Efficient parallel algorithms for molecular dynamics simulations

✍ Scribed by Ravi Murty; Daniel Okunbor

• Publisher: Elsevier Science
• Year: 1999
• Tongue: English
• Weight: 223 KB
• Volume: 25
• Category: Article
• ISSN: 0167-8191
• DOI: 10.1016/s0167-8191(98)00114-8

✦ Synopsis

The study of many-particle systems has increased signi®cantly 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 ®rst 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 eciencies of 98.63% and 98.88%, respectively.