Site config updates and bugfixes for NRL systems (Atlantis, Nautilus)

[climbfuji]

Summary

General

• Require variant ~libbsd for expat package to avoid duplicate packages when building unified environment on Narwhal

Atlantis

Update compilers.yaml and packages_gcc.yaml: remove unneeded environment modifications, add missing module dependencies.

Narwhal

Fixing the underlying issue for the wrong/old/not-even-default libsci libraries being linked by several packages is not straightforward and will require the HPE Cray admins to make modifications. Therefore, this PR provides a utility script util/narwhal/fix_libsci.sh as a workaround. This script needs to be run after each successful spack-stack environment build.

# Utility script to work arounds issues on Narwhal, where an old cray-libsci
# implementation is found and used by spack packages that use autotools,
# libtool, and configure. This is because of symbolic links in /opt/cray/pe/lib64
# pointing to the old (v21) libsci installation, and /etc/ld.so.conf.d/ containing
# a file that tells the build system to include libraries from /opt/cray/pe/lib64.

# The approach is to scan all shared libraries in a spack-stack environment and
# use patchelf to replace the "bad" libsci references in those with references
# to the "good" libsci version (determined by looking at the module that is loaded).

Nautilus

Revert gcc from 12.2.1 to 11.2.1 to address a known problem with the version of ld from binutils that ships with gcc@12. This particular version leads to compilation errors of downstream packages (e.g. py-pandas) when using openblas as provider for blas, lapack, fftw-api in spack-stack. See https://github.com/OpenMathLib/OpenBLAS/wiki/Faq#ELFoffset for more information.

Testing

• Atlantis: Built spack-stack with gcc, intel, oneapi, oneapi-ifx, ran NEPTUNE with these stacks
• Narwhal: Built spack-stack with oneapi + libsci/23 (default is libsci/22, the offending version in `/opt/cray, ran NEPTUNE with this stack
• Nautilus: Built spack-stack with gcc + openblas, ran NEPTUNE with this stack
• readthedocs output: https://spack-stack--1449.org.readthedocs.build/en/1449/PreConfiguredSites.html#navy-hpcmp-narwhal

(NRL colleagues, please see https://github.nrlmry.navy.mil/NEPTUNE/neptune-atmos/pull/1096 for a testing-only PR (not to be merged) for these changes)

Applications affected

NEPTUNE and JEDI-NEPTUNE on Atlantis, Nautilus, Narwhal

Systems affected

Atlantis, Nautilus, Narwhal

Dependencies

None

Issue(s) addressed

Atlantis

Resolves #1445

Narwhal

Working towards #1447 (this is not a full solution)

Nautilus

Resolves #1446

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.