SFU gets speedy research computers
The following backgrounder relates to today’s announcement from the Compute Canada/WestGrid project.
Dugan O’Neil, 778.782.5623, firstname.lastname@example.org
Martin Siegert, 778.782.4691, email@example.com
Marianne Meadahl, PAMR, 778.782.3210/9017; firstname.lastname@example.org
Upgraded high-performance computing (HPC) systems with massive memory and exceptional speed were officially launched today at Simon Fraser University — giving researchers the tools to solve problems that have previously been beyond their reach.
Nearly $17 million has been invested through the Compute Canada/WestGrid project towards upgrades at SFU and the University of British Columbia, with contributions from the Canada Foundation for Innovation (CFI), the BC Knowledge Development Fund, SFU, UBC, Dell and Hewlett-Packard (HP).
The work supported by this infrastructure covers “big data” projects, such as those mapping the genetics of individual disease strains.
SFU physics professor Dugan O’Neil says: “Researchers who need to access and manipulate large datasets are well-served by the SFU facility. This expansion more than doubles the available storage at the site and more than triples the computing power.”
The resources will also enable researchers to collaborate on international projects, including the Large Hadron Collider (the world’s biggest atomic particle accelerator) in Europe.
The expanded Dell HPC system at SFU is called Bugaboo. Martin Siegert, SFU’s head of research computing, notes Bugaboo’s new storage capacity is 2,400 times that of modern desktop computer.
“A petabyte is one thousand terabytes, a million gigabytes. We now have 2.4 petabytes of storage,” he explains. And Bugaboo is 4,300 times faster than the typical desktop computer.
“I think the way computing in Canada is going is actually quite exciting. We're no longer working on a per-university basis. This is a facility that is open to all researchers in Canada and likewise SFU researchers can use any other research facility in the country.”
Mario Pinto, SFU’s vice-president of research, adds: “The key to international collaboration is rapid data collection and communication.
“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 neurogical disorders with neuroinformatics.
“In all of these endeavors, collaboration assisted by electronic data storage and exchange is a critical component.”
One beneficiary of the Bugaboo upgrade is Jack Chen, associate professor in SFU’s department of molecular biology and biochemistry.
“WestGrid is a critical platform for our genomics research on pathogens, which aims to identify genomic variations that define disease conditions [particularly malaria],” says Chen. “The volume of genomic sequences is large and beyond the power of normal computers to process, but with WestGrid, we have been able to expand our sequencing and analysis work.”
SFU’s Bugaboo platform acts as one of five Canadian Tier-2 data centres for ATLAS, a particle-physics experiment at the Large Hadron Collider. Physics profs Bernd Stelzer and Mike Vetterli are the other key SFU users for the ATLAS project.
At SFU, the Bugaboo platform offers 414 computer nodes containing 4,328 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).
Those 4,328 cores make Bugaboo some 4,300 times faster than a desktop computer, which would have only one or two cores.
WestGrid User Profiles – SFU:
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.
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 behavior 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.
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.