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Stony Brook University Scientist Uses NCSA’s SGI Altix System to Earn Top Prize for Humanitarian Research


SGI (NASDAQ: SGIC) today announced that several researchers honored in the Itanium Solutions Alliance Innovation Contest conducted their acclaimed work on SGI® Altix® systems.

Dr. Carlos Simmerling at Stony Brook University in New York won $50,000 and top honors for his breakthrough medical research, while the University of California-Riverside (UCR) earned Honorable Mention and $5,000. Four other Altix users were named finalists: Imperial College, London; Interactive Supercomputing, Inc; McLaren Racing; and Stanford University.

The contest recognizes projects that utilize the full potential of systems based on Intel® Itanium® 2 processors, such as SGI Altix. From a pool of 25 finalists in three categories, winners were announced today at the Intel Developer Forum in Beijing and Gelato ICE: Itanium Conference and Expo in San Jose, Calif. Stony Brook’s Simmerling won the top award in the Humanitarian Impact Innovation category. Working on an SGI Altix system located at the National Center for Supercomputing Applications (NCSA), Simmerling and his team have developed simulation methods that can explore the molecular basis for diseases such as AIDS, cancer and tuberculosis. The team recently achieved the most extensive computer simulations ever done on HIV protease, a molecule that slices a pre-HIV protein chain into the pieces that ultimately assemble into a mature and infectious virus. The simulations modeled how the viral protease changes structure over time, revealing for the first time how it transiently opens during its function, allowing drugs to gain access to the interior and inactivate it. The results provide vital data in the effort to develop new treatments for the 40 million people currently living with AIDS.

“This is a tremendous honor — one that recognizes what human effort and technological advances can achieve when brought to bear on a problem that had previously proved insurmountable,” said Simmerling, an associate professor in Stony Brook’s Department of Chemistry and director of Computational Biology for Stony Brook’s Institute for Chemical Biology and Drug Discovery.

Simmerling has concluded that using NCSA’s powerful Altix system has made a dramatic difference in his research. “The Altix allows us to obtain new medical advances in months, rather than in years,” he said.

Another Altix user, the University of California-Riverside, earned Honorable Mention in the Entrepreneurial Innovation category for its use of an SGI Altix system outfitted with an SGI® RASC™ (Reconfigurable Application Specific Computing) blade. Biological scientists leveraged solutions provided by UCR’s Department of Computer Science and Engineering to develop and run a new compilation tool called ROCCC (Riverside Optimizing Compiler for Configurable Computing). The tool makes it easy to customize Field Programmable Gate Array (FPGA) technology, which is used in SGI RASC solutions, for specific uses.

Four other SGI Altix users were named finalists in the competition:

-Imperial College, London. The National Service for Computational Chemistry Software (NSCCS) is sponsored by Imperial College and provides researchers with access to 20 different software applications. Recently, escalating needs were fast outpacing its aging compute resources. After an investment in a powerful shared-memory SGI Altix system driven by 224 Intel Itanium 2 cores, NSCCS users now have access to four times the number of processors as before, an improvement that translates to shorter time to solution and the ability to compute problems that before were not even feasible. (Humanitarian Innovation finalist.)

-Interactive Supercomputing, Inc. (ISC). Researchers at the National Cancer Institute mine a vast public database of genomic information for potential discoveries. On a desktop, MATLAB-based statistical analyses took more than two days to compute, but using ISC’s Star-P software to transparently execute the MATLAB algorithms on an SGI Altix system, the computations are done in 15 minutes or less. That acceleration is significant to researchers looking to continually extend the reach of their studies. (Humanitarian Innovation finalist.)

-McLaren Racing. McLaren Racing needed a system that could scale to meet new challenges relating to the aerodynamics of all aspects of the car including wings, floor and topbody. The HPC power of the Itanium 2-based SGI Altix allowed McLaren Racing to reach exacting Formula 1 standards and timescales. The Formula 1 CFD models are up to 10 times larger than typical industrial CFD projects. By automating much of the process, the SGI Altix systems have been able to accelerate work on the car model many times over. (Enterprise Business Application finalist.)

-Stanford University. To improve available treatments for cardiovascular disease, Stanford researchers developed a software solution that incorporates computational mechanics and scientific visualization. That combination that requires the kind of exceptional floating-point performance found in Intel Itanium 2 processors and SGI Altix systems. Now, even complex computations can be performed quickly and accurately enough to guide treatment decisions for often life-threatening ailments. (Humanitarian Innovation finalist.)

“The Innovation Contest submissions operating on SGI Altix servers showed that exciting and innovative computing on Itanium-based systems is taking place in sectors ranging from pharmaceutical research to weather forecasting,” said Mark K. Smith, Innovation Contest judge and managing director of the Gelato Federation. “In the future, these data-intensive deployments will continue to evolve and Itanium 2-based systems will continue to grow and scale to the needs of innovative users.”

“SGI applauds the remarkable work of these researchers, and we are delighted that they have been honored by the Itanium Solutions Alliance,” said Ravi Pendakanti, director of marketing, SGI. “Powered by Intel Itanium 2 processors, SGI Altix systems regularly help scientists and engineers achieve what just a short time ago was considered impossible. The achievements of these visionaries illustrate that SGI Altix truly delivers Innovation for Results.”


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