Please use this identifier to cite or link to this item: http://hdl.handle.net/1959.3/34537

Title

Parallelization algorithms for three-body interactions in molecular dynamics simulation

Author(s)

Li, Jianhui;  Zhou, Zhongwu;  Sadus, Richard J.

Abstract

Two force decomposition algorithms are proposed for parallelizing three-body interactions in Molecular Dynamics (MD) simulations. The first algorithm divides the entire 3D force matrix into equal sized force cubes that are assigned to parallel processors. In the second strategy, the force matrix is decomposed into slices of two-dimensional force matrixes, and those slices are distributed among processors cyclically. The proposed decomposition algorithms are implemented using MPI and tested in computational experiments. The performances of proposed decomposition methods are studied and compared with computational load theoretical analysis. Both theoretical prediction and computation experiments demonstrate that the load balance is a key factor that impacts the parallel performance of the examined system, and the cyclic force decomposition algorithm produced reasonably good overall performances.

Publication type

Conference paper

Research centre

Swinburne University of Technology. Faculty of Engineering and Industrial Sciences. Industrial Research Institute Swinburne

Source

Lecture Notes in Computer Science : Parallel and Distributed Processing and Applications : 4th International Symposium, ISPA 2006, Sorrento, Italy, December 4-6, 2006, Vol. 4330 (2006), pp. 374-382

Publication year

2006

Publisher

Springer

ISBN

9783540680673

Publisher URL

http://dx.doi.org/10.1007/11946441_37

Peer reviewed