An 8.61 Tflop/s molecular dynamics simulation for NaCl with a special-purpose computer: MDM

Authors:
Tetsu Narumi;Atsushi Kawai;Takahiro Koishi
Affiliations:
RIKEN Genomic Sciences Center, Totsuka, Yokohama, Japan;Advanced Computing Center, RIKEN;Advanced Computing Center, RIKEN
Venue:
Proceedings of the 2001 ACM/IEEE conference on Supercomputing
Year:
2001

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Abstract

We performed molecular dynamics (MD) simulation of 33 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 8.61 Tflop/s. In this calculation we used a special-purpose computer, MDM, which we have developed for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large scale MD simulations without truncating the Coulomb force. It is composed of MDGRAPE-2, WINE-2 and a host computer. MDGRAPE-2 accelerates the calculation for real-space part of the Coulomb and van der Waals forces. WINE-2 accelerates the calculation for wavenumber-space part of the Coulomb force. The host computer performs other calculations. With the completed MDM system we performed an MD simulation similar to what was the basis of our SC2000 submission for a Gordon Bell prize. With this large scale MD simulation, we can dramatically decrease the fluctuation of the temperature less than 0.1 Kelvin.