apptainer_wrapper / singularity_wrapper

This small script helps with running apptainer / singularity images.

It is especially useful when using Lmod or other module system that can set environment variables.

Usage

Set the $PATH to point to the bin-folder.

Afterwards, you can set these two environment variables:

• $CONTAINER_IMAGE - Path to the apptainer / singularity image that should be used.
• $CONTAINER_FLAGS - Extra flags that should be added to every apptainer / singularity call (e.g -B /my_folder, --nv).

After these have been set one can run:

• apptainer_wrapper run - same as running apptainer run $CONTAINER_FLAGS $CONTAINER_IMAGE
• apptainer_wrapper exec my_executable - same as running apptainer exec $CONTAINER_FLAGS $CONTAINER_IMAGE my_executable
• apptainer_wrapper shell - same as running apptainer shell $CONTAINER_FLAGS $CONTAINER_IMAGE
• apptainer_wrapper shell /bin/bash - same as running apptainer shell -s /bin/bash $CONTAINER_FLAGS $CONTAINER_IMAGE

Example Lmod module

-- -*- lua -*-
--
-- Module file for singularity-wrapper
--

whatis([[Name : my-image]])
whatis([[Version : latest]])
help([[A software in ]])

family("container")

prepend_path("PATH", "/path/to/singularity_wrapper/bin")
setenv("CONTAINER_IMAGE", "/path/to/singularity/image/my-image-latest.sif")
setenv("CONTAINER_FLAGS", " -B /my_binding --nv ")