Japan's RIKEN Bases New Protein Modeling Solution on SGI Altix 350 System

Demonstration at SC2004 Spotlights Versatility of Altix 350 as Engine for

Driving Complex Protein Model Calculations

Nov 09, 2004, 00:00 ET from SGI

    PITTSBURGH, Nov. 9 /PRNewswire-FirstCall/ -- Using a 16-processor SGI(R)
 Altix(R) 350 system from Silicon Graphics (NYSE:   SGI) as a cost-effective
 compute engine, Japan's Institute of Physical and Chemical Research (RIKEN)
 this week is demonstrating a new molecular dynamics simulation solution at the
 Supercomputing Conference 2004. RIKEN will demonstrate its MDGRAPE-3 system in
 SGI's SC2004 Booth No. 1311 and in RIKEN's SC2004 Booth No.2748D at the David
 L. Lawrence Convention Center.
     RIKEN recently chose Altix 350, based on 16 Intel(R) Itanium(R) 2
 processors and featuring 16GB of memory, as the host computer of its MDGRAPE-3
 system, which also incorporates a special chip for force calculations. RIKEN's
 SC2004 demonstration will show how this low-cost, high-performance accelerator
 will become an important solution for computational biology, computer-aided
 drug design, nanotechnology and other demanding scientific applications.
 MDGRAPE-3 is a special-purpose computer system for molecular dynamics
 simulations developed by RIKEN to accelerate calculations of protein models,
 the most time-consuming part in simulations.
     By combining a 16-processor Altix 350 and eight MDGRAPE-3 units, RIKEN
 expects to achieve 32 teraflops (trillion calculations per second) of
 performance in a single rack. At RIKEN's Genomics Science Center in Yokohama,
 Japan, researchers plan to build an even more powerful simulation system
 capable of generating a full petaflop (thousand trillion operations per
 second) of performance using 32 racks totaling 512 Itanium 2 processors and
 6,144 MDGRAPE-3 chips.
     "Molecular dynamics simulations present an exceptionally difficult test
 for even the most powerful of today's computer systems, which is why RIKEN
 worked to develop the MDGRAPE-3 solution to address this and other demanding
 fields of study," said Makoto Taiji, Ph.D., Team Leader of High Performance
 Biocomputing Research Team RIKEN. "The versatility and leading
 price/performance of the Altix 350 system made it an ideal host computer for
 the MDGRAPE-3 simulation system, while the Altix 350 system's remarkable
 scalability will allow us to extend MDGRAPE-3 to a full petaflop of
     "With Altix 350 in widespread use at commercial, government and research
 customer sites around the world, it is exciting to see another ingenious
 application of this powerful and broadly adaptable mid-range system," said
 Dave Parry senior vice president and general manager, Server and Platform
 Group, SGI. "As the RIKEN's latest demonstration shows, Altix 350 achieves the
 price/performance and scalability that make it a strategic element for
 everything from high-performance computing deployments to departmental
 technical computing configurations."
     SGI Altix 350 provides the performance and technology of SGI Altix at a
 breakthrough price point. Altix 350 delivers a superior Linux(R) OS-based
 alternative to the proprietary solutions that dominate the technical mid-range
 market. This mid-range powerhouse delivers more real-world performance than
 any other system in its class, and provides breakthrough capabilities for
 technical database and traditional cluster applications. Its modular "expand
 on demand" architecture allows users to independently scale processors,
 memory, and I/O, enabling them to cost-effectively build exactly the system
 they need, and reconfigure it easily as requirements change.
     Altix 350 incorporates the same high-performance shared-memory SGI(R)
 NUMAflex(TM) architecture and optimized Linux tools originally implemented in
 the award-winning Altix(R) 3000 servers and supercomputers. It supports up to
 16 processors in a single system image, and features the industry leading
 6.4GB/second SGI(R) NUMAlink(TM) interconnect.
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      Ginny Babbitt