(closes #2629) Fix NEMOv5 issues

[sergisiso]

No description provided.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 99.86%. Comparing base (92fbf60) to head (07fec74).
Report is 18 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master    #2698   +/-   ##
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  Coverage   99.86%   99.86%           
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  Files         353      353           
  Lines       48996    49024   +28     
=======================================
+ Hits        48932    48960   +28     
  Misses         64       64           

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[sergisiso]

@arporter This is ready for review, it compiles NEMOv5 and LFRic with the new spack repository, where there is software stack to build the applications with gfortran-14 nvhpc-24.5 and intel-24.2.

I addition:

• I updated the version of LFRic, which we now compare using the produced checksum file, so it can be tested with MPI. (note that before we compiled with mpi but run serially which could hide some bugs)
• I deleted NEMOv5 build system logic to exclude files in order to have them all in the provided script. This allows us to be explicit about what is failing, and fix the problems without having to update the files inside gh_runner manually.
• I disabled the addition of parallelisation directives inside pure or elemental functions, this produced a compiler bug in NEMOv5 and it seems to be invalid by definition.
• I fix an issue where we lost the pure/elemental function attributes

I have not yet deleted the current NEMOv5 version that there is in the nemo_test workflow, because the output is very slightly different:
it : 10 |ssh|_max: 0.6483453724882898D+01 |U|_max: 0.5701938594625860D-02 |V|_max: 0.4920016849737715D-01 S_min: 0.2996960233984670D+02 S_max: 0.3102375152368392D+02
it : 10 |ssh|_max: 0.6483453724938688D+01 |U|_max: 0.5701938594606864D-02 |V|_max: 0.4919999106597320D-01 S_min: 0.2996960234052442D+02 S_max: 0.3102375152367826D+02

If the reviewer I ok with this numbers I could update the KGO file, do the nemov5 check for this compiler with exact output match and deleted from the nemov4 workflow.

[sergisiso]

@arporter We are now down to 1 NEMOv4 passthrough error (#717) and 0 NEMOv5 passthrough errors! Although I am wondering if we should enable TOP and ICE at least in the passthrough in order to cover more code.

[sergisiso]

@arporter This is ready for next review

[sergisiso]

I just realised that I made a typo in the branch name and some commits by referring to 2692, but this PR solves issue 2629, sorry for the confusion

[arporter]

Looking good now. I think we 'just' need to get to the bottom of the configuration to use for these tests. As you say, we could include other keys to maximise our exposure but, if that causes problems, we can delay that step.

[sergisiso]

@arporter Ready for another review, I just slightly updated the test filenames and removed del_keys on the workflow.

[arporter]

All good now.
Integration tests were all green.
Will proceed to merge.