Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation

Timothy R. Law; Jonny Hancox; Tammy M.K. Cheng; Raphael A.G. Chaleil; Steven A. Wright; Paul A. Bates; Stephen A. Jarvis

doi:10.1109/SBAC-PAD.2016.24

Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation

Timothy R. Law, Jonny Hancox, Tammy M.K. Cheng, Raphael A.G. Chaleil, Steven A. Wright, Paul A. Bates, Stephen A. Jarvis

Engineering and Physical Sciences

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

1 Citation (Scopus)

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.

Original language	English
Title of host publication	Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016
Publisher	IEEE Computer Society
Pages	126-133
Number of pages	8
ISBN (Electronic)	9781509061082
DOIs	https://doi.org/10.1109/SBAC-PAD.2016.24
Publication status	Published - 16 Dec 2016
Event	28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016 - Los Angeles, United States Duration: 26 Oct 2016 → 28 Oct 2016

Publication series

Name	Proceedings - Symposium on Computer Architecture and High Performance Computing
ISSN (Print)	1550-6533

Conference

Conference	28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016
Country/Territory	United States
City	Los Angeles
Period	26/10/16 → 28/10/16

Bibliographical note

Funding Information:
This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003), and by the Engineering and Physical Sciences Research Council and Intel Corporation (CASE award 1365607).

Publisher Copyright:
© 2016 IEEE.

ASJC Scopus subject areas

Hardware and Architecture
Software

Access to Document

10.1109/SBAC-PAD.2016.24

Cite this

Law, T. R., Hancox, J., Cheng, T. M. K., Chaleil, R. A. G., Wright, S. A., Bates, P. A., & Jarvis, S. A. (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 (pp. 126-133). Article 7789332 (Proceedings - Symposium on Computer Architecture and High Performance Computing). IEEE Computer Society. https://doi.org/10.1109/SBAC-PAD.2016.24

Law, Timothy R. ; Hancox, Jonny ; Cheng, Tammy M.K. et al. / Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation. Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016. IEEE Computer Society, 2016. pp. 126-133 (Proceedings - Symposium on Computer Architecture and High Performance Computing).

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title = "Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation",

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.",

author = "Law, {Timothy R.} and Jonny Hancox and Cheng, {Tammy M.K.} and Chaleil, {Raphael A.G.} and Wright, {Steven A.} and Bates, {Paul A.} and Jarvis, {Stephen A.}",

note = "Funding Information: This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001003), the UK Medical Research Council (FC001003), and the Wellcome Trust (FC001003), and by the Engineering and Physical Sciences Research Council and Intel Corporation (CASE award 1365607). Publisher Copyright: {\textcopyright} 2016 IEEE.; 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016 ; Conference date: 26-10-2016 Through 28-10-2016",

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Law, TR, Hancox, J, Cheng, TMK, Chaleil, RAG, Wright, SA, Bates, PA & Jarvis, SA 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., 7789332, Proceedings - Symposium on Computer Architecture and High Performance Computing, IEEE Computer Society, pp. 126-133, 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016, Los Angeles, United States, 26/10/16. https://doi.org/10.1109/SBAC-PAD.2016.24

Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation. / Law, Timothy R.; Hancox, Jonny; Cheng, Tammy M.K. et al.
Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016. IEEE Computer Society, 2016. p. 126-133 7789332 (Proceedings - Symposium on Computer Architecture and High Performance Computing).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

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Law TR, Hancox J, Cheng TMK, Chaleil RAG, Wright SA, Bates PA et al. 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. IEEE Computer Society. 2016. p. 126-133. 7789332. (Proceedings - Symposium on Computer Architecture and High Performance Computing). doi: 10.1109/SBAC-PAD.2016.24

Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation

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