Intel K.K. (Intel Corp.'s Japanese unit) and NEC subsidiary SGI Japan Ltd. collaborated with Riken on development of the system, which was designed as a dedicated machine for molecular dynamics simulation. The supercomputer is installed at Riken's Yokohama Institute, and Riken plans to show it off at an open house scheduled for Saturday (June 24).
Dubbed the MDGrape-3, the molecular dynamics simulator comprises 201 units of Riken's proprietary system and two types of Intel Xeon-based servers. Each Riken unit has 24 MDGrape-3 chips, each offering 230 Gflops. The chip was developed in 2004 as the core processing element for the supercomputer. Foundry partner Hitachi Ltd. fabricated the chips on its HDL4N 130-nanometer process technology.
Supporting the proprietary computing cluster are 65 parallel servers based on Intel's 5000 series dual-core Intel Xeon processor (code named Dempsey) and 37 parallel servers based on a 3.2-GHz Xeon with 2 Mbytes of Level 1 cache. The Dempsey-based servers use 256 dual-core processors each; the others use 74 3.2-GHz cores each. Intel provided technical support along with the processors.
SGI Japan integrated the component units into a parallel computing system.
MDGrape-3 does not run Linpack and thus cannot be directly compared with the supercomputers ranked in the Top 500 listing based on the Linpack benchmarks, said Makoto Taiji, team leader of the molecular dynamics simulation project at the Riken Genomic Sciences Center. But the system has a theoretical peak performance of 1 petaflops in targeted areas, which is the next milestone for supercomputer developers and is about three times higher than BlueGene/L's 360 Gflops.
Riken developed the computer as a part of Japan's Protein 3000 Project, launched in 2002 as a post-genome-project investigation into the workings of proteins. The machine is expected to facilitate simulation of proteins' molecular connections in a bid to shrink the development time for new drug therapies. In a broader sense, MDGrape-3 is expected to accelerate the advancement of nanometer-level life sciences.