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On our clusters, you will want to use a number of additional options (that appear after <code>run</code> and before <code>your-container-name.sif</code>). These options will include <code>-C</code>, <code>-c</code>, <code>-e</code>, <code>-W</code> as well as various bind mount options to make your disk space available to the programs that run in your container. For example: | On our clusters, you will want to use a number of additional options (that appear after <code>run</code> and before <code>your-container-name.sif</code>). These options will include <code>-C</code>, <code>-c</code>, <code>-e</code>, <code>-W</code> as well as various bind mount options to make your disk space available to the programs that run in your container. For example: | ||
apptainer shell -C -W $SLURM_TMPDIR -B /home -B /project -B /scratch your-container-name.sif | apptainer shell -C -W $SLURM_TMPDIR -B /home:/cluster_home -B /project -B /scratch your-container-name.sif | ||
For more information on these options see the following sections on this page: | For more information on these options see the following sections on this page: | ||
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i.e., <code>-B ./my_data_file.txt:/special/input.dat</code> bind mount maps the file <code>./my_data_file.txt</code> to be the file <code>/special/input.dat</code> inside the container and the <code>wc</code> command now processes that file. This feature can be useful when programs/scripts inside the container have hard-coded paths to files and directories that must be located in certain locations. | i.e., <code>-B ./my_data_file.txt:/special/input.dat</code> bind mount maps the file <code>./my_data_file.txt</code> to be the file <code>/special/input.dat</code> inside the container and the <code>wc</code> command now processes that file. This feature can be useful when programs/scripts inside the container have hard-coded paths to files and directories that must be located in certain locations. | ||
If you need to bind-mount the <code>/home</code> filesystem in your container, use an alternate destination directory: | |||
* <code>-B /home:/cluster_home</code> | |||
This ensures that configuration files and programs in your home directory do not interfere with the software in your container. For example, programs in <code>$HOME/bin</code> and Python packages in <code>$HOME/.local/lib/python3.x</code> could be used instead of the corresponding files in your container in you used <code>-B /home</code>. | |||
Finally, <b>don't mount our CVMFS paths</b> inside your containers as this is fraught with perils and defeats many reasons to use a container. The programs that have to run inside a container need to be completely inside the container. Don't introduce even more programs inside the container if they don't need to be there. | Finally, <b>don't mount our CVMFS paths</b> inside your containers as this is fraught with perils and defeats many reasons to use a container. The programs that have to run inside a container need to be completely inside the container. Don't introduce even more programs inside the container if they don't need to be there. | ||