Law, Timothy R., Hancox, Jonny, Cheng, Tammy M.K. et al. (4 more authors) (2016) Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation. In: Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016. 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016, 26-28 Oct 2016 IEEE Computer Society , USA , pp. 126-133.
Abstract
We present optimisations applied to a bespoke bio-physical molecular dynamics simulation designed to investigate chromosome condensation. Our primary focus is on domain-specific algorithmic improvements to determining short-range interaction forces between particles, as certain qualities of the simulation render traditional methods less effective. We implement tuned versions of the code for both traditional CPU architectures and the modern many-core architecture found in the Intel Xeon Phi coprocessor and compare their effectiveness. We achieve speed-ups starting at a factor of 10 over the original code, facilitating more detailed and larger-scale experiments.
Metadata
Item Type: | Proceedings Paper |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © Copyright 2018 IEEE - All rights reserved. Use of this web site signifies your agreement to the terms and conditions. |
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: | 04 Sep 2018 15:30 |
Last Modified: | 08 Feb 2025 00:11 |
Published Version: | https://doi.org/10.1109/SBAC-PAD.2016.24 |
Status: | Published |
Publisher: | IEEE Computer Society |
Identification Number: | 10.1109/SBAC-PAD.2016.24 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:135317 |
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