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Comparison between parallel and distributed molecular dynamics simulations of Lennard-Jones systems

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3 Author(s)
Baja, V. ; Comput. Sci. Dept., Tech. Univ. of Cluj-Napoca, Cluj-Napoca, Romania ; Gorgan, D. ; Beu, T.

This paper concerns mainly with parallel and distributed implementations of molecular dynamics simulations of the Lennard-Jones potential model. The reported research work studies and experiments different algorithms and parallelization techniques for shared memory and message passing architectures, and the programs are executed on single-core processors, multi-core processors, GPU, and GPU cluster. The solution based on efficient versions of the neighbor list algorithm and space division technique is further discussed. The obtained speedups for multi-core processor, GPU, and GPU cluster, relative to the single-core processor implementation of the program, are analyzed, and the advantages of the algorithms are highlighted.

Published in:

Intelligent Computer Communication and Processing (ICCP), 2012 IEEE International Conference on

Date of Conference:

Aug. 30 2012-Sept. 1 2012

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