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UK, Thai researchers use Tesla GPUs to combat H1N1

Posted: 20 Jun 2012 ?? ?Print Version ?Bookmark and Share

Keywords:H1N1 Virus? Tesla? GPU?

The fight against H1N1 has been difficult with many anti-influenza drugs being rendered ineffective due to the virus' rapid mutations. However, researchers at the University of Bristol in the United Kingdom, and the Bansomdejchaopraya Rajabhat and Chulalongkorn Universities in Bangkok, have used computer simulation to observe how H1N1 mutations change the chemical and biological structural dynamics of a key enzyme of the virus, revealing its mechanism of resistance to existing anti-influenza drugs. With this breakthrough, development of inhibitor drugs addressing these mutations can now progress, possibly reducing the impact of future epidemics.

Using a small cluster equipped with Nvidia Corp.'s Tesla GPUs running simulations with the AMBER molecular dynamics application, the research team uncovered the H1N1 mechanism of resistance in half the time and using one-fifth the servers that it would have taken using a CPU-only cluster. A paper detailing the researchers' findings has already been published in a recent edition of Biochemistry.

In detailing how Nvidia's GPU helped them, Christopher Woods, lead investigator for the U.K. research team stated that the four-node, eight-GPU cluster allowed them to quickly run and repeat a much larger number of complex simulations. This enabled them to exhaustively explore all virus mutations, building up a detailed picture that allowed them to quickly identify the key steps in the mechanism of resistance, in a much shorter time. He further stated that a CPU-only system with 16 to 24 CPUs would have taken twice as long and would have made it difficult for the team to concentrate all their time on the cluster, given the high demand for compute cycles by other researchers across the university.

Following the outbreak of H1N1 influenza cases in 2009, researchers worldwide have been racing to discover how virus mutations led to the ineffectiveness of leading anti-influenza drugs. However, studying viruses in laboratory experiments was difficult because reactions were often too fast and delicate to capture. Advanced computer simulations of these systems have previously been beyond the reach of researchers without access to expensive, high-powered supercomputers.

With Nvidia's small and affordable GPU-based server now available, researchers now have access to a high-performance system. Nvidia has also launched its GPU Test Drive program, aiming to aid more researchers experience GPU-accelerated research. It enables computational chemists and biologists to experience GPU acceleration of their molecular dynamics simulations for free on a remotely hosted GPU cluster.





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