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Hardware accelerator for molecular dynamics: MDGRAPE-2 |
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| Authors: | Ryutaro Susukita Toshikazu Ebisuzaki Hideaki Furusawa Atsushi Kawai Takahiro Koishi Tetsu Narumi |
| Affiliation: | a Computational Science Division, Advanced Computing Center, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan b T.J. Watson Research Center, IBM Co., Ltd., PO Box 218, Yorktown Heights, NY 10598, USA c EDA Solutions, Information Technology Solutions Co., Ltd., 1623-14 Shimotsuruma, Yamato, Kanagawa 242-8502, Japan d Tokyo Research Laboratory, IBM Japan Co., Ltd., 1623-14 Shimotsuruma, Yamato, Kanagawa 242-8502, Japan e High Performance Biocomputing Team, Computer/Informatics Science Facilities, Genomic Sciences Center, RIKEN (The Institute of Physical and Chemical Research), 214 Maeda, Totsuka-ku, Yokohama 244-0408, Japan f Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan |
| Abstract: | We developed MDGRAPE-2, a hardware accelerator that calculates forces at high speed in molecular dynamics (MD) simulations. MDGRAPE-2 is connected to a PC or a workstation as an extension board. The sustained performance of one MDGRAPE-2 board is 15 Gflops, roughly equivalent to the peak performance of the fastest supercomputer processing element. One board is able to calculate all forces between 10 000 particles in 0.28 s (i.e. 310000 time steps per day). If 16 boards are connected to one computer and operated in parallel, this calculation speed becomes ∼10 times faster. In addition to MD, MDGRAPE-2 can be applied to gravitational N-body simulations, the vortex method and smoothed particle hydrodynamics in computational fluid dynamics. |
| Keywords: | Molecular dynamics Special purpose computer |
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