Law, Timothy R., Hancox, Jonny, Wright, Steven A. orcid.org/0000-0001-7133-8533 et al. (1 more author) (2019) An Algorithm for Computing Short-Range Forces in Molecular Dynamics Simulations with Non-Uniform Particle Densities. Journal of Parallel and Distributed Computing. pp. 1-11. ISSN 0743-7315
Abstract
We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5x overall speedup and good scaling to large problem sizes and processor counts.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2019 The Author(s). |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Computer Science (York) |
Depositing User: | Pure (York) |
Date Deposited: | 20 Mar 2019 13:00 |
Last Modified: | 17 Dec 2024 00:12 |
Published Version: | https://doi.org/10.1016/j.jpdc.2019.03.008 |
Status: | Published online |
Refereed: | Yes |
Identification Number: | 10.1016/j.jpdc.2019.03.008 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:143924 |