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U.S. university utilizes ATI processors in protein programme

Posted: 11 Oct 2006     Print Version  Bookmark and Share

Keywords:ATI Technologies Inc.  Stanford University  ATI processors 

ATI Technologies Inc. has recently announced that Stanford University has released software to utilize ATI processors for Stanford University's [email protected] distributed computing project, yielding an enormous increase in the speed of disease research.

By enabling [email protected] participants to make use of the powerful processing architectures found in ATI's Radeon X1900 and Radeon X1950 graphics cards, Stanford said it expects to gain new capabilities that have never been possible before. With this new processing power now tapped, said the press release, researchers expect to discover even more about the science of protein folding and folding-related diseases, with potentially dramatic effect for studies into Alzheimer's, cancer, Huntington's and Parkinson's diseases among others.

"The quest to understand diseases like cancer and Alzheimer's is the reason why the [email protected] program exists, and with the phenomenal acceleration provided by ATI processors, we can truly say this is life-changing work," said Vijay Pande, associate professor of chemistry, and director of [email protected] distributed computing project, Stanford University.

The [email protected] programme studies the ways in which proteins fold, assembling themselves in order to carry out important functions in the body. While protein folding is critical and fundamental to virtually all of biology, today the concept is still considered to be a mystery. When proteins do not fold correctly, consequences include a number of diseases, so to better understand this area, the [email protected] program groups hundreds of thousands of home computers together worldwide, studying folding by taking advantage of each computer's processing power to form a distributed supercomputer. Today the program consists of approximately 200,000 computers, using various computer processors.

[email protected] is made up of a number of engine cores  software designed to calculate various aspects of molecular dynamics associated with protein folding. Stanford's Gromacs software core, introduced in May 2003, remains the fastest and one of the most optimized molecular dynamics codes in the world. Through the work of Stanford University researchers, the Gromacs software was tuned to take advantage of ATI's Radeon X1900 and Radeon X1950 products, delivering the massive speed up in processing referenced above. However, as versatile as the Gromacs code is when combined with ATI processors, some protein folding calculations cannot be performed on ATI hardware, and require the use of computer processors and other engine cores.

With support for ATI processors, [email protected] participants and disease researchers are tapping into the new capabilities offered by these advanced architectures, with a Radeon X1900 card performing scientific calculations at 20x times to 40 times the speed of traditional computer processors.2 At that rate, using the processing power of one ATI Radeon X1900, three years worth of research can now be done in just one month. The processing power of just 5,000 ATI processors is also enough to rival that of the existing 200,000 computers currently involved in the [email protected] project; and it is estimated that if a mere 10,000 computers were to each use an ATI processor to conduct folding research, that the [email protected] program would effectively perform faster than the fastest supercomputer in existence today, surpassing the 1 petaFLOP level.




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