Update ECMWF libs ecbuild, eckit, fckit, atlas, fiat, ectrans

[fmahebert]

Description

Update ECMWF's packages to the following versions,

ecbuild 3.12.0
eckit 1.32.3
fckit 0.14.1
fiat 1.6.1
ectrans 1.7.0
atlas 0.44.1

This is following the validation work of https://github.com/JCSDA-internal/oops/issues/3052

Dependencies

• waiting on Cherry-pick spack-packages 2366: "ecmwf_atlas: add new versions, and new dependency versions" spack-packages#23 (corresponding upstream PR ecmwf_atlas: add new versions, and new dependency versions spack/spack-packages#2366)

Issues addressed

Closes #1723

Applications affected

Impacts JEDI applications

Systems affected

Impacts all systems

Testing

• CI:
  • 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:
• Additional testing:
  • jedi-bundle ctests using gcc 13.3 and intel 2024.2 as detailed https://github.com/JCSDA-internal/oops/issues/3052

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]

@fmahebert We need a PR for https://github.com/JCSDA/spack-packages that cherry-picks your commit(s) from spack/spack-packages#2366. Do you want me to create it and point your spack-stack PR to that branch?

[fmahebert]

@climbfuji

• I opened a cherry-picking PR to jcsda/spack-packages here: Cherry-pick spack-packages 2366: "ecmwf_atlas: add new versions, and new dependency versions" spack-packages#23
• I've force-pushed changes to this branch to update the base branch to update_to_spack_v1 and to update the submodule pointer

Please let me know if this is the correct configuration!

[climbfuji]

I don't see the actual submodule pointer update here, just the .gitmodules update.

[fmahebert]

Hopefully fixed...

[climbfuji]

Looks good now. We'll merge #1817 first, then update this PR, and wait for the CI tests to succeed.

[climbfuji]

Looks good now. We'll merge #1817 first, then update this PR, and wait for the CI tests to succeed.

Can you fix the merge conflicts, please? All that's needed is pulling in develop and "adding" (confirming) that the head of your current spack-packages branch is correct (because it is up to date with spack-stack-dev).

[climbfuji]

Looks good now. We'll merge #1817 first, then update this PR, and wait for the CI tests to succeed.

Can you fix the merge conflicts, please? All that's needed is pulling in develop and "adding" (confirming) that the head of your current spack-packages branch is correct (because it is up to date with spack-stack-dev).

Actually, I just merged JCSDA/spack-packages#22 - can you pull this into your spack-packages branch and update the submodule pointer while you are resolving the conflicts, please?

[fmahebert]

Ahh, I was too fast / too slow! Yes, I will do that second step as well

[fmahebert]

Done, hopefully correctly

[climbfuji]

@fmahebert I merged JCSDA/spack-packages#23, please update the spack-package submodule ptr to hash JCSDA/spack-packages@ea29f11 and revert the gitmodules change. Also, please pull in spack-stack develop once more, because we just merged #1821