Move to manylinux_2_28 base image for wheels

[JCGoran]

• use new Docker image tags (manylinux_2_28_x86_64 and manylinux_2_28_aarch64) in CI for building wheels
• use image-provided flex, mpich, and openmpi instead of building from source (still need custom readline and ncurses as the *-static versions do not use -fPIC)
• unify MPI headers when building wheels
• remove BBP-specific tests for wheels
• show warning in Python wrapper if host machine is using GCC<10

[pramodk]

I didn’t check the details but just asking for clarity - moving to 2.28 changed anything about old platforms supported?

[JCGoran]

I didn’t check the details but just asking for clarity - moving to 2.28 changed anything about old platforms supported?

This is mostly in reference to #1963 (comment) to assess how much work is needed.
The change would only have an impact on users who have older systems, but would like to run a newer version of NEURON (9 and above), and only via wheels (source/Spack builds would remain unaffected), i.e. personal machines, since cluster deployments should anyway use a Spack/source install (for performance reasons).

The new min. system requirements would be:

• Debian 10+ (10 reached EOL in July 2024)
• Ubuntu 18.10+ (the previous LTS version, 18.04.6, reached EOL in May 2023)
• Fedora 29+ (reached EOL years ago)
• CentOS/RHEL 8+ (CentOS 7 reached EOL July 2024)

[azure-pipelines]

✔️ 952d3d9 -> Azure artifacts URL

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 67.07%. Comparing base (74dcdd5) to head (4ffe46c).

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #3306   +/-   ##
=======================================
  Coverage   67.07%   67.07%           
=======================================
  Files         571      571           
  Lines      111055   111055           
=======================================
  Hits        74488    74488           
  Misses      36567    36567           

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[pramodk]

Thanks for checking. Those all looks good! 👍

[JCGoran]

Okay, some additional findings about this:

• GCC major versions are not backwards compatible, i.e. we cannot reliably compile and link mod files w/GCC vOlder if we compiled a manylinux wheel w/GCC vNewer (if we didn't have to compile and link anything on the host machine, but just use it, we'd most likely be fine)
• the version of the compiler in the manylinux image is actually too new for us (GCC 14); fortunately, we can install GCC 10 from the repos and use that as the compiler toolchain
• why GCC 10? Because it's available for installation (may not be default) on at least Ubuntu 20.04 LTS, Debian 11, and (trivially) Almalinux 8, which are all rather old, but best be safe than sorry
• I've also changed the min. version of GCC checked by the _binwrapper.py script (from 9 to 10) because we used to build things with GCC 10 anyway, and due to the first point above, there is no guarantee that NEURON would compile and link mod files properly w/ GCC 9
• with the above in mind, we should also be more explicit about the min. version of GCC needed on the user system in the docs

In summary, I think the move to manylinux_2_28 without too many changes is more than feasible.

[azure-pipelines]

✔️ 44ef470 -> Azure artifacts URL

[azure-pipelines]

✔️ 4ffe46c -> Azure artifacts URL

[sonarqubecloud]

Quality Gate passed

Issues
2 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[JCGoran]

This is mostly to fix an issue with Podman on MacOS:

Error: invalid symlink "/var/tmp/libpod_builder742187951/build/README.md" -> "../../docs/install/python_wheels.md"

It also makes it more GitHub-friendly since GitHub doesn't follow symlinks, it just displays where it's pointing to; now it's actually clickable.

[azure-pipelines]

✔️ fae53da -> Azure artifacts URL

[nrnhines]

Many details I'm not familiar with. But if it works...