A cyclic force decomposition algorithm for parallelising three-body interactions in molecular dynamics simulations
JH Li and ZW Zhou and RJ Sadus, FIRST INTERNATIONAL MULTI-SYMPOSIUMS ON COMPUTER AND COMPUTATIONAL SCIENCES (IMSCCS 2006), PROCEEDINGS, VOL 1, 338-+ (2006).
A cyclic force decomposition algorithm is examined for parallelising three body interactions. The algorithm is based on the decomposition of a 3D force matrix into slices of 2D force matrixes in cyclic task assignments. The proposed decomposition algorithm is implemented using MPI and tested in computational experiments of AM simulations. The performance of the decomposition method is studied in terms of load balance, achieved speedup and parallel efficiency. Theoretical analysis of effective triplets is proposed and conducted by which load balance status can be predicted and compared with benchmark measurements. Reasonably good overall performance is achieved with the proposed algorithm. Both theoretical analysis and computation experiments demonstrate that the load balance is a key factor that impacts the parallel efficiency of the system examined in this study.
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