Software Stack

Software on Pawsey computers includes vendor-supplied operating systems, compiler suites, numerical libraries and research-domain-specific packages. There may be multiple Software Stacks deployed on the Setonix, see The pawseyenv module section for more information.The software stack of Setonix is organised on three levels, all residing under the /software filesystem.

  • The system-wide level is accessible by all users of the supercomputer and is maintained by the Pawsey staff.
  • The project-wide level is the set of applications and libraries accessible by all members of a project. Each project is provided with a dedicated directory on the /software filesystem. The path is /software/projects/<project-id>. Project members are responsible for managing their installations.
  • Each user also has a dedicated directory in which to install personal software. The path is /software/projects/<project-id>/<user-name>

Module systems are available on our HPC systems to help manage software and keep the shell environment as tidy and reproducible as possible. In particular, Setonix adopts Lmod. For instance, the command

$ module load gromacs/2023-double

would load the required variables to run the molecular dynamics software Gromacs for double precision.

Container technology is emerging in HPC as an alternative effective tool for building, managing and running software. Singularity is the container engine currently installed on all Pawsey Supercomputing systems. On Setonix, Singularity can be loaded as a module using the syntax

      $ module load singularity/4.1.0-<FLAVOUR>

(Check the differences in flavours in our Singularity at Pawsey documentation.)

Among other features, Singularity is fully compatible with the Docker engine and Docker containers. Singularity can be run on Nimbus cloud as well as on personal computers and workstations.

A listing of the packages that are installed on Pawsey machines is available. Dedicated pages with additional details are available for the most popular applications within our user base.

The pawseyenv module

The pawseyenv module makes the software installed by Pawsey staff visible. It has versions, reflecting the fact that there may exist multiple software stack deployments on Setonix at any given time. At the time of writing, there are two deployments on Setonix: 2022.11  and 2023.08 . The version represents the date when the deployment was executed.
You can select which deployment to use using the following sequence of commands.

Terminal 1. Changing software stack version.
module unload gcc
module swap pawseyenv/<loaded-version> pawseyenv/<desired-version>
module load gcc

Despite the fact that you may choose, we always suggest users to transition to the newer stack. We may deploy a new stack because the supercomputer may have been updated, and so have the MPI libraries. Your executable may point to old libraries that do not exist anymore.

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External references