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

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.

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INDEX TERMS

Primary Classification:
  C. Computer Systems Organization
  C.5 COMPUTER SYSTEM IMPLEMENTATION
      C.5.1 Large and Medium ("Mainframe") Computers
          Subjects: Super (very large) computers

Additional Classification:
  I. Computing Methodologies
  I.6 SIMULATION AND MODELING
      I.6.8 Types of Simulation
          Subjects: Continuous

  J. Computer Applications
  J.2 PHYSICAL SCIENCES AND ENGINEERING
      Subjects: Chemistry

General Terms:
Algorithms, Design, Performance

Keywords:
ewald method, molecular dynamics simulation, special-purpose computer