Helping the bioinformatics community harness the computing resources they need
Exploring GPUs with Sarah at the ABACBS Conference workshop
The challenges researchers face when accessing high performance computing was addressed at a recent workshop led by a national group of experts. More than 40 researchers and bioinformaticians explored strategies for the adoption, usage, and optimisation of Graphics Processing Units (GPUs) at ABACBS 2024 in December.
The workshop was co-ordinated by Dr Andrew Lonsdale (Peter MacCallum Cancer Centre), Dr Sarah Beecroft (Pawsey Supercomputing Research Centre) and Dr Johan Gustafsson (Australian BioCommons). It featured a wide range of speakers covering practical insights on resource availability, portable code that runs efficiently on multiple GPU platforms (NVIDIA, AMD, and Intel), and real-world use cases.
The availability of GPUs in the Australia context was introduced by Andrew Lonsdale (Peter Mac), and Georgie Samaha (BioCommons) offered practical guidance on accessing GPUs via national resources and access schemes. Sarah Beecroft (Pawsey) provided a concise introduction to high performance computing principles including GPU access, to ensure everyone shared similar foundational knowledge. George Bouras (University of Adelaide) then demonstrated how to integrate machine learning frameworks like PyTorch with the Slurm scheduler, while Edward Yang (WEHI) presented best practices for writing interoperable, maintainable GPU code.
Highlighting real-world applications, Keiran Rowell, Nathan Glades, and Josh Caley (UNSW Structural Biology Facility) showcased how GPUs are empowering researchers to handle large, complex structural biology datasets, and Wytamma Wirth (University of Melbourne) illustrated the power of online GPU resources to accelerate in Bayesian phylogenetics analyses.
Feedback showed that attendees appreciated the variety of speakers and the balance of technical depth with practical applicability. They particularly highlighted the workshop’s interactive approach, which included live polling and ample Q&A sessions.
Half of the attendees reported they were already using GPUs, and the other half planned to adopt them soon. Two-thirds were keen to integrate existing GPU-enabled bioinformatics tools, while one-third aimed to develop new GPU-accelerated algorithms, underscoring the community’s readiness to embrace GPUs both as a means of immediately accelerating current workflows, and as a basis for innovative tool development.
This workshop aimed to support researchers with the knowledge, skills, and resources they need to unlock the full potential of GPU computing, and participants reported that they were keen to go on to investigate GPU applications beyond AI/ML, gain deeper insights into GPU architectures, and participate in more hands-on training sessions.
Attending the ABACBS Conference is a great way to connect and strengthen the GPU-enabled bioinformatics community in Australia, and Australian BioCommons sponsors and attends the conference each year to hear from researchers and bioinformaticians and to share responses to their research infrastructure priorities. Stay tuned for more information about ABACBS 2025 in Adelaide!