NCI Leases New Supercomputer

National Cancer Institute
Monday, 2 August 1999

The National Cancer Institute (NCI) today announced the signing of a three-year, $6.5 million agreement with Silicon Graphics, Inc., (SGI) to lease a Cray SV1 supercomputer. The new machine will be operated at NCI's Advanced Biomedical Computing Center (ABCC) in Frederick, Md., where it will replace a Cray Y-MP supercomputer that has been in use there since 1991.

According to Jacob Maizel, Jr., Ph.D., chief of NCI's Laboratory of Experimental and Computational Biology and a founder of the Frederick center, the SGI supercomputer has a combined computing power of 115 gigaflops, or enough capacity to process in one day a computational task that would take a high-end Pentium computer about four years to complete. A gigaflop is a measure of a computer's speed that, in the terminology of the trade, equals 1 billion floating point operations per second.

Maizel said the new SGI supercomputer, which should be fully operational by the end of the year, provides about 48 times more computing capacity than ABCC's previous supercomputer. It also has about 96 times the disk and memory capacity of the older computer and features 96 processors, a plus in simulating biological problems that require large amounts of computer memory.

Richard Klausner, M.D., NCI director, said the Institute's decision to lease the Cray SV1 comes as cancer researchers worldwide have shown a growing interest in implementing the latest, high-speed computational methods into their studies. "The last decade has shown that supercomputing has an important place in cancer research, and its importance will only increase in the coming years as studies move forward in defining the molecular causes of cancer," he said.

Klausner said supercomputing will likely play a key role in translating recent advances in gene discovery into new, more targeted cancer treatments. "One of the great opportunities now in cancer research is to find molecules in tumor cells that are driving their growth and target them directly with drugs or other treatments," he said. "As more of these molecular targets are identified, computational biology can play a key role in defining their precise chemical structure, critical information in designing compounds that can reliably hit these targets."

Supercomputers are broadly defined as the most technologically advanced, or high performance, computers in existence at any time. Though computational speed is one major asset in supercomputing, scientists say that supercomputers also must be technologically mature and reliable in generating useful data. "Supercomputing is still in its infancy," said Maizel. "But the field is so fluid that the computer power at our disposal continues to grow exponentially every few years."

For biologists, supercomputing studies can generate a resolution of detail that is almost impossible to obtain from laboratory work. Current supercomputers produce models in a relatively brief time predicting the complete chemical structure of various regions of a human protein all the way down to fine electronic detail. These calculations, in turn, can be used to predict the folding patterns of the protein, now a major area of research interest, and how these structures move or interact with other proteins and drugs.

Though several supercomputing centers currently are in operation in the United States, Stan Burt, Ph.D., ABCC director, said the Frederick facility continues to fill a unique niche. "The ABCC remains the only supercomputing center available to the public and dedicated solely to biological research," he said. "It's also unique in that the center employs a staff of trained computational scientists who can assist in problem solving and formulating computations. Requests here do not go into a processing vacuum."

Among its past accomplishments, the ABCC played a critical role in solving the 3-D structure of HIV-1 protease, an enzyme that HIV utilizes to infect human immune cells. With the 3-D structure clarified, scientists were able to design highly effective protease inhibitors, now the mainstay of AIDS therapy.

Burt said that with the new Cray SV1, the prospects for future computational successes only will be enhanced. "The Cray SV1 represents a significant resource for the entire biological research community," said Burt. "It is a powerful machine with lots of memory, and users will find it to be a valuable tool in sorting out the functions of the genes and proteins involved in their diseases of interest."

Other SGI systems that also will be available in Frederick are an SGI Origin™2000 and two Cray J90™ supercomputers, and a PowerChallenge™ system. Further details can be found at http://www.abcc.ncifcrf.gov.

For more information, or to contact National Cancer Institute, see their website at: www.cancer.gov