Hardware accelerator for molecular dynamics

MDGRAPE-2

Ryutaro Susukita, Toshikazu Ebisuzaki, Bruce G. Elmegreen, Hideaki Furusawa, Kenya Kato, Atsushi Kawai, Yoshinao Kobayashi, Takahiro Koishi, Geoffrey D. McNiven, Tetsu Narumi, Kenji Yasuoka

Research output: Contribution to journalArticle

53 Citations (Scopus)

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 10000 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.

Original languageEnglish
Pages (from-to)115-131
Number of pages17
JournalComputer Physics Communications
Volume155
Issue number2
DOIs
Publication statusPublished - 2003 Oct 1

Fingerprint

Particle accelerators
Molecular dynamics
hardware
accelerators
molecular dynamics
Hardware
supercomputers
Supercomputers
workstations
computational fluid dynamics
Printed circuit boards
Computational fluid dynamics
Vortex flow
Hydrodynamics
simulation
hydrodynamics
high speed
vortices
Computer simulation
Processing

Keywords

  • Molecular dynamics
  • Special purpose computer

ASJC Scopus subject areas

  • Computer Science Applications
  • Physics and Astronomy(all)

Cite this

Susukita, R., Ebisuzaki, T., Elmegreen, B. G., Furusawa, H., Kato, K., Kawai, A., ... Yasuoka, K. (2003). Hardware accelerator for molecular dynamics: MDGRAPE-2. Computer Physics Communications, 155(2), 115-131. https://doi.org/10.1016/S0010-4655(03)00349-7

Hardware accelerator for molecular dynamics : MDGRAPE-2. / Susukita, Ryutaro; Ebisuzaki, Toshikazu; Elmegreen, Bruce G.; Furusawa, Hideaki; Kato, Kenya; Kawai, Atsushi; Kobayashi, Yoshinao; Koishi, Takahiro; McNiven, Geoffrey D.; Narumi, Tetsu; Yasuoka, Kenji.

In: Computer Physics Communications, Vol. 155, No. 2, 01.10.2003, p. 115-131.

Research output: Contribution to journalArticle

Susukita, R, Ebisuzaki, T, Elmegreen, BG, Furusawa, H, Kato, K, Kawai, A, Kobayashi, Y, Koishi, T, McNiven, GD, Narumi, T & Yasuoka, K 2003, 'Hardware accelerator for molecular dynamics: MDGRAPE-2', Computer Physics Communications, vol. 155, no. 2, pp. 115-131. https://doi.org/10.1016/S0010-4655(03)00349-7
Susukita R, Ebisuzaki T, Elmegreen BG, Furusawa H, Kato K, Kawai A et al. Hardware accelerator for molecular dynamics: MDGRAPE-2. Computer Physics Communications. 2003 Oct 1;155(2):115-131. https://doi.org/10.1016/S0010-4655(03)00349-7
Susukita, Ryutaro ; Ebisuzaki, Toshikazu ; Elmegreen, Bruce G. ; Furusawa, Hideaki ; Kato, Kenya ; Kawai, Atsushi ; Kobayashi, Yoshinao ; Koishi, Takahiro ; McNiven, Geoffrey D. ; Narumi, Tetsu ; Yasuoka, Kenji. / Hardware accelerator for molecular dynamics : MDGRAPE-2. In: Computer Physics Communications. 2003 ; Vol. 155, No. 2. pp. 115-131.
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