Lab Canada

Fast, powerful computing resources open research doors

Vancouver, BC – Upgraded high-performance computing (HPC) systems with massive memory and exceptional speed are being launched at two universities in British Columbia.

Nearly $17 million has been provided through the Compute Canada / WestGrid project toward upgrades at the University of British Columbia (UBC) and Simon Fraser University (SFU), with contributions from the Canada Foundation for Innovation (CFI), as well as the BC Knowledge Development Fund, SFU, UBC, Dell and HP.

The expanded computational tools include an HP system at UBC, called Orcinus, and the Dell HPC system at SFU, called Bugaboo. Orcinus provides 928 compute nodes containing 9,600 cores (processors that read and execute program instructions), 19.2 TB of memory and 0.5 PB of storage capacity (equivalent to 250 billion pages of standard printed text). It also offers a theoretical computational performance of more than 90 TeraFLOPS, meaning it enables trillions of calculations to be performed every second.

“Big science requires the latest and most robust tools, and the Compute Canada/WestGrid investment not only provides our researchers with the resources they need to tackle complex scientific investigations, but it will help attract international collaborations and the brightest minds around the world to BC and Canada,” says John Hepburn, UBC’s vice president research and international.

WestGrid projects at UBC include:

1) Gren Patey, Department Of Chemistry: Gren Patey’s research group is using WestGrid’s HPC resources to simulate and measure the structure of ion-water behaviour in nanopores. This information offers important clues in understanding and influencing the transport of ions and water through systems such as nanotubes and biological channels. Preliminary results from the WestGrid simulations have alluded to new methods of altering ion transport.

2) Ryan Brinkman, Terry Fox Laboratory, BC Cancer Agency: The analysis of cancer particles lies at the heart of Ryan Brinkman’s work with the Terry Fox Laboratory. Flow cytometry can produce millions of multiparametric descriptions of individual cancer cells. The Orcinus system at UBC is used to archive and analyze the data gathered on lymphoma, immunity and graft vs. host diseases. This dissemination will be used to develop a systemic approach for capturing, modeling and analyzing flow cytometry data.

3) Joerg Bohlmann, Michael Smith laboratories; and Colette Breuil, Faculty of Forestry: The Tria Project is using genomics to study the destructive interaction of bark beetles, fungal pathogens and host pine trees. The results from the project’s genomics and system biology approach, funded by Genome Canada, Genomes BC and Genome Alberta, are informing, in real-time, ecological risk models and economic analyses. These outcomes, in turn, advance resource management and policies. Joerg Bohlmann and Colette Breuil’s co-ordinated research groups are using WestGrid to assemble the massive data sets of the genome and transcription sequences of the bark beetles and fungi to provide insights into the molecular mechanisms that allow them to undermine or disarm pine trees’ defenses.

At SFU, the Bugaboo platform offers 414 compute nodes containing over 4,300 cores, nearly 9 TB of memory and 2.4 PB of storage capacity (enough space to store the content of nearly every academic research library in the USA). This effectively doubles the site’s available storage, and triples its computing power. Such an efficient system will allow researchers to contribute to large-scale computational projects, such as ATLAS, an experiment within the Large Hadron Collider that is investigating particle physics in order to discover the nature of the universe.

“The key to international collaboration is rapid data collection and communication,” said Mario Pinto, SFU’s vice president, research. “Investment in the Compute Canada/WestGrid initiative will provide the necessary portals for the exchange of information in such diverse domains as particle physics, tracking epidemics in infectious diseases using bioinformatics, mapping genetic and epigenetic factors in chronic diseases, and studying degenerative neurological disorders with neuroinformatics. In all of these endeavours, collaboration assisted by electronic data storage and exchange is a critical component.”

WestGrid projects at SFU include:

1) Jack Chen, Department of Molecular Biology and Biochemistry: Jack Chen’s group is using WestGrid to help identify genomic differences that may be responsible for the virulence of malaria parasites. This understanding will help identify necessary drug targets and design. The volume of these genomic sequences is large and beyond the power of normal computers to process. As well as aiding with this analysis, the WestGrid resources have enabled Chen’s group to expand the scope of its work, and initiate collaborative work with scientists in China.

2) Andrew Calvert, Earth Sciences: Seismologist Andrew Calvert is creating improved images of the Earth’s sub-surface using seismic reflection and refraction data. These images could help monitor and predict the behaviour of earthquake-prone fault lines that are up to 40km below ground. He is using WestGrid’s computing power to support his seismogram modeling and simulations, as well as process the large volumes of imaging data he is gathering.

3) Michael Eikerling, Chemistry: Polymer electrolyte fuel cells are among the more promising systems for high-efficiency, low-emission energy sources. Michael Eikerling is modeling the physiochemical processes of low-temperature fuel cells (design, structure and energy flow) to find optimized ways to create and operate them. He is using WestGrid to develop advanced models for the structure and performance of these fuel cells at a phenomenological and kinetic level, and study their dynamics and energetics.