Debug gdas.x NaN abort: update sorc/fv3-jedi to Gaussian-grid read path (RussTreadon-NOAA fork @81a8e1c)

[Copilot]

gdas.x (3D-Var) aborts with NaN in H(x) when reading backgrounds from Gaussian-grid GFS files via the new IOStructuredGrid read path. Root cause: missing std::isnan guard in readVarToStructuredAtlasField.

Root cause

In IEEE 754, std::abs(NaN) > threshold and NaN == x both return false, so the existing fill-value check in IOStructuredGrid::readVarToStructuredAtlasField silently passes NaN float values from the NetCDF background files into the Atlas FieldSet. Those NaN values survive GlobalInterpolator::apply() onto the cubed-sphere grid and propagate into H(x).

// 81a8e1c — NaN bypasses every test; propagates silently to H(x)
const bool isMissing = (std::abs(val) > kMissingThreshold)
                     || (val == fillValue)
                     || (val == missingValue);

// Fix (companion PR to RussTreadon-NOAA/fv3-jedi)
const bool isMissing = std::isnan(val)           // must be first
                     || (std::abs(val) > kMissingThreshold)
                     || (val == fillValue)
                     || (val == missingValue);

Confirmed by examining atmanlvar.yaml: background uses filetype: structured grid, gridtype: gaussian with files gdas.t18z.atm.f006.nc / gdas.t18z.sfc.f006.nc on a C96 (F96) geometry.

Changes

• .gitmodules — sorc/fv3-jedi URL/branch updated from jcsda/fv3-jedi@develop (SHA 3d29a037, partial Gaussian path) to RussTreadon-NOAA/fv3-jedi@copilot/debug-segmentation-fault-issue (SHA 81a8e1c), which provides the complete Gaussian-grid read/write path and MPI GlobalInterpolator desync fixes. TODO comment added to restore upstream once fixes land in jcsda/fv3-jedi.
• sorc/fv3-jedi — submodule pointer bumped 3d29a037 → 81a8e1c.

Companion PRs

• RussTreadon-NOAA/fv3-jedi — add std::isnan(val) as the first term of isMissing in IOStructuredGrid::readVarToStructuredAtlasField (required before the NaN abort is fully resolved; submodule pointer will need a second bump to that SHA).

Issues

Automated CI tests to run in Global Workflow

• atm_jjob
• C96C48_ufs_hybatmDA
• C96C48_hybatmsnowDA
• C96_gcafs_cycled
• C48mx500_3DVarAOWCDA
• C48mx500_hybAOWCDA
• C96C48_ufsgsi_hybatmDA
• C48_ufsenkf_atmDA
• C96C48_hybatmDA

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[RussTreadon-NOAA]

The attached file, atmanlvar.yaml, is the input yaml read by gdas.x
atmanlvar.yaml

Note: https://github.com/RussTreadon-NOAA/fv3-jedi/tree/copilot/debug-segmentation-fault-issue at RussTreadon-NOAA/fv3-jedi@81a8e1c contains code to read backgrounds from gaussian grid GFS atmospheric and surface files.