Rework file I/O in mesh converters for thread-safety

[dengwirda]

This PR reworks the way the C++ MpasMeshConverter.x and MpasCellCuller.x, as well as the MPAS-Tools conversion.py wrapper, handles file I/O to eliminate the need to change into local directories to account for hard-coded relative file names (e.g. graph.info).

Eliminating the os.getcwd() + os.chdir() pattern in conversion.py makes these routines thread-safe, allowing them to be called across parallel threads.

These changes write all output files generated by the mesh-converter/culler (e.g. graph.info, cellMapForward.txt, etc) into the directory defined by the output filename.

[dengwirda]

To run additional tests (attached):

cd conda_package
conda env create -y -n mpas_tools_dev --file dev-spec.txt
conda activate mpas_tools_dev
python -m pip install -e .
cd ..
cd mesh_tools/mesh_conversion_tools
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=$CONDA_PREFIX -DCMAKE_BUILD_TYPE=Debug ..
make
make install

python test_sphere.py
python test_planar.py

test_mesh_converter.zip

[xylar]

For now, just requesting a few formatting fixes. I'll test this in compass tomorrow. Thanks for the nice example tests and instructions!

[xylar]

@mgduda, @akturner, @matthewhoffman and @mark-petersen, this work is needed as part of working on supporting parallel tasks via Parsl. If we make meshes in parallel with threads, it turns out that we can't be doing chdir type operations because these aren't thread-safe in python.

[xylar]

@dengwirda, could you add to the PR description that the approach for modifying the C++ code is to use the directory of the output file also as the directory for the other files (e.g. graph.info)? I think that's missing.

[matthewhoffman]

I'm just going to approve by inspection. This makes sense and the changes look appropriate. Thank for working on this Darren.

[xylar]

@dengwirda, I tested this in compass on both my Linux laptop and Chrysalis. I needed to build the conda package (so that conda-forge compilers were used instead of system compilers) rather than following the instructions above, which used system compilers. When I did that, I got bit-for-bit identical results with the ocean nightly test suite for all tests.

I will approve as soon as the formatting issues are fixed.

[akturner]

Built and ran successfully for me

[mark-petersen]

I compiled the c++ MpasCellCuller and MpasMeshConverter on grizzly with both gnu and intel and tested them individually with a QU240 mesh. Everything appears to work fine. Thanks!

[mgduda]

I'll second @xylar's suggestion to fix the whitespace in mpas_cell_culler.cpp and mpas_mesh_converter.cpp.

[xylar]

@mgduda, I went ahead and fixed the white space since it seems like @dengwirda hasn't had time. Could you give it another look to make sure you're okay with the changes otherwise? I would like to do a new release of MPAS-Tools soon and it would be nice if this were included.

[xylar]

Approving now that white space issues are fixed.

[xylar]

@mgduda, is this something you might have time to try out soon? If so, the timing would be good with other fixes we want to make for another MPAS-Tools release.

[mgduda]

Sorry about the delay!

[xylar]

Thanks @mgduda!