An SPMD-Like Algorithm for Parallelizing Molecular Dynamics Using OpenMP

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 a...

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Bibliographic Details
Published in:Computing in science & engineering 2013-07, Vol.15 (4), p.48-56
Main Authors: Bai, Mingze, Sun, Shixin, Tang, Hong, Dou, Yusheng, Lo, Glenn V.
Format: Article
Language:English
Subjects:
Biological system modeling
Computational modeling
Heuristic algorithms
Message systems
Molecular computing
molecular dynamics
Multicore processing
OpenMP
parallel computing
single program multiple data
spatial decomposition
SPMD-like
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Summary: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.
ISSN:1521-9615
1558-366X
DOI:10.1109/MCSE.2012.66