Parallel Processing by PC Cluster for Optimization of Molecular Structure Using Hamiltonian Algorithm

Hiroyuki TERAMAEa* and Kazushige OHTAWARAb,c

aDepartment of Chemistry, Faculty of Science, Josai University
1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
bATR Adaptive Communication Research Laboratories
2-2-2 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0288, Japan
c Present address: Technology Development Division, Victor Company of Japan, Ltd.
58-7 Shinmei-cho, Yokosuka, Kanagawa 239-8550, Japan

(Received: August 7, 2008; Accepted for publication: November 7, 2008; Advance publication: January 19, 2009)

The Hamiltonian Algorithm combined with ab initio molecular orbital calculation is applied to the optimization of molecular structure. In order to carry out an optimization within a reasonable time frame even in the systems of many atoms, we perform parallel processing of the two-electron integrals by personal computer (PC) cluster consisting of 8 CPU's with Pentium 4 (3.0GHz) processor. We attempt to clear up the relation between the computation time and the number of CPU's focusing particularly on the reduction of the elapsed time. The computation time for single-point 3-21G calculations of the molecules of minor tranquilizer drugs having the benzodiazepin or the thienodiazepin backbone are measured. In the calculation of flutoplazepam (1:C19H16ClFN2O), the acceleration ratio of the CPU time and the elapsed time are 4.1 and 4.3 with 4 CPU's, 7.9 and 42.1 with 8 CPU's, respectively. Increasing the number of CPU's achieves an extensive improvement of the elapsed time more than the number of the CPU's used, because calculated two-electron integrals are able to be buffered on the memory of the PC cluster. The number of CPU's needed to buffer the two-electron integrals is estimated through a series of the calculations of the glycine oligomers.

Keywords: Parallel processing, PC cluster, Geometry optimization, Hamiltonian algorithm

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