Parallelization algorithms for three-body interactions in molecular dynamics simulation

Authors:
Jianhui Li;Zhongwu Zhou;Richard J. Sadus
Affiliations:
Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Victoria, Australia;Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Victoria, Australia;Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Victoria, Australia
Venue:
ISPA'06 Proceedings of the 4th international conference on Parallel and Distributed Processing and Applications
Year:
2006

Citing 3
Cited 0

Molecular dynamics of clusters of particles interacting with pairwise forces using a massively parallel computer

Journal of Computational Physics
Fast parallel algorithms for short-range molecular dynamics

Journal of Computational Physics
Molecular Simulation of Fluids: Theory, Algorithms and Object-Orientation

Molecular Simulation of Fluids: Theory, Algorithms and Object-Orientation

Quantified Score

Hi-index	0.00

Visualization

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.