Japans Petaflop computer: MDGRAPE-3

On June 19, Japan’s Institute of Physical and Chemical Research (Riken), SGI Japan and Intel announced the development of a supercomputer with a theoretical peak performance of 1 petaflops The computer is called MDGRAPE-3 It is a special-purpose computer for molecular dynamics simulations. The system will have 5120 chips of 200 Gflops performance, therefore its peak performance will reach 1 petaflops in total. It will perform simulations with million particles at 0.1 sec/step and will enable simulation with 10M particles using Ewald method. The power dissipation will be 300 kW. The specialization enables high-performance at low-power.

More details on the system is here at EEtimes Hitachi Ltd. fabricated the chips on its HDL4N 130-nanometer process technology. (Therefore, an MDGRAPE-4 could get a 4-10 times speed boost by going to a 65 nanometer or 45 nanometer process). 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. MDGrape-3 does not run the Linpack benchmark.

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