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A comparison between parallelization approaches in molecular dynamics simulations on GPUs

Lorenzo Rovigatti, Petr Sulc, Istvan Z. Reguly, Flavio Romano
Dipartimento di Fisica, Sapienza-Universit’a di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
arXiv:1401.4350 [physics.comp-ph], (17 Jan 2014)

@article{2014arXiv1401.4350R,

   author={Rovigatti}, L. and {{v S}ulc}, P. and {Reguly}, I.~Z. and {Romano}, F.},

   title={"{A comparison between parallelization approaches in molecular dynamics simulations on GPUs}"},

   journal={ArXiv e-prints},

   archivePrefix={"arXiv"},

   eprint={1401.4350},

   primaryClass={"physics.comp-ph"},

   keywords={Physics – Computational Physics, Condensed Matter – Soft Condensed Matter},

   year={2014},

   month={jan},

   adsurl={http://adsabs.harvard.edu/abs/2014arXiv1401.4350R},

   adsnote={Provided by the SAO/NASA Astrophysics Data System}

}

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We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a newly proposed "edge-based" approach, where a thread is started per each potentially non-zero interaction. We find that the former is more efficient for systems with many simple interactions per particle, while the latter is more efficient if the system has more complicated interactions or fewer of them. By comparing computation times on more and less recent GPU technology, we predict that, if the current trend of increasing the number of processing cores – as opposed to their computing power – remains, the "edge-based" approach will gradually become the most efficient choice in an increasing number of cases.
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