pmd into Workflow

[Malmahrouqi3]

Description

(#646), I am attempting to implement PMD GitHub Action to the Test Suite.

Fixes #(issue) [optional]

None

Please delete options that are not relevant.

• New feature (non-breaking change which adds functionality)

Scope

• This PR comprises a set of related changes with a common goal

If you cannot check the above box, please split your PR into multiple PRs that each have a common goal.

How Has This Been Tested?

Please describe the tests that you ran to verify your changes.
Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration

• Test A
• Test B

Test Configuration:

• What computers and compilers did you use to test this:

Checklist

• I have added comments for the new code
• I added Doxygen docstrings to the new code
• I have made corresponding changes to the documentation (docs/)
• I have added regression tests to the test suite so that people can verify in the future that the feature is behaving as expected
• I have added example cases in examples/ that demonstrate my new feature performing as expected.
  They run to completion and demonstrate "interesting physics"
• I ran ./mfc.sh format before committing my code
• New and existing tests pass locally with my changes, including with GPU capability enabled (both NVIDIA hardware with NVHPC compilers and AMD hardware with CRAY compilers) and disabled
• This PR does not introduce any repeated code (it follows the DRY principle)
• I cannot think of a way to condense this code and reduce any introduced additional line count

If your code changes any code source files (anything in src/simulation)

To make sure the code is performing as expected on GPU devices, I have:

• Checked that the code compiles using NVHPC compilers
• Checked that the code compiles using CRAY compilers
• Ran the code on either V100, A100, or H100 GPUs and ensured the new feature performed as expected (the GPU results match the CPU results)
• Ran the code on MI200+ GPUs and ensure the new features performed as expected (the GPU results match the CPU results)
• Enclosed the new feature via nvtx ranges so that they can be identified in profiles
• Ran a Nsight Systems profile using ./mfc.sh run XXXX --gpu -t simulation --nsys, and have attached the output file (.nsys-rep) and plain text results to this PR
• Ran a Rocprof Systems profile using ./mfc.sh run XXXX --gpu -t simulation --rsys --hip-trace, and have attached the output file and plain text results to this PR.
• Ran my code using various numbers of different GPUs (1, 2, and 8, for example) in parallel and made sure that the results scale similarly to what happens if you run without the new code/feature

[Malmahrouqi3]

• The github action is not yet supporting Python and Fortran so I guess the other way is by cloning https://github.com/pmd/pmd and running terminal commands to generate violations.
  ./pmd cpd -l fortran src/*
  ./pmd cpd -l python toolchain/*

[sbryngelson]

• The github action is not yet supporting Python and Fortran so I guess the other way is by cloning pmd/pmd and running terminal commands to generate violations.
  ./pmd cpd -l fortran src/*
  ./pmd cpd -l python toolchain/*

Yeah I can imagine that being the case. That's no problem, we have much messier GH action workflows. I'll review this soon.

[Malmahrouqi3]

The PMD Analysis failed due to mainly what I suspect the need to set environment variable alias pmd="$HOME/pmd-bin-<version>/bin/pmd". Currently, I am building the project locally on WSL and have been waiting forever to double check that. Aside from that, maybe miscellaneous non-buggy adjusts might be needed - like additional flags, processing PMD reports, etc.