New GPUs Set AMBER Performance Record

May 18, 2011

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The fastest acceleration to date of AMBER 11, a molecular modeling software used to simulate the behaviors of biomolecules, has been reported by researchers at the San Diego Computer Center. Ross Walker, a principle contributor to the AMBER code and professor at SDCC, used four Nvidia Tesla M2090 GPUs together with four standard CPUs to achieve a record performance of 69 nanoseconds of simulation per day compared to the previous record on a supercomputer which is 46 nanoseconds of simulation per day.

These new GPU chips will be made available in servers such as the new HP ProLiant SL390 G7 4U server, which is built to cater to computing environments that require both CPUs and GPUs.

In other GPU news, Nortech has installed an 88,000 core GPU cluster in the "world's greenest data center" at Syracuse University. The cluster, which is being used for physics research and data analysis, uses Nvidia chips and uses 100,000 watts of power when running at maximum loads.

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The Cystic Fibrosis Interactome

Sandra Pankow is currently a research associate in John Yates' lab at Scripps Research Institute, studying protein-protein interactions involved in cystic fibrosis.

"I'm interested in trying to understand genetic diseases from a systems biology point of view," she says. "I've found that proteomics is the ideal tool for this because it gives the researcher the possibility to investigate thousands of proteins at the same time rather than just having to guess which one or two you should look at."

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With it, Pankow says, "we've reached about 30-fold to 100-fold higher sensitivity than previous methods. We're now able to profile an interactome to near completeness."
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