Stop GCHP build if CMake detects library conflicts from a Conda environment

[yantosca]

Your name

Bob Yantosca

Your affiliation

Harvard + GCST

Provide a clear and concise overview of the new feature requested.

We have seen that building GCHP when a conda environment containing ESMF is activated can lead to comipilation warnings. Or worse, GCHP can be linked against the wrong library version:

runtime library [libstdc++.so.6] in /n/sw/helmod-rocky8/apps/Core/gcc/12.2.0-fasrc01/\
lib64/../lib64 may be hidden by files in:
      /n/jacob_lab/Users/ryantosca/mamba/envs/gcpy_env/lib
    runtime library [libnetcdff.so.7] in /n/sw/helmod-rocky8/apps/MPI/gcc/12.2.0-fasrc01/\
openmpi/4.1.4-fasrc01/netcdf-fortran/4.6.0-fasrc02/lib may be hidden by files in:
      /n/jacob_lab/Users/ryantosca/mamba/envs/gcpy_env/lib
    runtime library [libnetcdf.so.19] in /n/sw/helmod-rocky8/apps/MPI/gcc/12.2.0-fasrc01/\
openmpi/4.1.4-fasrc01/netcdf-c/4.9.2-fasrc01/lib64 may be hidden by files in:
      /n/jacob_lab/Users/ryantosca/mamba/envs/gcpy_env/lib
    runtime library [libgomp.so.1] in /n/sw/helmod-rocky8/apps/Core/gcc/12.2.0-fasrc01/li\
b64 may be hidden by files in:
      /n/jacob_lab/Users/ryantosca/mamba/envs/gcpy_env/lib

  Some of these libraries may not be found correctly.

We could add a check in the relevant CMakeLists.txt to stop the build if hidden libraries are found. Or at the very least, if a conda environment is activated (i.e. if the $CONDA_DEFAULT_ENV envvar is defined).

Tagging @lizziel

Reference(s)

No response

Will you be implementing this feature yourself?

Yes, but I will need some help

Additional information

No response

[lizziel]

I believe this is a problem for non-ESMF libraries as well, such as netcdf as shown in the warnings above.

[yantosca]

We should also stop to GCHP integration tests as well if a conda env is activated.

[yantosca]

AI says we can implement an error trap like this in the CMakeLists.txt... basically fail if it detects the CONDA_DEFAULT_ENV to be non-blank.

# Fail if conda/mamba environment is active
if(DEFINED ENV{CONDA_DEFAULT_ENV} AND NOT "$ENV{CONDA_DEFAULT_ENV}" STREQUAL "")
    message(FATAL_ERROR 
        "\n====== CONDA ENVIRONMENT DETECTED ======\n"
        "Active environment: $ENV{CONDA_DEFAULT_ENV}\n"
        "Location: $ENV{CONDA_PREFIX}\n"
        "\n"
        "This will cause library conflicts during linking!\n"
        "Please deactivate the conda environment:\n"
        "\n"
        "  conda deactivate\n"
        "\n"
        "Then re-run cmake.\n"
        "==========================================\n")
endif()

[lizziel]

I don't think all python environments are bad and would prefer not to stop if any conda/mamba env is activated.

[yantosca]

@lizziel: Maybe there is a way to check if a conda env has netCDF or ESMF libraries. If so then we could stop.

[yantosca]

See geoschem/geos-chem#3220, which will stop integration tests if a conda env with netCDF is activated. We can extend this to the build sequence at a later time. I just wanted to prevent my GCHP int tests from dying when I forget to deactivate the gcpy_env.