Compaq, nuclear lab teaming on supercomputer

The PC maker is teaming with Sandia National Laboratories and life science company Celera Genomics to build what is anticipated to be one of the fastest supercomputers in the world.

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Compaq Computer is teaming with nuclear research facility Sandia National Laboratories and biotechnology company Celera Genomics to build what is anticipated to be one of the fastest supercomputers in the world.

The deal, announced Friday at a Department of Energy news conference in Washington, will result in a computer that can perform 100 trillion calculations per second--100 "teraflops"--by 2004, Bill Blake, vice president of high-performance technical computing at Compaq, said in an interview. A second phase, which will be open to other bidders besides Compaq, will result in a "petaflop" machine 10 times faster, the same speed as the Blue Gene machine under design at IBM.

The machine will benefit from computer hardware and software research from all three partners, Blake said. The computer will be used to extract medically useful information from raw databases of genetic information, but Sandia officials said the advances also will benefit the nation's nuclear weapons program.

The deal is one of a series of major contracts for Compaq, whose Unix computers using the Alpha chip are selling well with technical customers but not as well with commercial buyers who prefer computers from Sun Microsystems, Hewlett-Packard and IBM.

Other major Compaq victories include a $36 million partnership with the Pittsburgh Supercomputing Center to build a 2,728-CPU machine for academic use and ASCI Q, a $200 million nuclear weapons simulation machine with 12,000 CPUs to be built at Los Alamos National Laboratory.

Compaq must reckon with competitor Sun, which is trying to convert its business success into supercomputer success, and IBM, which has jumped into the top spot in supercomputer popularity and speed rankings and has the current fastest machine, a $110 million, 8,192-CPU machine that can perform 12.3 teraflops, about one-eighth the projected speed of the upcoming Compaq machine.

Houston-based Compaq is also developing a supercomputer for the Department of Energy's National Nuclear Security Administration, which is expected to be able to perform 30 trillion operations per second once delivered in 2002.

Rockville, Md.-based Celera for years competed with the federally funded Human Genome Project to compile a map of human genetic information. The two efforts joined forces at the last minute, and now Celera and other companies are trying to benefit from the research.

The new supercomputer will help in further genomics research and the study of the structure, function and interactions of proteins in the cells of humans and other organisms, according to a joint press release.

Celera will provide applications that life science researchers can use in their work, such as further mapping of the human genome and other biological research.

Although terms of the agreement were not disclosed, the three companies plan to spend millions of dollars, employ hundreds of workers, and develop new technology as part of the effort, scheduled to be completed in 2004.

At the press conference Friday, government officials, researchers and industry executives hailed the supercomputer as the next step in the Human Genome Project.

With years of experience building computer models of nuclear explosions, Sandia will assist Celera in building software to analyze biological data.

The supercomputer will help "to advance the knowledge from the human genome to improve human health," said Sandia President Paul Robinson. "Nothing beats the complexity of the Human Genome Project and the opportunities ahead. We look forward to working in these fields."

For Compaq, the deal is an example of its ongoing push to add servers and other high-end computing products to its successful PC business.

"Compaq has been reforming itself into providing computer and Internet technology to a whole span of different fields," said Compaq Vice President Bill Blake. "Part of this move from the desktop to the supercomputer has been with these partners."

The new supercomputer likely will have 10,000 to 20,000 CPUs, Blake said. That number is sufficiently large that the system designers must grapple with reliability problems not seen in typical business machines, even those with a few dozen CPUs.

"You start out on the basis that something will always be broken in the system somewhere," Blake said. Then designers build monitoring and job scheduling features that make sure jobs are reassigned to functioning CPUs if one fails.

The Compaq machine will take advantage of future Compaq Alpha chip designs that build networking abilities straight into the chip itself, Blake said in the interview. This feature will allow more CPUs to communicate directly with each other or to route shared information along from one chip to another as fast as possible.

"We're optimizing a special form of network between all the Alphas," Blake said.

This architecture varies considerably from that used by IBM, which prefers to have a smaller number of nodes, each with multiple CPUs and connected to central high-speed switches.