Japan's RIKEN bases new protein modelling solution on SGI Altix 350 system

Pittsburgh 09 November 2004Using a 16-processor SGI Altix 350 system from Silicon Graphics as a cost-effective compute engine, Japan's Institute of Physical and Chemical Research (RIKEN) has demonstrated a new molecular dynamics simulation solution at the Supercomputing Conference 2004. RIKEN demonstrated its MDGRAPE-3 system in SGI's SC2004 Booth and in RIKEN's SC2004 Booth at the David L. Lawrence Convention Center.

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RIKEN recently chose Altix 350, based on 16 Intel Itanium 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 showed 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 or 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 or thousand trillion operations per second of performance using 32 racks totaling 512 Itanium 2 processors and 6144 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", stated 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 performance."

"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", stated 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 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 NUMAflex architecture and optimized Linux tools originally implemented in the award-winning Altix 3000 servers and supercomputers. It supports up to 16 processors in a single system image, and features the industry leading 6,4GB/second SGI NUMAlink interconnect.


Leslie Versweyveld

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