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Singularity is a container platform: it lets you create and run containers that package up pieces of software in a way that is portable and reproducible. With a few basic commands, you can set up a workflow to run on Pawsey systems using Singularity. This page introduces how to get or build a Singularity container image and run that image on HPC systems. |
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Once you've written a Dockerfile, you can use it to build a container image.
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There are websites which provide detailed instructions for writing good Docker recipes, such as Best practices for writing Dockerfiles (external site). We also have some base images and specific examples listed on our Pawsey GitHub containers page (external page).
A simple snippet is provided in listing 1:
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Singularity allows users to make use of GPUs within their containers, by adding the runtime flag --nv (enable NVIDIA support).for both NVIDIA and AMD GPUs. Topaz and Nimbus use NVIDIA GPUs, while Setonix uses AMD GPUs. To enable NVIDIA support, add the runtime flag --nv. To use AMD GPUs, add the --rocm flag to your singularity command instead of --nv.
Listing 3 shows an example of running Gromacs, a popular molecular dynamics package, among the ones that have been optimised to run on GPUs through NVIDIA containers:
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