Xios interface with tests

[TomMelt]

Nextsim XIOS Interface

The previous XIOS work has diverged from the current development branch.

This PR has a minimum working example (MWE) in the form of a test testXiosInit (source ./core/test/XiosInit_test.cpp).

The test checks most of the functionality added by the XIOS C++ interface

• ./core/src/Xios.cpp
• ./core/src/include/Xios.hpp

which depend on a C interface included here: ./core/src/include/xios_c_interface.hpp

The core functionality of XIOS is included as part of this PR as the other two components will require it.

XIOS functionality

Still to discuss:

• [x] we need to discuss Dockerfile because building without one will become more complicated going forward (more dependencies, lxios, lpnetcdf etc.
• [x] ~Also how do we want to handle mac builds going forward? I cannot simulate mac (virt OS/docker) so it's not easy for me to "fix" CI~ we will not support MPI/xios on mac

This PR does the following:

• [x] add XIOS to cmake
• [x] add XIOS to the CI workflow
• [x] add unit tests to check core functionality of the C++ wrapper
• [x] uses mpi-aware doctest

I think this can be merged in relatively soon. The remaining steps are (for a future PR):

• [ ] to actually integrate XIOS into nextsim (because testXiosInit is a stand-alone binary)
• [ ] to replace the XIOS datetime types with nextsim's
• [ ] produce diagnostic output files

Steps required to run testXiosInit

• Install XIOS (see the github workflow for an idea how to install XIOS)
• Build nextsim with XIOS support using -DENABLE_XIOS=ON and -Dxios_DIR=/path/to/xios/install
• cd to build/core/test and run mpirun -n 2 ./testXiosInit

The test should pass all tests:

[doctest] doctest version is "2.4.11"
[doctest] run with "--help" for options
step 0===============================================================================
[doctest] test cases:  1 |  1 passed | 0 failed | 0 skipped
[doctest] assertions: 19 | 19 passed | 0 failed |
[doctest] Status: SUCCESS!
===============================================================================
[doctest] assertions on all processes:     38 |     38 passed |      0 failed |
===============================================================================
[doctest] Status: SUCCESS!

And produce the following output:

xios_client_1.err
xios_client_0.err
diagnostic.nc
xios_client_1.out
xios_client_0.out
doctest_1.log
doctest_0.log

I don't currently verify the output of diagnostic.nc as part of testXiosInit but this can be added.

This PR is to update the state of XIOS related PRs and Issues. This will close some stale issues closes #218 closes #291 closes #293

[MarionBWeinzierl]

I can see that you have the same netcdf_par.h error on Ubuntu that I had previously. Did you try setting the same include path to the parallel netcdf version?

https://github.com/nextsimhub/nextsimdg/blob/8066f6725e3c10435dfa3e8a3bef5f0d85d0ff1c/Dockerfiles/Dockerfile_Ubuntu_MPI#L10

[MarionBWeinzierl]

When I try to run (cd xios && ./make_xios --arch GCC_LINUX --netcdf_lib netcdf4_seq) to install xios I am getting

    /home/workspace/nextsimdg_xios/xios/extern/remap/src/earcut.hpp:26:29: error: ‘uint32_t’ in namespace ‘std’ does not name a type; did you mean ‘wint_t’?
   26 | template <typename N = std::uint32_t>
      |                             ^~~~~~~~
      |                             wint_t
    fcm_internal compile failed (256)
    gmake: *** [/home/workspace/nextsimdg_xios/xios/Makefile:756: meshutil.o] Error 1 
    gmake -f /home/workspace/nextsimdg_xios/xios/Makefile -j 1 all failed (2) at /home/workspace/nextsimdg_xios/xios/tools/FCM_OLD/bin/../lib/Fcm/Build.pm line 597.

[TomMelt]

I can see that you have the same netcdf_par.h error on Ubuntu that I had previously. Did you try setting the same include path to the parallel netcdf version?

https://github.com/nextsimhub/nextsimdg/blob/8066f6725e3c10435dfa3e8a3bef5f0d85d0ff1c/Dockerfiles/Dockerfile_Ubuntu_MPI#L10

Yeah but I figured there's no point fixing it if we move to a Docker container anyway. That's why I have left it for now. It will get worse when we add XIOS dependencies. So my plan is, get the docker build working first and then we can just build Nextsim with the dev environment configured already