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Phoenix, Arizona
Nov. 15, 2003 to Nov. 21, 2003
ISBN: 1-58113-695-1
pp: 15
Makoto Taiji , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Tetsu Narumi , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Yousuke Ohno , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Noriyuki Futatsugi , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Atsushi Suenaga , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Naoki Takada , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
Akihiko Konagaya , Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
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.
CITATION
Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya, "Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations", SC, 2003, SC Conference, SC Conference 2003, pp. 15, doi:10.1109/SC.2003.10017
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