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An SPMD-Like Algorithm for Parallelizing Molecular Dynamics Using OpenMP
July-Aug. 2013 (vol. 15 no. 4)
pp. 48-56
Mingze Bai, University of Electronic Science and Technology of China
Shixin Sun, University of Electronic Science and Technology of China
Hong Tang, Chongqing University of Posts and Telecommunications
Yusheng Dou, Chongqing University of Posts and Telecommunications
Glenn V. Lo, Nicholls State University
The efficiency and scalability of early efforts to parallelize molecular dynamics calculations on shared-memory systems using OpenMP have been limited by attempts to avoid data race. Recent work has produced better performance, but involves significant revisions to the serial code. A new algorithm addresses these limitations.
Index Terms:
Computational modeling,Molecular computing,Heuristic algorithms,Biological system modeling,Multicore processing,Message systems,spatial decomposition,molecular dynamics,parallel computing,OpenMP,SPMD-like,single program multiple data
Citation:
Mingze Bai, Shixin Sun, Hong Tang, Yusheng Dou, Glenn V. Lo, "An SPMD-Like Algorithm for Parallelizing Molecular Dynamics Using OpenMP," Computing in Science and Engineering, vol. 15, no. 4, pp. 48-56, July-Aug. 2013, doi:10.1109/MCSE.2012.66
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