Apptainer on OzSTAR

Apptainer (formerly Singularity) enables users to have full control of their environment. Apptainer containers can be used to package entire scientific workflows, software and libraries, and even data. This means that you don't have to ask your cluster admin to install anything for you - you can put it in a Apptainer container and run.

You can use Apptainer by loading the module

module load apptainer/latest


For documentation on how to create Apptainer containers, please visit the official documentation:

Binding the filesystem to a container

To bind /fred from OzSTAR to /fred in your container:

apptainer run -B /fred mycontainer.simg

To bind your project directory to a specific location in your container (In this case /fred/oz123 from OzSTAR to /oz123 inside the container):

apptainer run -B /fred/oz123:/oz123 mycontainer.simg

Using a GPU with a container

If you are on a login node, or you have requested one or more Nvidia GPU's in your batch job, you can access the GPU's in your container using the --nv switch. This will automatically bind the GPU's in to your container. You may still need to have your own cuda installation in your container.

apptainer run --nv mycontainer.simg

Increasing the speed of your container on OzSTAR

Depending on your workload, it is often better to request --tmp storage and copy your image to there before you use your container. In many cases this will provide better performance. It is important that your requested --tmp size is bigger than your apptainer image, or --tmp will run out of space and your job will crash.

For example, in your batch script:

#SBATCH --tmp=10G

cp /path/to/my/container.simg $JOBFS/container.simg

apptainer run $JOBFS/container.simg