Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations

Authors:
Makoto Taiji;Tetsu Narumi;Yousuke Ohno;Noriyuki Futatsugi;Atsushi Suenaga;Naoki Takada;Akihiko Konagaya
Affiliations:
Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan;Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Venue:
Proceedings of the 2003 ACM/IEEE conference on Supercomputing
Year:
2003

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Abstract

We are developing the 'Protein Explorer' system, a petaflops special-purpose computer system for molecular dynamics simulations. The Protein Explorer is a PC cluster equipped with special-purpose engines that calculate nonbonded interactions between atoms, which is the most time-consuming part of the simulations. A dedicated LSI 'MDGRAPE-3 chip' performs these force calculations at a speed of 165 gigaflops or higher. The system will have 6,144 MDGRAPE-3 chips to achieve a nominal peak performance of one petaflop. The system will be completed in 2006. In this paper, we describe the project plans and the architecture of the Protein Explorer.