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[feature/update_to_spack_v1] [email protected], bug fix netcdf-c+mpi, bug fix setup-meta-modules, Nautilus gcc stack update#1817

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climbfuji merged 12 commits intoJCSDA:feature/update_to_spack_v1from
climbfuji:feature/spack_v1_nautilus_esmf891_netcdf_c
Nov 17, 2025
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[feature/update_to_spack_v1] [email protected], bug fix netcdf-c+mpi, bug fix setup-meta-modules, Nautilus gcc stack update#1817
climbfuji merged 12 commits intoJCSDA:feature/update_to_spack_v1from
climbfuji:feature/spack_v1_nautilus_esmf891_netcdf_c

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@climbfuji climbfuji commented Nov 13, 2025 •
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Description

  1. Update configs/sites/tier1/nautilus/packages_gcc-13.3.1.yaml

  2. Bug fix in spack-ext/lib/jcsda-emc/spack-stack/stack/meta_modules.py: when creating MPI meta module, set environment variables from MPI spec (not compiler spec), and use correct compiler/mpi aliases. Check that meta modules are created.

  3. Update submodule pointer for repos/builtin for netcdf-c+mpi bug fix and [email protected] addition: Add [email protected] + bug fix for netcdf-c to find MPI functions when build system is cmake (replaces #18) spack-packages#21

  4. Update configs/** for [email protected]

Dependencies

Issues addressed

Closes #1809
Closes #1820
Closes #1819

Applications affected

JEDI (netcdf-c), NEPTUNE (esmf)

Systems affected

Nautilus

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
    • ...

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 on readthedocs are included in this PR
    • For site config updates, check in particular doc/source/PreConfiguredSites.rst and doc/source/MaintainersSection.rst
  • All necessary updates to the spack-stack wiki will be made when this PR is merged

@climbfuji climbfuji mentioned this pull request Nov 13, 2025
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@climbfuji climbfuji self-assigned this Nov 13, 2025
@climbfuji climbfuji moved this to In Progress in spack-stack-2.0.x (2025 Q4) Nov 13, 2025
@climbfuji climbfuji marked this pull request as ready for review November 14, 2025 22:34
@climbfuji climbfuji enabled auto-merge (squash) November 17, 2025 17:50
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mathomp4 commented Nov 17, 2025

@climbfuji Would you mind if we also updated the geos-gcm-env and jedi-geos-env to ESMF 8.9.1 as well? I mean, we tend to be at the bleeding edge (technically we are running an 9 beta in Baselibs, but that's only required for our MAPL3 development).

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climbfuji commented Nov 17, 2025

@climbfuji Would you mind if we also updated the geos-gcm-env and jedi-geos-env to ESMF 8.9.1 as well? I mean, we tend to be at the bleeding edge (technically we are running an 9 beta in Baselibs, but that's only required for our MAPL3 development).

No problem, but note that 8.9.1 is not an official release yet. We are pointing to a commit (head of the 8.9.1 patch branch) of ESMF.

Also, after pulling in your PR (as updates from develop), CI tests are failing for my code with duplicate py-colorama packages. Before pulling in your changes, I didn't have these. Have you seen this in your tests? I'll try to fix it by pinning py-colorama to one version before attempting anything else.

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climbfuji commented Nov 17, 2025

@climbfuji Would you mind if we also updated the geos-gcm-env and jedi-geos-env to ESMF 8.9.1 as well? I mean, we tend to be at the bleeding edge (technically we are running an 9 beta in Baselibs, but that's only required for our MAPL3 development).

No problem, but note that 8.9.1 is not an official release yet. We are pointing to a commit (head of the 8.9.1 patch branch) of ESMF.

Also, after pulling in your PR (as updates from develop), CI tests are failing for my code with duplicate py-colorama packages. Before pulling in your changes, I didn't have these. Have you seen this in your tests? I'll try to fix it by pinning py-colorama to one version before attempting anything else.

@mathomp4 Updated to 8.9.1 in 054b141

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mathomp4 commented Nov 17, 2025

@climbfuji Would you mind if we also updated the geos-gcm-env and jedi-geos-env to ESMF 8.9.1 as well? I mean, we tend to be at the bleeding edge (technically we are running an 9 beta in Baselibs, but that's only required for our MAPL3 development).

No problem, but note that 8.9.1 is not an official release yet. We are pointing to a commit (head of the 8.9.1 patch branch) of ESMF.

Oh. Ha! I guess I thought "I missed a release". I think it'll be fine for us.

Also, after pulling in your PR (as updates from develop), CI tests are failing for my code with duplicate py-colorama packages. Before pulling in your changes, I didn't have these. Have you seen this in your tests? I'll try to fix it by pinning py-colorama to one version before attempting anything else.

Huh. I didn't go near py-colorama at all. I mean, mepo does depend on it:

    depends_on("[email protected]:", type=("build", "run"))

but that hasn't changed in ever.

And I guess we did say 0.4.6 since that's the version that was out at the time (and still the latest).

Maybe some other package is asking for an older version?

@climbfuji climbfuji mentioned this pull request Nov 17, 2025
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@climbfuji climbfuji merged commit d857097 into JCSDA:feature/update_to_spack_v1 Nov 17, 2025
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@github-project-automation github-project-automation bot moved this from In Progress to Done in spack-stack-2.0.x (2025 Q4) Nov 17, 2025
@climbfuji climbfuji deleted the feature/spack_v1_nautilus_esmf891_netcdf_c branch November 17, 2025 23:35
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climbfuji commented Nov 18, 2025

@climbfuji Would you mind if we also updated the geos-gcm-env and jedi-geos-env to ESMF 8.9.1 as well? I mean, we tend to be at the bleeding edge (technically we are running an 9 beta in Baselibs, but that's only required for our MAPL3 development).

No problem, but note that 8.9.1 is not an official release yet. We are pointing to a commit (head of the 8.9.1 patch branch) of ESMF.

Oh. Ha! I guess I thought "I missed a release". I think it'll be fine for us.

Also, after pulling in your PR (as updates from develop), CI tests are failing for my code with duplicate py-colorama packages. Before pulling in your changes, I didn't have these. Have you seen this in your tests? I'll try to fix it by pinning py-colorama to one version before attempting anything else.

Huh. I didn't go near py-colorama at all. I mean, mepo does depend on it:

    depends_on("[email protected]:", type=("build", "run"))

but that hasn't changed in ever.

And I guess we did say 0.4.6 since that's the version that was out at the time (and still the latest).

Maybe some other package is asking for an older version?

Yeah, the [email protected] was the reason. I pinned it to that version in configs/common/packages.yaml, and now the duplicates are gone.

I merged your spack-packages PR, do you need another PR to update the versions in configs/common/packages.yaml?

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@mathomp4 mathomp4 mathomp4 approved these changes

@eap eap eap approved these changes

@rickgrubin-noaa rickgrubin-noaa rickgrubin-noaa approved these changes

@AlexanderRichert-NOAA AlexanderRichert-NOAA Awaiting requested review from AlexanderRichert-NOAA

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