Description

Update spack and spack-packages submodules from upstream spack/spack-packages develop as of the beginning of June, 2026.

This requires

• pinning a few Python packages to work with the older Python 3.11 stack that we currently have
• changing the way the Intel oneAPI modules are loaded in the site config (load compiler modules for MPI, don't load modules for MKL)
• update cylc versions for compatibility with current Python 3.11 stack

Dependencies

• waiting on Update spack-packages from spack-packages/develop 2026/06/04 spack-packages#67
• waiting on Update spack-stack-dev from spack develop 2026/05/20 spack#577

Issues addressed

• working toward [INSTALL]: cylc-flow@8.6.x to fix memory leak in 8.4.2 #1944
• closes Use spack-packages develop as base for spack-stack-dev #1878

Applications affected

Potentially all. This PR has been tested for the end-to-end NEPTUNE ecosystem so far. Testing and bug fixes for other applications will be made by the respective stakeholders in follow-up pull requests.

Systems affected

Potentially all. Changes are made here for Atlantis only. Other site config updates will be made by the respective site maintainers in follow-up pull requests.

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
  • On NRL's Atlantis: run NEPTUNE ecosystem end-to-end tests (including cylc workflow), run NEPTUNE CI tests

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. see note above, section "Systems affected"
• All dependency PRs/issues have been resolved and this PR can be merged.
• All necessary updates to the documentation (spack-stack wiki) will be made when this PR is merged