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Exploring SIMD for molecular dynamics, using Intel Xeon processors and Intel Xeon Phi coprocessors
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Pennycook, Simon J., Hughes, C. J., Smelyanskiy, M. and Jarvis, Stephen A. (2013) Exploring SIMD for molecular dynamics, using Intel Xeon processors and Intel Xeon Phi coprocessors. In: IEEE International Parallel & Distributed Processing Symposium, Boston, MA, 20-24 May 2013. Published in: 2013 IEEE 27th International Symposium on Parallel & Distributed Processing (IPDPS) pp. 1085-1097. ISBN 9781467360661. ISSN 1530-2075.
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Official URL: http://dx.doi.org/10.1109/IPDPS.2013.44
Abstract
We analyse gather-scatter performance bottlenecks in molecular dynamics codes and the challenges that they pose for obtaining benefits from SIMD execution. This analysis informs a number of novel code-level and algorithmic improvements to Sandia's miniMD benchmark, which we demonstrate using three SIMD widths (128-, 256- and 512-bit). The applicability of these optimisations to wider SIMD is discussed, and we show that the conventional approach of exposing more parallelism through redundant computation is not necessarily best.
In single precision, our optimised implementation is up to 5x faster than the original scalar code running on Intel Xeon processors with 256-bit SIMD, and adding a single Intel Xeon Phi coprocessor provides up to an additional 2x performance increase. These results demonstrate: (i) the importance of effective SIMD utilisation for molecular dynamics codes on current and future hardware; and (ii) the considerable performance increase afforded by the use of Intel Xeon Phi coprocessors for highly parallel workloads.
| Item Type: | Conference Item (Paper) | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software | ||||
| Divisions: | Faculty of Science > Computer Science | ||||
| Library of Congress Subject Headings (LCSH): | SIMD (Computer architecture), Molecular dynamics -- Computer programs | ||||
| Journal or Publication Title: | 2013 IEEE 27th International Symposium on Parallel & Distributed Processing (IPDPS) | ||||
| Publisher: | Conference Publishing Services | ||||
| ISBN: | 9781467360661 | ||||
| ISSN: | 1530-2075 | ||||
| Official Date: | May 2013 | ||||
| Dates: |
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| Date of first compliant deposit: | 28 July 2016 | ||||
| Page Range: | pp. 1085-1097 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Funder: | Royal Society (Great Britain) | ||||
| Grant number: | IF090020/AM (RS) | ||||
| Conference Paper Type: | Paper | ||||
| Title of Event: | IEEE International Parallel & Distributed Processing Symposium | ||||
| Type of Event: | Conference | ||||
| Location of Event: | Boston, MA | ||||
| Date(s) of Event: | 20-24 May 2013 | ||||
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