinity and set_affinity calls to routines in fms_affinity.F90, and fixed arguments in set_affinity removed extraneous calls to open file from write_field_noDD routines, added pelist definition and argument to open_file call in write_scalar declared variable i in write_scalar removed extraneous open_file and pelist definition from write_field_1d_nodd
…ongkindofdoctor/MOM6 into user/jml/operation_fms2_the_reckoning * 'user/jml/operation_fms2_the_reckoning' of github.com:wrongkindofdoctor/MOM6: added procedure to set the io_layout for 1-pe jobs to restore_state changed get_affinity and set_affinity to point to new wrappers in fms_affinity.F90 changed file_exist to file_exists in MOM_domains Replaced intent(out) with intent(inout) in EOS Segment index added for several OBC segment flags Adds MOM_random module Adds global extents to hor_index type Correct spelling in HI doxumentation Added option to trailer.py for line length excluding comments replaced get_cpu_affinity with fms_cpu_affinity_get and set_cpu_affinity with fms_cpu_affinity_set
…the sum to set_affinity if true, and 1 if false to prevent the new fms_affinity_set routine from evaluating cpuset_sz as 0 for 1-pe/1-thread jobs with openMP enabled
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Hi Jess, given that there are still lots of commits coming in to this PR, and since it will also require a squash at some point, can I request that we close this and re-open once it's ready? |
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@marshallward Sorry about that! I had to resolve issues incorporating the new thread affinity module in the latest FMS updates. but this should be it. If all of the Travis CI tests pass, you, @adcroft, and @MJHarrison-GFDL can proceed with the review of the code when you are able. In the mean time, I will start updating SIS2. |
…et_cpu_affinity cleaned up whitespace and commented out code fixed line length issue in MOM_domains
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Closed while I work through updates for internal gitlab CI tests. |
adcroft
referenced
this pull request
in adcroft/MOM6-examples
Jun 19, 2020
- This version of FMS is a prerequisite to updating calls to FMS ready to try FMS2 I/O behind NOAA-GFDL/SIS2#117 and NOAA-GFDL/MOM6#1033
This was referenced Jun 19, 2020
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This is a draft PR for the MOM6 code with the new fms-io calls so that MOM6 developers can see what the preliminary round of changes looks like. The code compiles with gnu7 in debug on gaea, but still needs more thorough testing. I will change the PR status ( and branch head, if the MOM6 team would prefer to have separate branch to test the new IO similar to fms-io-dev in the FMS repo) when I have finished regression testing. The PR for the alpha tag will also include thorough descriptions of the major changes.