Apptainer

Apptainer is the most widely used container system for HPC. It is a replacement (or next generation) for Singularity supported by the Linux Foundation.

Containers are a way to isolate your software and make it portable and reproducible. It is a valuable asset for reproducible science and, in addition, Its use is especially recommended when

1. Users rely on “old” libraries (e.g., HDF4);
2. Users need to update their library constantly;
3. It also makes the user more independent of the cluster admins.

Instructions

The steps to build a container always start with loading the apptainer module as follows

module load apptainer

For the next step, users have two options: 1) to just use a prebuilt image, or 2) to use a .def file (called recipe) that will contain the instructions to build the container. When using the latter option, we can build our container on top of another prebuilt image.

Building the container takes only one line of code, the structure (when building directly from a prebuilt image) is as follows

apptainer build [OPTION] <name-for-the-container> <library>://<prebuilt-image>

In order to know all the available “options”, one can run apptainer build --help. For the <library> part, usually we rely on DockerHub (for more options see the apptainer documentation). In general, we are interested in building a container image that is a single .sif file that can be transferred between computers. However, there is an interesting option called --sandbox, which creates an expandable container image. Sandboxes will be useful when trying to build a custom image. However, this type of container has two side effects. First, these containers take up more space. Secondly, they are not reproducible.