Derecho site config update for develop; bug fix in setup-meta-modules

[climbfuji]

Note

Added @rickgrubin-noaa/@jim-p-w for the Derecho site config updates, and @AlexanderHrabski-NOAA/@eap for the setup-meta-modules updates.

Description

1. Site config update for Derecho. New environments are based on ncarenv-basic; these require unsetting environment variables (removing entries from PATH and LD_LIBRARY_PATH that ncarenv-basic and ncarenv set and that absolutely shouldn't be in there).
2. Uncovered while working on the Derecho site config: The syntax for Spack's environment modification unset is different than the others: it takes a list of environment variable names, not a dictionary (key : value). This PR fixes it and configures an additional environment modification (remove_path) in spack stack setup-meta-modules.

Dependencies

None

Issues addressed

Add any issues here that this PR closes or is related to. Use "Resolves" or "Closes" to automatically close issues when the PR is merged. Using "Working towards" or "Related to" for other cases.

Applications affected

List all known applications (UFS WM, JEDI, SRW, etc.) intentionally or unintentionally affected by this PR.

Systems affected

List all systems intentionally or unintentionally affected by this PR.

Testing

• CI: Note whether the automatic tests (GitHub actions tests that run automatically for every commit) pass or not
  • GitHub actions CI tests pass
  • GitHub actions CI tests do not pass (provide explanation)
  • GitHub actions CI tests skipped (provide explanation if necessary)
• New tests added: List and describe any new tests added to GitHub actions
  • ...
• Additional testing: Add information on any additional tests conducted
  • See below

Additional testing on Derecho

THIS SECTION IS STILL BEING UPDATED

jedi-bundle

GCC

Built jedi-bundle with gcc@14.3.0 stack and ran ctests. Had to comment out pyiri-jedi because it complained about a missing fortranformat module, even though the py-fortranformat module was loaded.

Module load instructions

module --force purge

module use /lustre/desc1/scratch/heinzell/spst-derecho-20260717/envs/ue-gcc-14.3.0/modules/Core
module load stack-gcc/14.3.0
module load stack-cray-mpich/8.1.32
module load jedi-fv3-env/1.0.0
module load jedi-mpas-env/1.0.0
module load py-fortranformat

Ctest failures:

Total Test time (real) = 2692.59 sec

The following tests FAILED:
        215 - oops_qg_increment (Failed)                        executable oops
        2114 - ioda_bufr_python_encoder (Failed)                 ioda script
        2115 - ioda_bufr_python_parallel (Failed)                ioda mpi script
        3426 - fv3jedi_staticb_nicas_gfs (Failed)                ci_flake_disable fv3-jedi fv3jedi mpi script
        3428 - fv3jedi_staticb_split_nicas_gfs (Failed)          ci_flake_disable fv3-jedi fv3jedi mpi script
        3429 - fv3jedi_staticb_dirac_local_gfs_6pe (Failed)      ci_flake_disable fv3-jedi fv3jedi mpi script
        3430 - fv3jedi_staticb_dirac_local_gfs_12pe (Failed)     ci_flake_disable fv3-jedi fv3jedi mpi script
        3431 - fv3jedi_staticb_dirac_global_gfs_6pe (Failed)     ci_flake_disable fv3-jedi fv3jedi mpi script
        3432 - fv3jedi_staticb_dirac_global_gfs_12pe (Failed)    ci_flake_disable fv3-jedi fv3jedi mpi script
        3441 - fv3jedi_staticb_cor_geos (Failed)                 ci_flake_disable fv3-jedi fv3jedi mpi script
        3442 - fv3jedi_staticb_nicas_geos (Failed)               ci_flake_disable fv3-jedi fv3jedi mpi script
        3460 - fv3jedi_hyb-3dvar_gfs (Failed)                    ci_flake_disable fv3-jedi fv3jedi mpi script

Intel oneAPI

WORK IN PROGRESS

UFS Weather Model

WORK IN PROGRESS

GCC

WORK IN PROGRESS

Intel oneAPI

WORK IN PROGRESS

Checklist

• This PR addresses one issue/problem/enhancement or has a very good reason for not doing so.
• These changes have been tested on the affected systems and applications.
• All dependency PRs/issues have been resolved and this PR can be merged.
• All necessary updates to the documentation (spack-stack wiki) will be made when this PR is merged

[climbfuji]

Probably not needed

[rickgrubin-noaa]

Questions to help my clarity of the situation:

• using the sytem-provided oneAPI compiler version rather than the EPIC-installed version
  • better to use the system-provided version for "better interoperability" with MPI, etc., or ?
• using the GCC compilers @ 14.3.0
  • package versions for release/2.1 all build? I vaguely (incorrectly?) recall that v14.x was a no-go for some packages

and

Uncovered while working on the Derecho site config: The syntax for Spack's environment modification unset is different than the others

where "others" is the shell, or ?

[climbfuji]

Questions to help my clarity of the situation:

• using the sytem-provided oneAPI compiler version rather than the EPIC-installed version

  • better to use the system-provided version for "better interoperability" with MPI, etc., or ?

• using the GCC compilers @ 14.3.0

  • package versions for release/2.1 all build? I vaguely (incorrectly?) recall that v14.x was a no-go for some packages

and

Uncovered while working on the Derecho site config: The syntax for Spack's environment modification unset is different than the others

where "others" is the shell, or ?

This pull request is for develop. release/2.1 is not addressed here.

The Derecho ncarenv doesn't provide a GCC 13 module, only 14 or 12.

The system-provided Intel oneAPI compiler means avoiding one manual MODULEPATH, and it's slightly newer (2025.3.2 instead of 2025.3.1).

unset takes a list of variable names. All others (remove_path, prepend_path, set, ...) take key : value pairs in the Spack yamls.

[rickgrubin-noaa]

This pull request is for develop. release/2.1 is not addressed here.

Thanks for clarifying.

I'll let EPIC folks know that issue Derecho-specific issues for the WM spack-stack v2.1.x upgrade #3306 and adjacent PR Upgrade WM to spack-stack 2.1.x- #3174 are OBE.

unset takes a list of variable names. All others (remove_path, prepend_path, set, ...) take key : value pairs in the Spack yamls.

So a spack-specific command; thanks.

[eap]

I didn't test this manually, but I assume you have. I read through the meta-module logic and the new extra modules, the changes look sensible to me.