Upgrade FMS IO to FMS2 IO by DavidNew-NOAA · Pull Request #1239 · JCSDA-internal/soca

DavidNew-NOAA · 2026-04-28T19:53:41Z

Description

Update FMS IO to FMS2 IO

Issue(s) addressed

Resolves #1225

Dependencies

N/A

Impact

Expected impact on downstream repositories:

N/A

Manual Testing Instructions (optional)

If you would like your reviewers to manually build and test the change, please include
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Checklist

I have performed a self-review of my own code
I have made corresponding changes to the documentation
I have run the unit tests before creating the PR

Replace fms_io_mod with fms2_io_mod across all Fortran source files: - soca_balance_mod.F90: Replace read_data from fms_mod with open_file/read_data/close_file from fms2_io_mod - soca_geom_mod.F90: Replace restart_file_type with FmsNetcdfDomainFile_t, register_restart_field/restore_state/save_restart with open_file/register_restart_field/read_restart/write_restart/close_file, remove fms_io_init/fms_io_exit and associated counter - soca_fields_mod.F90: Same pattern replacements plus replace file_exist/field_exist with open_file/variable_exists Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Agent-Logs-Url: https://github.com/DavidNew-NOAA/soca/sessions/79ffa8fd-153d-4e6d-a50b-0f9b31130309

Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Agent-Logs-Url: https://github.com/DavidNew-NOAA/soca/sessions/79ffa8fd-153d-4e6d-a50b-0f9b31130309

…art for writes Use read_data() for all file reads instead of register_restart_field + read_restart, since input files (gridspec, ocean data, ice data) may not have restart metadata. Add is_restart=.true. to open_file for write operations so register_restart_field + write_restart works correctly when creating new files. Agent-Logs-Url: https://github.com/DavidNew-NOAA/soca/sessions/40ac97e7-ffa8-4a2f-bc1b-e089f96badc9 Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>

FMS2's register_restart_field requires explicit dimension names when writing (non-read-only). Added: - ["xaxis_1"] for 1D x-axis variables (lonh, lonq) - ["yaxis_1"] for 1D y-axis variables (lath, latq) - ["xaxis_1", "yaxis_1"] for 2D domain-decomposed variables - ["xaxis_1", "yaxis_1", "zaxis_1"] for 3D domain-decomposed variables Agent-Logs-Url: https://github.com/DavidNew-NOAA/soca/sessions/4a7f62e8-b633-428b-acfa-7788b715560a Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com>

Copilot

Pull request overview

Updates SOCA’s Fortran I/O integration to use fms2_io_mod (FMS I/O v2) APIs, addressing build failures when fms_io_mod is unavailable/incompatible (Issue #1225).

Changes:

Replace legacy fms_io_mod / fms_mod: read_data usage with fms2_io_mod (open_file, read_data, close_file).
Rework geometry gridspec read/write paths to use FMS2 NetCDF domain file objects and restart-writing APIs.
Update field reading/writing and variable existence checks to use FMS2 (variable_exists) and file-object-based access.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 6 comments.

File	Description
`src/soca/LinearVariableChange/Balance/soca_balance_mod.F90`	Switches dc/dT Jacobian input read to FMS2 file-object I/O.
`src/soca/Geometry/soca_geom_mod.F90`	Migrates gridspec read/write from legacy restart API to FMS2 open/read/close and restart writing with axis/field registration.
`src/soca/Fields/soca_fields_mod.F90`	Migrates restart/state I/O and existence checks to FMS2, including overwrite/write-restart workflow.

Comments suppressed due to low confidence (1)

src/soca/Fields/soca_fields_mod.F90:580

This if (variable_exists(...)) then block has an empty THEN branch, which makes the intent unclear and is easy to misread. Consider inverting the condition (e.g., if (.not. variable_exists(...)) then ...) so the non-default path is explicit.

              if(variable_exists(restart, self%fields(f)%metadata%io_name)) then
              else
                call seaice_categories_vars%push_back(self%fields(f)%name)
                cycle
              end if

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Copilot · 2026-04-28T19:58:21Z

+      do v = 1, size(atlasVars)
+        call read_data(geom_restart, atlasVars(v), fieldDataVars(:,:,v))
+      end do
+      call close_file(geom_restart)


If open_file(geom_restart, ...) fails here, fieldDataVars stays at its default values and the code proceeds to populate atlas fields, which can silently corrupt the geometry-derived fields. Consider failing fast (or at least logging) when the gridspec cannot be opened/read.

Suggested change

call close_file(geom_restart)

call close_file(geom_restart)

else

write(*,*) "ERROR: failed to open geom_grid_file: ", trim(str)

error stop "Unable to read geometry gridspec file"

Copilot · 2026-04-28T19:58:21Z

+    end do
+
+    call write_restart(geom_restart)
+    call close_file(geom_restart)


If open_file(geom_restart, ...) fails, this routine silently produces no output file. Given this is a write path, consider handling the failure explicitly (abort or log an error including the target path) so failures aren't missed in batch workflows.

Suggested change

call close_file(geom_restart)

call close_file(geom_restart)

else

write(*, '(A)') 'ERROR: soca_geom_write failed to open geometry restart file for writing: ' // trim(str)

error stop

Copilot · 2026-04-28T19:58:22Z

-     call free_restart_type(restart)
+     if (open_file(restart, str, "read", self%geom%Domain%mpp_domain)) then
+       call read_data(restart, 'h', h_common)
+       call close_file(restart)


When remap_filename is provided, failing to open_file leaves h_common as all zeros and the code continues, which will produce incorrect vertical remapping results. Consider treating an open_file failure here as fatal (or at least emitting a clear error) since h_common is required for the remap path.

Suggested change

call close_file(restart)

call close_file(restart)

else

error stop "soca_fields_mod: failed to open remap_filename; common vertical coordinate 'h' is required for remapping"

Copilot · 2026-04-28T19:58:22Z

        allocate(vars(n))

-        ! for each variable, setup to read
+        ! open the file for reading
+        if (.not. open_file(restart, filename, "read", self%geom%Domain%mpp_domain)) cycle
+


If open_file(restart, ...) fails, the code cycles after allocate(vars(n)) without deallocating vars, leaking memory and leaving partially-initialized state for the next loop iterations. Deallocate vars (and any nested allocations if added later) before cycle, or move the allocation to after a successful open_file call.

Copilot · 2026-04-28T19:58:22Z

+    ! open file, register fields, write, and close
+    if (open_file(restart, domain_filename, "overwrite", self%geom%Domain%mpp_domain, is_restart=.true.)) then
+      n=0
+      do f=1,size(self%fields)
+        if (self%fields(f)%metadata%io_file /= domains(d)) cycle
+        n = n + 1
+        if (vars(n)%afield%shape(1) == 1) then
+          call register_restart_field(restart, self%fields(f)%metadata%io_name, &
+              vars(n)%data(:,:,1), ["xaxis_1", "yaxis_1"])
+        else
+          call register_restart_field(restart, self%fields(f)%metadata%io_name, &
+              vars(n)%data(:,:,:), ["xaxis_1", "yaxis_1", "zaxis_1"])
+        end if


register_restart_field is called with axis names (xaxis_1, yaxis_1, zaxis_1) but this routine never registers those axes on the file object (unlike soca_geom_write, which calls register_axis). If fms2_io_mod does not auto-create these axes, this will fail at runtime or create malformed files. Register the required axes (including zaxis_1 when needed) before registering fields, and ensure the axis definitions (sizes/metadata) are consistent with the arrays being written.

Copilot · 2026-04-28T19:58:22Z

+      call read_data(geom_restart, "mask2d",  self%mask2d)
+      call read_data(geom_restart, "mask2du", self%mask2du)
+      call read_data(geom_restart, "mask2dv", self%mask2dv)
+      call close_file(geom_restart)


If open_file(geom_restart, ...) fails, geometry arrays remain at their default/placeholder values and initialization continues, which can lead to hard-to-diagnose downstream errors. Consider handling the failure explicitly (e.g., abort with a clear message including the filename) rather than silently skipping the reads.

Suggested change

call close_file(geom_restart)

call close_file(geom_restart)

else

error stop "Failed to open geometry restart file for reading: " // trim(str)

Copilot AI and others added 8 commits March 23, 2026 17:12

Initial plan

47e0039

Fix endif/end if consistency in ice variable checks

f2f3bbd

Co-authored-by: DavidNew-NOAA <134300700+DavidNew-NOAA@users.noreply.github.com> Agent-Logs-Url: https://github.com/DavidNew-NOAA/soca/sessions/79ffa8fd-153d-4e6d-a50b-0f9b31130309

Merge branch 'develop' into copilot/upgrade-fms-io-to-fms2-io-again

7820ace

Update

575a5d0

Merge branch 'develop' into feature/fms-to-fms2

97cd6e8

DavidNew-NOAA requested a review from Copilot April 28, 2026 19:53

DavidNew-NOAA changed the title ~~Feature/fms to fms2~~ Upgrade FMS IO to FMS2 IO Apr 28, 2026

Copilot started reviewing on behalf of DavidNew-NOAA April 28, 2026 19:54 View session

Copilot AI reviewed Apr 28, 2026

View reviewed changes

Correct dimension character lenght

456d921

eap mentioned this pull request May 6, 2026

Migrate SOCA IO from fms_io to fms2_io #1241

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DavidNew-NOAA closed this May 6, 2026

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Upgrade FMS IO to FMS2 IO#1239

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DavidNew-NOAA commented Apr 28, 2026

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