Efficient parallel algorithms for molecular dynamics simulations

R Murty and D Okunbor, PARALLEL COMPUTING, 25, 217-230 (1999).

DOI: 10.1016/S0167-8191(98)00114-8

The study of many-particle systems has increased significantly over the past decade, because of the increasing number of useful applications it supports. Numerical experiences have shown that the force calculation contributes 90% of the total simulation time. This is an O(N-2) algorithm, mainly due to pairwise interactions, where N is the number of particles in the system. The interaction decomposition technique proposed by Taylor et al., uses a special mapping scheme and optimal communication to reduce the overall computation time. In this paper, we propose two algorithms based on the force decomposition approach. The first technique which we call Force-Row Interleaving (FRI) method, treats rows one at a time and the other approach, called Force-Stripped Row (FSR), computes a priori the block of rows that balances workload to be sent to a processor. These two algorithms were tested on a system of 32000 atoms of liquid argon and implemented on a distributed memory, 16-processor iPSC/860. The FRI and FSR were both comparable to existing parallel techniques with efficiencies of 98.63% and 98.88%, respectively. (C) 1999 Elsevier Science B.V. All rights reserved.

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