Apptainer: Difference between revisions

When Apptainer is used with the <code>-C</code> or <code>-c</code> options, one will notice that they cannot access their disk space when inside the container. The remedy for this is to explicitly bind mount the disk space they wish to access. For example, suppose a user was using <code>-C</code> like this in an sbatch job to use apptainer:

where <code>./my_data_file.txt</code> is a file in the current directory on the host, i.e., the file is not stored in the container at all. Because of the <code>-C</code> option, this file will not be accessible to the <code>wc</code> program inside the container --and so an access error will result. The fix is to bind mount the current directory, e.g.,

While one can have multiple bind mounts specified, often it is easier to specify the top directories of the filesystems one wishes to access. For example, on our clusters one might want to use: