IBM to build protein supercomputer

Each board will be capable of 2 teraflops

IBM is to spend $100m building a supercomputer that is far faster than any existing machine.

Called Blue Gene, it will be used initially to probe some of the body's most complex molecules, giving scientists a new insight into common diseases and helping them to develop a new generation of powerful drugs.

Blue Gene vital statistics

Capable of one million, billion mathematical operations per second

More than one million processors

Processors capable of one billion operations per second

32 processors on a single chip

64 chips on to a board capable of 2 teraflops

Eight boards placed in 2m-high racks

64 racks will link together

Computer will occupy about 200 square metres

Blue Gene will be capable of more than one million, billion mathematical operations per second (one petaflop). This will make it 1,000 times more powerful than the Deep Blue supercomputer that beat world chess champion Garry Kasparov in 1997, and about two million times more powerful than today's best desktop PCs.

IBM expects it will take four to five years to build Blue Gene, which will be based at the company's Watson Research Center in Yorktown Heights, New York, US.

The supercomputer will give scientists a unique view of proteins, the large molecules that build and maintain our bodies. Proteins are constructed from long chains of amino acids which, under the influence of complex electrical and chemical interactions, adopt highly complex structures.

Their precise shapes are crucial - failure to fold up correctly can trigger disease.

Scientists would like to understand the "rules" that govern how proteins fold. This would enable them to "build" their own molecules with perhaps novel properties or block the action of undesirable proteins such as the enzymes a virus might use to infect cells.

"With this project we have a chance not only to change the future of computing, but also the future of health care," said Paul Horn, senior vice president of research at IBM.

New design approach

"In many ways, Deep Blue got a better job today. If this computer unlocks the mystery of how proteins fold, it will be an important milestone in the future of medicine and healthcare."

The research project would start by understanding the folding mechanism in a sequence of just 50 amino acids, Paul Horn said. Once the Blue Gene computer system is fully installed in four to five years, IBM would start to provide clear information on folding behaviour in proteins that are some 300 to 600 acids in length.

The two fastest computers in the world today are part of the ASCI program run by the US Department of Energy, and which were recently tested at about two teraflops - two trillion operations per second each.

IBM Research believes it can exceed this level of performance using a new approach to computer design and architecture.

"We think a tremendous gain in performance will be made possible by the first major revolution in how computers are built since the mid-1980s," said Dr Ambuj Goyal, IBM Research's vice president of computer science.

"We call this new approach to computer architecture Smash, which stands for Simple, Many and Self-Healing."

IBM says its Smash architecture differs from existing approaches in three ways:

• It will dramatically simplify the number of instructions carried out by each processor.
• It will use a massive parallel system capable of more than eight million simultaneous threads of computation (compared to the maximum of 5,000 threads today).
• The computer will be self-stabilising and self-healing, automatically overcoming failures of individual processors and computing threads.