Pass the host environment LD_LIBRARY_PATH within a Singularity container

What would you like to see added?

We need to document a generic example of how to pass the host environment LD_LIBRARY_PATH and append it within a container-defined LD_LIBRARY_PATH. Can be added to this page https://docs.rc.uab.edu/workflow_solutions/getting_containers/#containers-on-cheaha.

For instance, executing the Parabricks container requires a CUDA library. In order to see host GPUs inside the container, we need to append the CUDA LD_LIBRARY_PATH to the containerized LD_LIBRARY_PATH.

The CUDA LD_LIBRARY_PATH in Cheaha is in "/cm/local/apps/cuda/libs/current/lib64".
Before appending the CUDA LD_LIBRARY_PATH, the environment inside the container is,

$ singularity exec parabricks.sif printenv LD_LIBRARY_PATH
/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/.singularity.d/libs

After appending the CUDA LD_LIBRARY_PATH to the containerized LD_LIBRARY_PATH we can see that the initial containerized definition is preserved by appending,

$ export SINGULARITYENV_LD_LIBRARY_PATH="/cm/local/apps/cuda/libs/current/lib64:\$LD_LIBRARY_PATH"
$ singularity exec parabricks.sif printenv LD_LIBRARY_PATH
/cm/local/apps/cuda/libs/current/lib64:$LD_LIBRARY_PATH:/.singularity.d/libs

In order to execute the container we need to bind the path of the CUDA library as well as set the LD_LIBRARY_PATH,

$ singularity run --nv -B /cm/local/apps/cuda/libs/current/lib64 parabricks.sif /bin/pbrun fq2bam ...

If required link the Parabricks page:https://docs.rc.uab.edu/education/case_studies/#parabricks-testing-on-pascalnodes-and-amperenodes-on-cheaha.

For reference see this github post to see how to append LD_LIBRARY_PATH to the containers LD_LIBRARY_PATH: https://github.com/apptainer/singularity/issues/5781

Update the “Containers on Cheaha” page linked in the issue with the generic SINGULARITYENV_LD_LIBRARY_PATH and bind-path examples shown here. Include the Parabricks command and link to the Parabricks page if useful; done means the documentation explains preserving the container value while appending the host CUDA path.