loading...
 This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
2006 First International Multi-Symposiums on Computer and Computational Sciences
A Cyclic Force Decomposition Algorithm for Parallelising Three-Body Interactions in Molecular Dynamics Simulations
Hangzhou, Zhejiang, China
June 20-June 24
ISBN: 0-7695-2581-4
Jianhui Li, Swinburne University of Technology, Australia
Zhongwu Zhou, Swinburne University of Technology, Australia
Richard. J. Sadus, Swinburne University of Technology, Australia
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 MD 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.
Index Terms:
Parallel computation; force decomposition; load balance, three body interactions
Citation:
Jianhui Li, Zhongwu Zhou, Richard. J. Sadus, "A Cyclic Force Decomposition Algorithm for Parallelising Three-Body Interactions in Molecular Dynamics Simulations," imsccs, vol. 1, pp.338-343, 2006 First International Multi-Symposiums on Computer and Computational Sciences, 2006
Usage of this product signifies your acceptance of the Terms of Use.