Chicoma: various path and testing issues

[mark-petersen]

Making a new issues just for the topic of getting MPAS-Ocean standalone testing using compass working.

[mark-petersen]

See change in netcdf and pnetcdf path listed here: #523 (comment)

After that was fixed locally the compile was successful. But setting up compass produced this:

compass suite -s -c ocean -t nightly -p /usr/projects/climate/mpeterse/repos/E3SM/master/components/mpas-ocean -w $n/ocean_model_230214_860eb7bf_ch_gfortran_openmp_master
Setting up test cases:
  ocean/baroclinic_channel/10km/default
  ocean/baroclinic_channel/10km/threads_test
  ocean/baroclinic_channel/10km/decomp_test
  ocean/baroclinic_channel/10km/restart_test
  ocean/global_ocean/QU240/mesh
  ocean/global_ocean/QU240/PHC/init
Downloading BedMachineAntarctica_v2_and_GEBCO_2022_0.05_degree_20220729.nc (1.4GiB)
  to /usr/projects/regionalclimate/COMMON_MPAS/mpas_standalonedata/mpas-ocean/bathymetry_database
  0% |                                                                                                                                   | ETA:  --:--:--Traceback (most recent call last):
...
  File "/usr/projects/climate/mpeterse/repos/compass/pr/compass/io.py", line 122, in download
    with open(dest_path, 'wb') as f:
PermissionError: [Errno 13] Permission denied: '/usr/projects/regionalclimate/COMMON_MPAS/mpas_standalonedata/mpas-ocean/bathymetry_database/BedMachineAntarctica_v2_and_GEBCO_2022_0.05_degree_20220729.nc'

@xylar can you change this to be group read and writable? I don't know why that would change from badger to chicoma, but that is the problem right now:

/usr/projects/regionalclimate/COMMON_MPAS/mpas_standalonedata/:
total 8
drwxrwxr-x  3 mhoffman climate 4096 Oct  7 12:59 mpas-albany-landice
drwx------ 11 xylar    climate 4096 Jan 10 07:42 mpas-ocean

[mark-petersen]

After that permissions change, everything is working. I can compile and run on chicoma, as described in #523 and #531. Thanks.