TY - JOUR
T1 - Hardware accelerator for molecular dynamics
T2 - MDGRAPE-2
AU - Susukita, Ryutaro
AU - Ebisuzaki, Toshikazu
AU - Elmegreen, Bruce G.
AU - Furusawa, Hideaki
AU - Kato, Kenya
AU - Kawai, Atsushi
AU - Kobayashi, Yoshinao
AU - Koishi, Takahiro
AU - McNiven, Geoffrey D.
AU - Narumi, Tetsu
AU - Yasuoka, Kenji
N1 - Funding Information:
We thank M. Taiji, M. Tateno and K. Sunouchi for useful discussions on the hardware design of MDGRAPE-2. This work was supported by the fund for “Heterogeneous Computer System” of the Ministry of Education, Culture, Sports, Science and Technology of Japan.
PY - 2003/10/1
Y1 - 2003/10/1
N2 - 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.
AB - 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.
KW - Molecular dynamics
KW - Special purpose computer
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U2 - 10.1016/S0010-4655(03)00349-7
DO - 10.1016/S0010-4655(03)00349-7
M3 - Article
AN - SCOPUS:0141754037
SN - 0010-4655
VL - 155
SP - 115
EP - 131
JO - Computer Physics Communications
JF - Computer Physics Communications
IS - 2
ER -