Sync config_machines.xml to E3SM 4487cd1 and update Frontier GNU Spack externals

[Copilot]

Daily drift detected changes in supported machine config for bebop,
frontier, and improv. This PR syncs
mache/cime_machine_config/config_machines.xml to upstream E3SM revision
4487cd1c5daf8ab1de910a9d0c74be4b8e813bfb and updates the affected Frontier
Spack templates for module/version drift.

• config_machines.xml upstream sync

  • Replaced mache/cime_machine_config/config_machines.xml with generated
    upstream content from E3SM 4487cd1c5daf8ab1de910a9d0c74be4b8e813bfb.
  • Removed the temporary generated file
    upstream_config_machines.xml from the repo root.

• Frontier Spack template alignment

  • Updated:
    • mache/spack/templates/frontier_craygnu_mpich.yaml
    • mache/spack/templates/frontier_craygnu-mphipcc_mpich.yaml
  • Aligned GNU toolchain/module and external package versions with upstream
    Frontier drift in the synced machine configuration:
    • cpe/24.11 → cpe/25.09
    • gcc-native/12.3 → gcc-native/14.2
    • hdf5 1.14.3.3 → 1.14.3.7
    • netcdf-c 4.9.0.15 → 4.9.2.1
    • parallel-netcdf 1.12.3.15 → 1.12.3.19
  • Per review feedback, Frontier prefix: paths keep gnu/12.3 (not
    gnu/14.2) for these externals.
  • Clarification: Frontier template updates were based on Frontier config
    drift, not on crux machine settings.

# frontier_craygnu_mpich.yaml
- spec: hdf5@1.14.3.7~cxx+fortran+hl~java+mpi+shared
  prefix: /opt/cray/pe/hdf5-parallel/1.14.3.7/gnu/12.3
- spec: netcdf-c@4.9.2.1+mpi~parallel-netcdf
  prefix: /opt/cray/pe/netcdf-hdf5parallel/4.9.2.1/gnu/12.3

Checklist

• User's Guide has been updated if needed
• Developer's Guide has been updated if needed
• API documentation lists any new or modified class, method, or function
• Documentation builds cleanly and changes look as expected
• Tests pass and new features are covered by tests
• PR description includes a summary and any relevant issue references
• Testing comment, if appropriate, in the PR documents testing used to verify the changes

Fixes #407

[xylar]

@copilot, you are making changes to Frontier files based on changes to config_machines.xml in for the machine crux. Why are you doing that?

[xylar]

@copilot, sorry, my mistake. There were, indeed, frontier changes. Your changes now look right to me. Again, sorry.

[Copilot]

@copilot, you are making changes to Frontier files based on changes to config_machines.xml in for the machine crux. Why are you doing that?

Good catch — those Frontier template edits were not intended to be driven by crux. In cf10241, I synced config_machines.xml and then updated Frontier templates to match Frontier module/version drift in that same upstream sync. The follow-up 88924b8 kept the Frontier prefix paths at gnu/12.3 per your review feedback.

[xylar]

These changes look good!

[xylar]

Testing

I was able to deploy all 7 spack environments for Polaris for the 6 compilers on Frontier with these changes.