By the same authors

Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Standard

Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation. / Law, Timothy R.; Hancox, Jonny; Cheng, Tammy M.K.; Chaleil, Raphael A.G.; Wright, Steven A.; Bates, Paul A.; Jarvis, Stephen A.

Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016. IEEE Computer Society Press, 2016. p. 126-133 7789332.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Harvard

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, IEEE Computer Society Press, 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

APA

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). [7789332] IEEE Computer Society Press. https://doi.org/10.1109/SBAC-PAD.2016.24

Vancouver

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 Press. 2016. p. 126-133. 7789332 https://doi.org/10.1109/SBAC-PAD.2016.24

Author

Law, Timothy R. ; Hancox, Jonny ; Cheng, Tammy M.K. ; Chaleil, Raphael A.G. ; Wright, Steven A. ; Bates, Paul A. ; Jarvis, Stephen A. / 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 Press, 2016. pp. 126-133

Bibtex - Download

@inproceedings{176cf5d64e14400cb6e60a34c2f35c86,
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 = "{\textcopyright} Copyright 2018 IEEE - All rights reserved. Use of this web site signifies your agreement to the terms and conditions. ; 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016 ; Conference date: 26-10-2016 Through 28-10-2016",
year = "2016",
month = dec,
day = "16",
doi = "10.1109/SBAC-PAD.2016.24",
language = "English",
pages = "126--133",
booktitle = "Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016",
publisher = "IEEE Computer Society Press",

}

RIS (suitable for import to EndNote) - Download

TY - GEN

T1 - Optimisation of a Molecular Dynamics Simulation of Chromosome Condensation

AU - Law, Timothy R.

AU - Hancox, Jonny

AU - Cheng, Tammy M.K.

AU - Chaleil, Raphael A.G.

AU - Wright, Steven A.

AU - Bates, Paul A.

AU - Jarvis, Stephen A.

N1 - © Copyright 2018 IEEE - All rights reserved. Use of this web site signifies your agreement to the terms and conditions.

PY - 2016/12/16

Y1 - 2016/12/16

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85010369507&partnerID=8YFLogxK

U2 - 10.1109/SBAC-PAD.2016.24

DO - 10.1109/SBAC-PAD.2016.24

M3 - Conference contribution

AN - SCOPUS:85010369507

SP - 126

EP - 133

BT - Proceedings - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016

PB - IEEE Computer Society Press

T2 - 28th IEEE International Symposium on Computer Architecture and High Performance Computing, SBAC-PAD 2016

Y2 - 26 October 2016 through 28 October 2016

ER -