BC Gov News

VANCOUVER - Upgraded high-performance computing (HPC) systems with massive memory and exceptional speed are being launched at two British Columbia universities. This will give 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 toward upgrades at the University of British Columbia (UBC) and Simon Fraser University (SFU), with contributions from the Government of Canada through the Canada Foundation for Innovation (CFI), as well as the B.C. Knowledge Development Fund, SFU, UBC, Dell and HP.

The work being supported by this infrastructure covers a wide range of fields that focus on computational challenges and "big data" projects, such as those mapping out the genetic composition of individual disease strains. These resources will also enable local academics to collaborate on international research endeavours, including the Large Hadron Collider in Europe.

"By investing another $9.4 million in WestGrid from our B.C. Knowledge Development Fund, we're helping create a super-fast, super-powerful computing platform to support world-class B.C. innovation," said Harry Bloy, MLA for Burnaby-Lougheed. "Our researchers will use it to tackle complex problems, including climate change, early detection of Alzheimer's, and other things that affect B.C. families, while creating jobs by driving the province's knowledge economy."

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 B.C. and Canada," says John Hepburn, UBC's vice president research and international.

For Joerg Bohlmann and Colette Breuil, professors at UBC (the Michael Smith laboratories and faculty of forestry), these computational resources are important for their genomics investigations into the mountain pine beetle epidemic, as part of the Tria project. "Genomes of fungi and beetles are several tens to hundreds of million bases long," says Breuil. "Assembling and analyzing them requires terabytes of storage and large memory nodes. Greater computing resources and powers are absolutely essential to harness the full benefits of these projects."

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."

One such beneficiary of the Bugaboo upgrade is Jack Chen, an associate professor in the department of molecular biology and biochemistry at SFU. "WestGrid is a critical platform for our genomics research on pathogens, which aims to identify genomic variations that define disease conditions [particularly malaria]," said 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."

"Today's launch is a powerful example of what can be achieved when various stakeholders come together as partners," said Gilles G. Patry, president and CEO of the CFI. "These installations will further enhance Canada's capacity to effectively compete in the global technology arena."

The resource upgrades at SFU and UBC complement an $8 million investment into HPC systems at the University of Victoria made through Compute Canada, WestGrid, CFI, IBM and the Government of B.C. in February, 2010.

Two backgrounders follow.

Media Contacts:

Cybera Inc.
Meagan Hampel
Communications Officer
403 210-5376

University of British Columbia
Brian Lin
Senior Communications Co-ordinator
604 822-2234

Simon Fraser University
Martin Siegert
Head, Research Computing

WestGrid/Compute Canada Site Lead
778 782-4691

Dugan O'Neil
Primary Investigator, WestGrid
778 782-5623

BACKGROUNDER 1

WestGrid User Profiles - UBC:

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.

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 (a technique for counting and inspecting microscopic particles) is a detailed bioinformatics method that 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.

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 B.C. 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.

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 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.

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.

Media Contacts:

Cybera Inc.
Meagan Hampel
Communications Officer
403 210-5376

University of British Columbia
Brian Lin
Senior Communications Co-ordinator
604 822-2234

Simon Fraser University
Martin Siegert
Head, Research Computing
WestGrid/Compute Canada Site Lead
778 782-4691

Dugan O'Neil
Primary Investigator, WestGrid
778 782-5623

BACKGROUNDER 2

Compute Canada/WestGrid

Compute Canada is a national platform that integrates High-Performance Computing (HPC) resources at seven partner consortia across the country to create a dynamic computational resource. Compute Canada brings together high-performance computers, data resources and tools, and academic research facilities from around the country. WestGrid is the HPC consortium that encompasses 14 partner institutions across British Columbia, Alberta, Saskatchewan and Manitoba. Compute Canada/WestGrid have built a user community across Canada in disciplines ranging from the sciences and engineering to arts and humanities. This user community is supported by a distributed and cohesive team of technical staff and system architects. For more information, visit www.computecanada.ca or www.westgrid.ca

British Columbia Knowledge Development Fund

The B.C. Knowledge Development Fund is the provincial government's major research infrastructure investment program. Since 2001, the fund has invested more than $423 million for 740-plus research projects in public post-secondary institutions, teaching hospitals and affiliated non-profit research agencies. This includes $15 million provided to WestGrid. The B.C. Knowledge Development Fund improves British Columbia's ability to attract and retain high-quality researchers and skilled technicians, and helps institutions compete successfully for private-sector and federal funding. In the past decade, the B.C. government has committed $1.8 billion to research in B.C., which has secured another $1.3 billion from other sources. For more information, visit: http://www.tted.gov.bc.ca/TRI/research/funding/BCKDF/Pages/default.aspx

Canada Foundation for Innovation

Created by the Government of Canada in 1997, the Canada Foundation for Innovation (CFI) strives to build our nation's capacity to undertake world-class research and technology development, to benefit Canadians through investments in state-of-the-art facilities and equipment at universities, colleges, research hospitals and non-profit research institutions. For more information, visit: www.innovation.ca

University of British Columbia

The University of British Columbia (UBC) is one of North America's largest public research and teaching institutions, and one of only two Canadian institutions consistently ranked among the world's 40 best universities. Surrounded by the beauty of the Canadian West, it is a place that inspires bold, new ways of thinking that have helped make it a national leader in areas as diverse as community service learning, sustainability and research commercialization. UBC offers more than 55,000 students a range of innovative programs and attracts $550 million per year in research funding from government, non-profit organizations and industry through 7,000 grants. For more information, visit: www.ubc.ca

Simon Fraser University

Simon Fraser University is a public research university with three campuses in the British Columbia Lower Mainland. It has more than 34,000 students and 950 faculty members. It has often been ranked Canada's No. 1 comprehensive university, most recently by Maclean's magazine in 2009 and 2010. The Times of London also rates it as one of the world's top 200 universities. The university's alumni include four B.C. premiers. For more information, visit: www.sfu.ca

Dell

Dell Inc. (NASDAQ: DELL) listens to customers and delivers innovative technology and services that give them the power to do more. For more information, visit: www.dell.ca

HP

HP creates new possibilities for technology to have a meaningful impact on people, businesses, governments and society. The world's largest technology company, HP brings together a portfolio that spans printing, personal computing, software, services and IT infrastructure at the convergence of the cloud and connectivity, creating seamless, secure, context-aware experiences for a connected world. More information about HP (NYSE: HPQ) is available at: www.hp.com

ATLAS

The ATLAS experiment at the Large Hadron Collider (LHC) at CERN, Geneva, Switzerland studies the basic forces that have shaped our Universe since the beginning of time. Among the possible unknowns are the origin of mass, extra dimensions of space, unification of fundamental forces, and evidence for dark matter candidates in the Universe. If all the data from ATLAS could be recorded, they would fill 100,000 CDs per second. However, ATLAS only records a fraction of the data (those that may show signs of new physics) at a rate that is equivalent to filling two CDs every minute. These data are then distributed to storage facilities around the world were they are stored for researchers to access and analyze. The WestGrid/ComputeCanada storage facility at SFU acts as one such storage facility for ATLAS within Canada.

Media Contacts:

Cybera Inc.
Meagan Hampel
Communications Officer
403 210-5376

University of British Columbia
Brian Lin
Senior Communications Co-ordinator
604 822-2234

Simon Fraser University
Martin Siegert
Head, Research Computing
WestGrid/Compute Canada Site Lead
778 782-4691

Dugan O'Neil
Primary Investigator, WestGrid
778 782-5623