DESIGN AND ANALYSIS OF A PARALLEL MOLECULAR-DYNAMICS APPLICATION

This paper investigates the parallelization of molecular dynamics simu lations. Topics addressed include the development of abstractions that support alternatives to traditional neighbor-list based approaches to molecular dynamics simulations, the evaluation of alternative methods for domain decomposition and program synchronization, and the design of a flexible framework for constructing realistic molecular dynamics simulations. Moreover, this framework is designed to be suitable for i mplementation of programs for both shared and distributed memory MIMD multiprocessors. One specific problem addressed by our research is tha t MD simulations often scale poorly with increases in system size and in numbers of processors, in part due to the commonly used neighbor li st approach. Our research uses a domain decomposition approach that ex ploits molecular locality to reduce overall computation and to attain good scalability. Experimental evidence concerning scalability and per formance is gathered on KSR supercomputers. (C) 1996 Academic Press, I nc.