release/1.9: Bug fixes for scotch and crtm-fix, update Ursa site config by climbfuji · Pull Request #1660 · JCSDA/spack-stack

climbfuji · 2025-06-04T17:09:22Z

Summary

Update of spack with three changes for release/1.9 (see dependencies below)
Update templates/config files for changes in 1.
Update ursa site config - builds without duplicates with the spack changes from 1. This introduces the use of MKL as the virtual provider for blas/lapack/fftw when using Intel/oneAPI, but keeps OpenBLAS/FFTW for GNU. Similar to what NRL systems do, what CI uses, and what we should move (back) to on all systems before the spack-stack 2.0.x releases.

Note. After this is merged, we need a final round of testing with all UFS regression tests. If successful, create release 1.9.2 and merge necessary changes back to develop.

Testing

CI
Built spack-stack on Ursa, testing done by @JessicaMeixner-NOAA with UFS (see Upgrade UFS-WM to spack-stack/1.9.2 ufs-community/ufs-weather-model#2650 (comment))
Built spack-stack on Nautilus and confirmed there are no version conflicts

Applications affected

release/1.9 applications that will use spack-stack-1.9.2 (UFS, JEDI, ...)

Systems affected

Ursa

Dependencies

Waiting on release/1.9: Yet another crtm-fix bugfix spack#546
Waiting on release/1.9.0: Add conflict for scotch with oneapi spack#547
Waiting on release/1.9.0: add mapl@2.53.4 spack#548

Issue(s) addressed

@ulmononian @rickgrubin-noaa please add issues here

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.

…d testing

…to use gcc

…s.yaml

climbfuji · 2025-06-06T13:31:05Z

configs/sites/tier1/ursa/compilers.yaml

      fc:  /usr/bin/gfortran
    flags: {}
    operating_system: rocky9
+    target: x86_64


The target entries are the magic that fixes all the version conflicts.

climbfuji · 2025-06-06T13:31:37Z

configs/sites/tier1/ursa/packages_oneapi.yaml

+    - spec: gcc-runtime@11.4.1%gcc@11.4.1
+      prefix: /usr

-  # If using intel-oneapi-mkl, make appropriate changes below


Since this is a new platform, let's just move straight back to Intel MKL instead of OpenBLAS+FFTW with Intel.

The GCC build still uses OpenBLAS and FFTW, as intended.

This is what Jessica Meixner tested in ufs-community/ufs-weather-model#2650 (comment)

@climbfuji will going "straight back to Intel MKL instead of OpenBLAS+FFTW with Intel" on ursa but not on other problems cause any inconsistencies? trying to understand if we are going to need to rebuild 1.9.1 entirely on all platforms or if we can hopefully just update scotch...

No, it won't. It's entirely transparent to the users or downstream application. I've asked for this move in general for a very long time. Before we had OpenBLAS with Intel, hpc-stack and jedi-stack used MKL with Intel by default. When spack-stack started, we had problems with getting MKL to work and out of necessity switched to OpenBLAS.

In fact, we already switched to MKL on all NRL systems with Intel (and use OpenBLAS with GNU), and nobody noticed.

The spack-stack CI runners are like that, too, by the way.

climbfuji · 2025-06-06T13:31:52Z

configs/sites/tier1/ursa/packages_gcc.yaml

+    - spec: gcc-runtime@11.4.1%gcc@11.4.1
+      prefix: /usr

-  ectrans:


…om/climbfuji/spack-stack into bugfix/rel19_scotch_oneapi_use_gcc

rickgrubin-noaa · 2025-06-09T18:54:21Z

@climbfuji would you please also add the following to this PR:

add mapl/2.53.4 ^esmf/8.8.0 to templates/unified-dev/spack.yaml, replacing mapl@2.53.0 ^esmf@8.8.0
change the mapl entry in common/packages.yaml from

    mapl:
      require: '@2.53.0 ~shared ~f2py'
      variants: '+pflogger'

to

    mapl:
      require: '@2.53 ~shared ~f2py'
      variants: '+pflogger'

add mapl@2.53.4 to mapl/package.py
- version("2.53.4", sha256="da38348a72fcbaa2b888578bfa630ab36261206136d33700344ed6792f9f9aeb")

climbfuji · 2025-06-09T20:58:21Z

@climbfuji would you please also add the following to this PR:

add mapl/2.53.4 ^esmf/8.8.0 to templates/unified-dev/spack.yaml, replacing mapl@2.53.0 ^esmf@8.8.0

change the mapl entry in common/packages.yaml from
    mapl:
      require: '@2.53.0 ~shared ~f2py'
      variants: '+pflogger'
to
    mapl:
      require: '@2.53 ~shared ~f2py'
      variants: '+pflogger' 
add mapl@2.53.4 to mapl/package.py

version("2.53.4", sha256="da38348a72fcbaa2b888578bfa630ab36261206136d33700344ed6792f9f9aeb")

Thanks, will do in a bit!

…d testing

…mf@8.8.0'

configs/templates/unified-dev/spack.yaml

ulmononian

thanks @climbfuji

rickgrubin-noaa

Only comment is to revert spack branch in .gitmodules when done.

JessicaMeixner-NOAA · 2025-06-10T14:02:13Z

configs/common/packages.yaml

  scotch:
-    require: '@7.0.4 +mpi+metis~shared~threads~mpi_thread+noarch+esmumps'
+    require:
+    - '@7.0.4 +mpi+metis~shared~threads~mpi_thread+noarch+esmumps'


Does this mean we are using scotch 7.0.4 or are we moving to 7.0.7? (sorry this is my lack of spack-stack knowledge question)

This is still scotch 7.0.4. If it works, then there is no need to update it. The purpose of spack-stack release 1.9.2 is to provide a bug fix / hot fix for the existing 1.9.0 and 1.9.1 releases. Bug fix releases only contain the necessary changes to fix bugs, no changes that aren't necessary.

Do we know if scotch 7.0.4 works on other machines? Or just Ursa... I'm assuming it's going to work on other machines but don't know. Either way WW3 is ready to handle a mix of the two if necessary.

I am pretty sure it will work. We'll install the 1.9.2 release candidate on two machines of your choice with both GNU and oneAPI, and hopefully that will confirm my guess. Ursa + ???

climbfuji · 2025-06-10T14:07:59Z

Only comment is to revert spack branch in .gitmodules when done.

Done.

climbfuji · 2025-06-10T15:51:33Z

I created tag spack-stack-1.9.2rc2 for spack-stack only. That is sufficient for testing, since the submodule pointer for spack is uniquely referenced by the hash stored in spack-stack.

climbfuji added 2 commits June 4, 2025 11:07

Update .gitmodules and submodule pointer for spack for code review an…

6bd15e6

…d testing

configs/common/packages_oneapi.yaml: with oneapi, force scotch build …

abc15f1

…to use gcc

climbfuji mentioned this pull request Jun 4, 2025

release/1.9: Yet another crtm-fix bugfix JCSDA/spack#546

Merged

climbfuji added 2 commits June 4, 2025 15:17

Revert .gitmodules and update submodule pointer for spack

df6dac1

Change require statements for qt and scotch in configs/common/package…

8861eed

…s.yaml

climbfuji added this to spack-stack-1.9.x (2024 Q4 - 2025 Q3) Jun 5, 2025

climbfuji moved this to In Progress in spack-stack-1.9.x (2024 Q4 - 2025 Q3) Jun 5, 2025

Fix ursa site config

22456d2

climbfuji commented Jun 6, 2025

View reviewed changes

configs/sites/tier1/ursa/packages_gcc.yaml

- spec: gcc-runtime@11.4.1%gcc@11.4.1

prefix: /usr

ectrans:

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climbfuji mentioned this pull request Jun 6, 2025

release/1.9.0: Add conflict for scotch with oneapi JCSDA/spack#547

Merged

Update submodule pointer for scotch

1c03d7d

climbfuji self-assigned this Jun 6, 2025

climbfuji added 2 commits June 9, 2025 11:55

Revert .gitmodules and update submodule pointer for spack

41f3b4f

Merge branch 'bugfix/rel19_scotch_oneapi_use_gcc' of https://github.c…

777c3ff

…om/climbfuji/spack-stack into bugfix/rel19_scotch_oneapi_use_gcc

climbfuji changed the title ~~release/1.9: bug fixes for scotch and crtm-fix (WIP)~~ release/1.9: Bug fixes for scotch and crtm-fix, update Ursa site config Jun 9, 2025

climbfuji added 2 commits June 9, 2025 16:09

Update .gitmodules and submodule pointer for spack for code review an…

44970e8

…d testing

In configs/** replace 'mapl@2.53.0 ^esmf@8.8.0' with 'mapl@2.53.4 ^es…

cb9a8d8

…mf@8.8.0'

climbfuji commented Jun 9, 2025

View reviewed changes

configs/templates/unified-dev/spack.yaml Outdated Show resolved Hide resolved

Update configs/templates/unified-dev/spack.yaml

500680f

ulmononian approved these changes Jun 9, 2025

View reviewed changes

climbfuji mentioned this pull request Jun 10, 2025

release/1.9.0: add mapl@2.53.4 JCSDA/spack#548

Merged

climbfuji marked this pull request as ready for review June 10, 2025 11:31

climbfuji requested review from AlexanderRichert-NOAA, RatkoVasic-NOAA and rickgrubin-noaa June 10, 2025 11:36

rickgrubin-noaa approved these changes Jun 10, 2025

View reviewed changes

JessicaMeixner-NOAA reviewed Jun 10, 2025

View reviewed changes

Revert .gitmodules and update submodule pointer for spack

751af11

climbfuji merged commit 7aeb006 into JCSDA:release/1.9.0 Jun 10, 2025
8 of 9 checks passed

climbfuji deleted the bugfix/rel19_scotch_oneapi_use_gcc branch June 10, 2025 15:50

github-project-automation bot moved this from In Progress to Done in spack-stack-1.9.x (2024 Q4 - 2025 Q3) Jun 10, 2025

climbfuji mentioned this pull request Jun 10, 2025

UFS having problem using spack-stack@1.9.1 installed SCOTCH@7.0.7 #1608

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