Removal of FMS1 I/O from FMS2 I/O infra

[marshallward]

This patch removes the calls to FMS1 I/O (fms_io_mod, mpp_io_mod) from the FMS2 infra layer, and now exclusively uses FMS2 for those operations.

FMS2 I/O is currently restricted to files which use domains; files which do not use them are delegated to the native netCDF layer. The reasoning for this is that FMS is required to define the formatting of domain-decomposed I/O; for single-file I/O, this is not necessary.

This does not remove all references to FMS1 I/O from MOM6, only those in the I/O layer.

Several minor changes are included to accommodate the change:

• MOM restart I/O now always reports its MOM domain. Previously, the domian was omitted when PARALLEL_RESTARTFILES was false, in order to trick FMS into handling this as a single file. We now generate a new domain with an IO layout of [1,1] when single-file restarts are requested.

• The interface acceleration (g') was incorrectly set to the layer grid (Nk) rather than the interface grid (Nk+1). This did not appear to change any answers, but when Vertical_coordinate.nc was moved to the netCDF layer, it detected this error. This is fixed in this patch.

[codecov]

Codecov Report

Merging #343 (d7d123b) into dev/gfdl (ded1382) will increase coverage by 0.01%.
The diff coverage is 72.00%.

❗ Current head d7d123b differs from pull request most recent head 411dde5. Consider uploading reports for the commit 411dde5 to get more accurate results

@@             Coverage Diff              @@
##           dev/gfdl     #343      +/-   ##
============================================
+ Coverage     38.12%   38.14%   +0.01%     
============================================
  Files           269      269              
  Lines         75622    75635      +13     
  Branches      13911    13915       +4     
============================================
+ Hits          28832    28849      +17     
+ Misses        41588    41584       -4     
  Partials       5202     5202              

Impacted Files	Coverage Δ
src/framework/MOM_restart.F90	32.76% <0.00%> (ø)
src/framework/MOM_io_file.F90	50.00% <60.00%> (+0.71%)	⬆️
config_src/infra/FMS1/MOM_domain_infra.F90	36.44% <80.00%> (+0.32%)	⬆️
src/ALE/MOM_ALE.F90	45.09% <100.00%> (ø)
src/ALE/MOM_regridding.F90	28.73% <100.00%> (ø)
src/framework/MOM_io.F90	30.49% <100.00%> (+0.06%)	⬆️
src/initialization/MOM_coord_initialization.F90	55.81% <100.00%> (ø)

... and 4 files with indirect coverage changes

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[marshallward]

I've tested this in our regression suite, but there's lots of potential points of I/O failure. @MJHarrison-GFDL @kshedstrom If either of you could test this on any OBC experiments, or point me to them, that would be very helpful.

[kshedstrom]

I see no problems except that some of my cases generated a Vertical_coordinate file instead of a Vertical_coordinate.nc file. The contents appear to match, though.

[marshallward]

Thanks, that is reassuring. As for Vertical_coordinate, we removed the logic which checks and adds the .nc if it's missing. We also set the default name to Vertical_coordinate.nc. Is it set to Vertical_coordinate in one of your files maybe?

[kshedstrom]

I don't think so. One example case is here: https://github.com/ESMG/ESMG-configs/tree/dev/esmg/ocean_only/seamount/z
Its friend the layer case has it right, while the sigma case is also wrong.

[klindsay28]

There's an occurrence of the string Vertical_coordinate without an .nc suffix in MOM_ALE.F90, in subroutine ALE_writeCoordinateFile, that this PR doesn't modify.

MOM6/src/ALE/MOM_ALE.F90

Lines 1457 to 1461 in 1bb66a4

	character(len=240) :: filepath
	filepath = trim(directory) // trim("Vertical_coordinate")
	call write_regrid_file(CS%regridCS, GV, filepath)

Could that be the cause of what @kshedstrom is seeing?

[kshedstrom]

Also, that's ocean_only behaving. Is there a SIS2 patch coming?

//import/c1/AKWATERS/kate/ESMG/ESMG-configs/src/SIS2/src/SIS_sum_output.F90:373:74:

                        action=APPEND_FILE, form=ASCII_FILE, nohdrs=.true.)
                                                                          1
Error: Type mismatch in argument ‘io_handle’ at (1); passed INTEGER(4) to TYPE(file_type)

[marshallward]

@klindsay28 That certainly looks like it would drop the .nc, thanks for finding that. I'll see if it can be safely renamed.

@kshedstrom The plan to is to get MOM6 updated while supporting the legacy API for SIS2, and then flip the SIS2 API. Not always possible, but I think that one might work.

(I guess none of our tests are calling write_ice_statistics...)

[kshedstrom]

That patch took care of the one problem.

[marshallward]

open_ASCII_file was added to MOM6 framework some time ago, so it should be safe to flip over to that in SIS2. I will test it at some point today.

[marshallward]

Hopefully this patch to SIS2 will fix the ASCII I/O issue.

https://github.com/NOAA-GFDL/SIS2/pull/193/files

[kshedstrom]

Yes, good to go!

[marshallward]

I've pushed the requested cleanups here (mainly refactor + resolving conflicts).

[Hallberg-NOAA]

All of my concerns with this PR have been addressed, and this PR is passing the pipeline testing at
gitlab.gfdl.noaa.gov/ogrp/MOM6/-/pipelines/18922.