Systolic loop methods for molecular dynamics simulation using multiple transputers

Abstract The implementation of molecular dynamics simulation on parallel computers needs a method which distributes over the processors both the evaluation of pair interactions and the integration of particle motions. This paper introduces several ways to achieve this, all based on the systolic loop concept. Each particle has a home processor which integrates its motion. In the evaluation of the interactions, the particle data circulate around the ring of processors in such a way that every particle meets every other particle, enabling all the pair interactions to be evaluated. The methods are suitable for use with a spherical cut-off or with a neighbour list. Three possible sources of inefficiency are discussed in detail. These are: imperfect load balancing during the force evaluation; communication delays during the force evaluation; and communication delays in accumulating thermodynamic quantities. In each case the loss of efficiency is only significant if the number of processors approaches the number of particles, which is unlikely to be the case in practice. Also, if the parallel computer is constructed from transputers, their ability to simultaneously calculate and communicate can reduce communication delays in the force evaluation. The methods have been tested on systems of up to 130 transputers.