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Japan's RIKEN Bases Protein Modeling Solution On SGI System

Using 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) demonstrated a new molecular dynamics simulation solution at the Supercomputing Conference 2004.

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 (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 at 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," 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 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 per second SGI NUMAlink interconnect.

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SGI, also known as Silicon Graphics Inc, is a leader in high-performance computing, visualization and storage. SGI's vision is to provide technology that enables the most significant scientific and creative breakthroughs of the 21st century. Whether it's sharing images to aid in brain surgery, finding oil more efficiently, studying global climate, providing technologies for homeland security and defense or enabling the transition from analog to digital broadcasting, SGI is dedicated to addressing the next class of challenges for scientific, engineering and creative users. With offices worldwide, the company is headquartered in Mountain View, Calif., and can be found on the Web at http://www.sgi.com.