BOSTON, BIO-IT WORLD, Booth 405, May 1 /PRNewswire-FirstCall/ -- A powerful new computing system from SGI (Nasdaq: SGIC) has shortened the time required to run complex calculations for biologists, chemists and engineers at East Carolina University (ECU) - in some cases, from several days to just a few hours.
BOSTON, BIO-IT WORLD, Booth 405, May 1 /PRNewswire-FirstCall/ — A powerful new computing system from SGI (Nasdaq: SGIC) has shortened the time required to run complex calculations for biologists, chemists and engineers at East Carolina University (ECU) – in some cases, from several days to just a few hours.
Purchased with a grant from the National Science Foundation (NSF), the new SGI(R) Altix(R) 4700 system is helping ECU researchers analyze computational models that were growing too large and complex for the university's existing resources. The resulting performance gains also have convinced evolutionary biologists at ECU that the shared-memory Altix platform can be a superior engine for the Bayesian inference analyses, routinely run on distributed clusters.
"When I learned that ECU was applying to the NSF for a large shared-memory system instead of a distributed cluster, you could say I was disappointed," said Dr. Jason Bond, an ECU professor of biology. "Everyone I talked to in my field disagreed with our plan to invest in a shared-memory machine."
But after seeing complex Bayesian and dynamic homology computations soar on the new 128-core SGI Altix 4700 system, Bond was sold on the advantages of a large-node, shared-memory solution. The Altix platform allows access to all data in the system's memory directly and efficiently, without having to move data through I/O or networking bottlenecks – a common problem with traditional distributed clusters.
"We're now running MrBayes analyses in a few hours that previously would take days to run on our dual-core processor machine here in the lab," said Bond, who also leverages the Altix system to run POY, a complex sequence alignment and tree search application, and other algorithms as part of ongoing NSF evolutionary studies of spiders and millipedes.
With the SGI Altix solution improving ECU's research productivity "many times over," continued Bond, "We now have the time to run lots of permutations to test our inferences. In the past, we'd run two permutations and wait days to get the results. We'd send the results for peer review, and they'd recommend dropping that analysis from the paper altogether. It just was not productive."
Installed in January, the new system includes 256GB of shared memory and 10TB of shared disk storage. For ECU, it represents an eight-fold increase in compute power and a 12-fold increase in disk storage.
ECU researchers are now turning their attention to the system's ability to make a broad range of studies more interactive and insightful by delivering results sooner. Research underway at the university includes:
— A study of the complex reaction mechanisms of catalytic chemical processes. Such investigations will lead to the design of new, more efficient catalysts that will aid in the synthesis of commercially important molecules. — Explorations into the structure and function of biological ion channels, or membrane proteins, in both normal and diseased cells — The design and development of advanced engine concepts by applying computational fluid dynamics studies. Future designs may also be destined for transfer to ECU industrial partners.
"Our goal in applying for the NSF grant was to secure a system that improved productivity across a wide array of applications, was easy to administer, and had a low cost of ownership," said Andrew Sargent, professor of chemistry and NSF grant principal investigator. "While highly distributed applications are often best suited for distributed clusters, the Altix 4700 platform provides a far more flexible, scalable and user-friendly environment for running the most complex codes. Now our researchers are conducting more in-depth chemical, biological and engineering studies than ever before, and are even pursuing areas of investigation that previously were closed to them."
Built on the powerful SGI(R) NUMAflex(TM) architecture and featuring a high-performance, industry-standard 64-bit Linux(R) environment, the Altix 4700 has ECU researchers looking toward the future. "It simply opens up other avenues of data exploration," said Bond. "Even with Bayesian analysis, which can be enormously involved and compute- and memory-intensive, we're able to construct larger trees and analyze larger data sets, without tying up all the desktops in the lab for hours or days."
James River Technical, Inc., SGI's designated partner for higher education and research, facilitated the sale.
SGI is demonstrating its acclaimed SGI Altix and SGI(R) InfiniteStorage solutions in Booth 405 at the Bio-IT World Conference and Expo through May 2 at the World Trade Center in Boston.
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