Trehv's Blogz!: World's Fastest Computer Now Twice as Fast

Trehv's Blogz!: What's the world's fastest supercomputer used for?

What's the world's fastest supercomputer used for?

by Julia Layton

The world's fastest supercomputer will probably never be known as the world's fastest supercomputer. RIKEN's MDGrape-3 is the first machine to break the petaflop barrier -- that's 1 quadrillion calculations (floating-point operations, to be specific) per second -- and it's three times faster than the currently ranked fastest computer in the world, IBM's BlueGene/L. But MDGrape-3 is so specialized that it can't run the software used to officially rank computing speed. What it can do is determine the effect of any chemical compound on one of the most intricate systems in the human body in a couple of seconds.
MDGrape-3 is designed for pharmaceutical research, specifically molecular dynamics simulation. In developing drugs, pharmaceutical companies have to analyze thousands on thousands of chemical compounds to find out how they'll affect the protein-bonding structures in the human body. Protein structures called enzymes are the building blocks that do all of the work within a cell, and the way these proteins bond with any drug compound introduced into the human body determines the body's response to that drug. MDGrape-3 produces simulations of these molecular interactions. What takes most computers hours or days to analyze takes MDGrape-3 a few seconds. This functionality is invaluable in drug research, and it could drastically cut the research time involved in the development of new cures. A subsidiary of pharmaceutical giant Merck has already booked time on the machine.
Structurally speaking, MDGrape-3 is a parallel computing system consisting of two main sections: a primary server unit and a specialized-engines unit. The latter component is a cluster of 201 engines running proprietary chips developed by Riken specifically for MDGrape-3. It's this huge set of engines, running 24 MDGrape-3 chips each, that does the heavy protein-analysis lifting. Each chip has a maximum processing speed of 230 gigaflops (one billion operations per second). The primary server unit manages the engine cluster. This parallel server setup runs two different types of processors: 65 servers run dual-core Intel 5000-series Xeon processors, 256 per server; and 37 servers run 3.3-GHz Intel Xeon processors, each with 2 MB of level 1 cache, at 74 processors per server. This hardware structure enables the 1-petaflop speed, which is the machine's theoretical maximum for certain processes.
MDGrape-3 took $9 million and about four years to build. And it's actually very efficient -- a total cost of $9 million breaks down to about $15 per gigaflop. The slower BlueGene/L cost about $140 per gigaflop to build.
BlueGene/L, which tops out at a theoretical 360 teraflops (trillion calculations per second), is also a biotechnology-specific machine. The advances in speed marked by these two supercomputers is indicative of a general trend in technology toward biologically-slanted systems. Some say the trend really started with the successful mapping of the human genome in 2000. Regardless of what spurred the current biotechnology race, most experts agree that the logical end of the surge is a state of DNA-based medicine. In several decades, we could make an appointment with our doctor for a quick DNA analysis to find out what diseases we're at risk for and pop a single, gene-targeting pill that eliminates all of those foreseeable risks.
For more information on MDGrape-3 and related topics, check out the following links:
How DNA Computers Will Work
What are the different types of computers?
What is the world's fastest computer?
CNNMoney.com: How biotech is driving computing - Aug. 31, 2006
RIKEN: Molecular Dynamics Simulation

Reference: http://www.howstuffworks.com/

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World's Fastest Computer Now Twice as Fast

By Matthew Fordahl, Associated Press

posted: 14 November 2005 12:05 pm ET

BlueGene/L, the fastest computer in the world, is located in the Terascale Simulation Facility at Lawrence Livermore National Laboratory. Credit: LLNL

SAN JOSE, Calif. (AP) -- An IBM-built computer that has topped the list of the world's 500 most powerful supercomputers has widened its lead in the latest ranking released Monday.

The computer named Blue Gene/L, deployed at Lawrence Livermore National Laboratory, has doubled its performance to 280.6 trillion calculations per second (teraflops), up from 136.8 teraflops from the list released in June.

The system, which is used to study the U.S. nuclear stockpile and perform other research, was officially completed this summer after it was doubled in size. Researchers expect it will hold the top spot for the foreseeable future.

"This is as fast as this will get under the contract we have, but it's not limited to be only this fast,'' said Dave Turek, vice president of deep computing at IBM. "If Livermore were to have an interest in taking it bigger, we could do that.''

International Business Machines Corp. built the top three systems on the list released Monday by the Top 500 project, an independent group of university computer scientists who release supercomputer rankings every six months.

Big Blue built 43.8 percent of the systems on the entire list.

The No. 2 machine is another Blue Gene system, with performance ranked at 91.2 teraflops. It's installed at IBM's Thomas Watson Research Center. The No. 3 system, also at LLNL, reached 63.4 teraflops in the test.

Hewlett-Packard Co. is the No. 2 manufacturer, with 33.8 percent of the machines on the list. No other computer maker has more than 7 percent in any category.

Of the chip makers, Intel Corp. microprocessors were used in a total of 333 systems, with 81 using the company's EM64T technology. IBM chips are in second place, with its Power microprocessors at the heart of 73 systems.

Advanced Micro Devices Inc.'s Opteron chips were used in 55 systems, up from 25 six months ago.

Of all the systems, the majority -- 305 -- are installed in the United States. Europe is represented by 100 systems on the list, while Asia has 66.

Japan's Earth Simulator, which topped five lists until it was dethroned by Blue Gene/L's prototype last November, slipped to the No. 7 spot. It was a source of much American angst when it first topped the list in 2002.

"One year after it was dethroned, it's kicked down to No. 7,'' said Erich Strohmaier, a compiler of the Top 500 list and a computer scientist at Lawrence Berkeley National Laboratory. "That shows the turnover in the top 10.''

The list, which has been issued twice a year since June 1993, is also compiled by Horst Simon of LBNL, Jack Dongarra at the University of Tennessee, Knoxville, and Hans Meuer of the University of Mannheim, Germany.

The latest list will be released officially Tuesday at a supercomputer conference in Seattle.

Reference: http://www.livescience.com/