New resources power long-running workflows at Pawsey Supercomputing Research Centre

Pawsey’s Setonix supercomputer (supplied by Karina Nunez).

Specialised nodes are now available at the Pawsey Supercomputing Research Centre that are designed to power long-running scientific workflows. Responding to researcher demand, new Workflow Nodes have been custom built on Setonix to optimise and support workflows managed by tools like Nextflow and Snakemake that surpass the regular 96 hour wall-time constraint.

Researchers voiced their challenges in running long workflows, including numerous reports from the BioCommons computational workflows community that they were running out of wall-time - the clock time it takes for a computation to run from start to finish. One of these researchers was Lauren Huet, Bioinformatics Research Officer at the Minderoo OceanOmics Centre at UWA:

Our Ocean Genomes project is addressing a key gap where over 95% of marine vertebrates lack sequenced genomes. Building such a comprehensive reference genome library requires intensive compute power, and the workflows can be quite long. This project would not be possible without the capacity to scale up to process tens or hundreds of genomes in parallel.

Dr Sarah Beecroft, Life Sciences Supercomputing Specialist at Pawsey, led the team effort to build dedicated Workflow Nodes on Pawsey’s Setonix - the most powerful research computer in the Southern Hemisphere. 

Setonix’s Workflow Nodes provide a stable and robust environment for workflow orchestration. Users can launch their master jobs interactively and keep their sessions alive for extended time periods, enhancing both productivity and performance. I’m really excited to see the new research that is enabled!

Lauren and the OceanOmics team are already benefiting greatly from the Workflow Nodes:

It’s been a game-changer for our research! The nodes enable us to run Nextflow pipelines directly in the terminal, offering unparalleled flexibility for developing and testing our workflows. The capability to execute long-running pipelines without interruptions has significantly increased our throughput, allowing us to produce results faster and more efficiently.

As a member of the BioCommons BioCLI project, Sarah is passionate about making command-line infrastructure accessible and well documented. Together with other supercomputing experts, the team has produced a new comprehensive technical user guide for users looking to run their workflows on the Setonix Workflow Nodes.

Learn how to run workflows on the Workflow Nodes in Pawsey’s user support documentation, or join the next meeting of the BioCommons computational workflows interest group to influence future research infrastructure developments.