Multicomputer Molecular Dynamics Simulation using Distributed Neighbour Lists

Abstract

A systolic loop method for parallel molecular dynamics, previously written in Occam, is reimplemented in Fortran using a general message-passing library. The method is extended to include a conventional neighbour list, fully distributed over the processors. A modification of the systolic loop method, called systolic replication, permits a parallel implementation of the fastest known sequential algorithm, in which a link-cell spatial decomposition is used to form the distributed neighbour list. The performance of each method, for a liquid argon simulation, is measured on a Transputer system and analysed in terms of the concept of scaleability. Some measurements are also made using i860 processors. The best performance achieved is 5000 particle moves per second, using 28 Transputers.

Key Words:

• systolic loop method
• distributed neighbour lists
• transputer
• molecular dynamics