Domain-Based Decomposition Parallel Molecular Dynamics Algorithm on Computer Clusters

Author

Zhao, Jiu-ling ; Zhao, Jiu-Fen

Author_Institution

Second Artillery Eng. Inst., Xi´´an

Volume

3

fYear

2007

fDate

24-27 Aug. 2007

Firstpage

49

Lastpage

52

Abstract

With MPI and C/C++, a parallel algorithm of molecular dynamics based on octal-tree domain decomposition method was implemented for micro canonical system (NVE), and run the code on a small cluster. The code speed-up was examined for a number of particles ranging from N = 192 to 10800 and for number of processors from P = 2 up to 8. As a result, the computing performance has been improved obviously, that is the computing speedup of the system can be three times or more than those computing on the single computer.

Keywords

C++ language; biology computing; message passing; molecular dynamics method; octrees; parallel algorithms; workstation clusters; C/C++ language; MPI; computer clusters; micro canonical system; molecular dynamics; octal-tree domain decomposition; parallel algorithm; Atomic measurements; Clustering algorithms; Computational modeling; Concurrent computing; Costs; Distributed computing; Heuristic algorithms; Mechanical factors; Parallel algorithms; Physics;

fLanguage

English

Publisher

ieee

Conference_Titel

Fuzzy Systems and Knowledge Discovery, 2007. FSKD 2007. Fourth International Conference on

Conference_Location

Haikou

Print_ISBN

978-0-7695-2874-8

Type

conf

DOI

10.1109/FSKD.2007.260

Filename

4406200