Optimization techniques for parallel molecular dynamics using domain decomposition
M Putz and A Kolb, COMPUTER PHYSICS COMMUNICATIONS, 113, 145-167 (1998).
In this paper we describe the implementation of a new parallelized Molecular Dynamics code for many-particle problems with short-ranged interactions. While the basic algorithms have their foundation in the fairly standard methods of domain decomposition, linked-cell pair search and Verlet pair list, we have developed some refined techniques for optimizing them. The rewards of these optimizations are a up to 45% overall improvement in the scalar performance and very good scaling behavior in the number of processors even down to a few hundred particles per processor on a GRAY T3E. The best speedup can be obtained for systems with pair forces only since then the data structures can be organized in a very simple manner. To deal with more complex situations as well, we have developed a partial replicated data scheme which is suitable to simulate many molecules consisting of many simple particles (e.g. polymer chains) for many types of short-range interactions. (C) 1998 Elsevier Science B.V.
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