A parallel scalable approach to short-range molecular dynamics on the CM-5

Abstract

Presents a scalable algorithm for short-range molecular dynamics which minimizes interprocessor communications at the expense of a modest computational redundancy. The method combines Verlet neighbor lists with coarse-grained cells. Each processing node is associated with a cubic volume of space and the particles it owns are those initially contained in the volume. Data structures for 'own' and 'visitor' particle coordinates are maintained in each node. Visitors are particles owned by one of the 26 neighboring cells but lying within an interaction range of a face. The Verlet neighbor list includes pointers to own-own and own-visitor interactions. To communicate, each of the 26 neighbor cells sends a corresponding block of particle coordinates using message-passing cells. The algorithms has the numerical properties of the standard serial Verlet method and is efficient for hundreds to thousands of particles per node allowing the simulation of large systems with millions of particles. Preliminary results on the new CM-5 supercomputer are described.<>