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New package adp-preprocessors (Navy only), use [email protected] with LLVM, bug fix for Intel oneAPI MPI in setup-meta-modules#1807

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climbfuji merged 10 commits intoJCSDA:feature/update_to_spack_v1from
climbfuji:feature/adp_preprocessors
Nov 6, 2025
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New package adp-preprocessors (Navy only), use [email protected] with LLVM, bug fix for Intel oneAPI MPI in setup-meta-modules#1807
climbfuji merged 10 commits intoJCSDA:feature/update_to_spack_v1from
climbfuji:feature/adp_preprocessors

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@climbfuji climbfuji commented Nov 5, 2025 •
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Description

  1. New package adp-preprocessors, enabled as a variant for jedi-neptune-env and off by default so that the unified environment builds out of the box on other systems.
  2. Use w3emc version 2.10.0 instead of the newer 2.11.0 with LLVM native, because 2.11.0 doesn't build. We only need 2.11.0 with Intel LLVM for now, because the older versions don't support the Intel LLVM compilers. In a future update, when grib-utils are updated to no longer require the deprecated extradeps variant from w3emc, we can hopefully update to 2.12.0 or a newer version that builds with all compilers.
  3. Update submodule pointer for spack-packages for the recently merged PR Use spack v1 syntax in MCT package to set -fPIC spack-packages#17 (use spack v1 syntax in MCT package to set -fPIC).
  4. Bug fix in spack-ext/lib/jcsda-emc/spack-stack/stack/meta_modules.py: set correct path to Intel oneAPI MPI compiler wrappers (this can be wrong, depending on how the external Intel oneAPI MPI was installed and is used (prefix vs modules).

Dependencies

Issues addressed

NRL-internal GitHub issue only, none created here

Applications affected

None directly

Systems affected

Atlantis (because it uses LLVM 21.1.0), Nautilus (setup-meta-modules bug fix)

Testing

  • CI: Note whether the automatic tests (GitHub actions tests that run automatically for every commit) pass or not
    • GitHub actions CI tests pass
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    • 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 self-assigned this Nov 5, 2025
@climbfuji climbfuji marked this pull request as ready for review November 5, 2025 16:01
@climbfuji climbfuji moved this to In Progress in spack-stack-2.0.x (2025 Q4) Nov 5, 2025
@climbfuji climbfuji changed the title New package adp-preprocessors (Navy only), use [email protected] with LLVM New package adp-preprocessors (Navy only), use [email protected] with LLVM, bug fix for Intel oneAPI MPI in setup-meta-modules Nov 5, 2025
climbfuji
climbfuji commented Nov 6, 2025
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repos/spack_stack/spack_repo/spack_stack/packages/adp_preprocessors/package.py

homepage = "https://github.nrlmry.navy.mil/ADP/adp-preprocessors/wiki"
#git = "https://github.nrlmry.navy.mil/ADP/adp-preprocessors.git"
git = "https://github.nrlmry.navy.mil/climbfuji/adp-preprocessors.git"
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@climbfuji climbfuji Nov 6, 2025

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Keep this git url and fake version 1.2.0 below until the spack updates for adp are merged and a new tag is created

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climbfuji commented Nov 6, 2025

areinecke is currently unable to submit a review, but he conveyed to me that the PR looks good as far as the NRL parts are concerned.

@AlexanderRichert-NOAA Would you be able to look at the rest, please?

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AlexanderRichert-NOAA commented Nov 6, 2025

For what it's worth, installing [email protected] ^[email protected] works for me using feature/update_to_spack_v1.
The w3emc-related dependencies/requirements for grib-util are:

    depends_on("w3emc", when="@1.2.4:")
    requires("^w3emc +extradeps", when="^[email protected]:2.11")
    requires("^w3emc precision=4,d", when="^[email protected]:")
    depends_on("[email protected]:", when="@1.3:")

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climbfuji commented Nov 6, 2025

For what it's worth, installing [email protected] ^[email protected] works for me using feature/update_to_spack_v1. The w3emc-related dependencies/requirements for grib-util are:

    depends_on("w3emc", when="@1.2.4:")
    requires("^w3emc +extradeps", when="^[email protected]:2.11")
    requires("^w3emc precision=4,d", when="^[email protected]:")
    depends_on("[email protected]:", when="@1.3:")

Would be good to know if w3emc2.12 compiles with LLVM. We can make that update in the near future if it does.

Thanks for the review!

@climbfuji climbfuji merged commit 8a52957 into JCSDA:feature/update_to_spack_v1 Nov 6, 2025
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@climbfuji climbfuji deleted the feature/adp_preprocessors branch November 6, 2025 17:49
@github-project-automation github-project-automation bot moved this from In Progress to Done in spack-stack-2.0.x (2025 Q4) Nov 6, 2025
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@AlexanderRichert-NOAA AlexanderRichert-NOAA AlexanderRichert-NOAA approved these changes

@areinecke areinecke Awaiting requested review from areinecke

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