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On HPC clusters, there are typically thousands if not tens of thousands of daily users who all have their own custom software stacks. Reproducibility crucial in scientific research, even down to the point of having the same version of the programming language. Updating the software stack on a whim quickly leads to a bunch of unhappy researchers.

Luckily, we have some nice software to help us manage everyone's custom software deployment: Lmod! Lmod is a Lua-based module system that enables you to dynamically load software as defined in Lua module files.

Creating a Lua module file

If you look in the /opt/sw directory on nfs-0, you will see the directory apptainer:

~# ls /opt/sw

This is the first program on our cluster that we will make available to our user test. To get started, open a text editor window using the following command:

~# nano 1.1.3.lua

Inside the text editor window, populate the 1.1.3.lua file with the content below:

help([[Apptainer is a container management software for HPC gurus like you and me]])

local root = "/opt/sw/apptainer"

app_bin = pathJoin(root, "bin")
app_libexec_bin = pathJoin(root, "libexec/apptainer/bin")
app_libexec_cni = pathJoin(root, "libexec/apptainer/cni")
app_libexec_lib = pathJoin(root, "libexec/apptainer/lib")
app_man = pathJoin(root, "share/man")

prepend_path("PATH", app_bin)
prepend_path("PATH", app_libexec_bin)
prepend_path("PATH", app_libexec_cni)
prepend_path("LIBRARY_PATH", app_libexec_lib)
prepend_path("LD_LIBRARY_PATH", app_libexec_lib)
prepend_path("MANPATH", app_man)

Save and close the file once you are done populating the file.

Setting up the module file

To set up the module file up on nfs-0, use the following commands:

~# echo /opt/sw/modules > /opt/apps/lmod/lmod/init/.modulespath
~# mkdir -p /opt/sw/modules/apptainer
~# mv 1.1.3.lua /opt/sw/modules/apptainer

Accessing apptainer

With the module file set in place, let us test that it works. Log into nfs-0 as user test, and then load the apptainer module:

~# sudo -i -u test
$ module load apptainer

To test that apptainer works, use the following command to print the version number:

$ apptainer version

If you see the version number printed out to the terminal, then it is time to move on to building a container image with apptainer!