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Developing performance-portable molecular dynamics kernels in Open CL
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Pennycook, Simon J. and Jarvis, Stephen A. (2012) Developing performance-portable molecular dynamics kernels in Open CL. In: 3rd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems, International Conference for High Performance Computing, Networking, Storage and Analysis, Salt Lake City, UT, 10-16 Nov 2012. Published in: 2012 SC Companion : High Performance Computing, Networking, Storage and Analysis (SCC) pp. 386-395. ISBN 9781467362184 .
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Abstract
This paper investigates the development of a molecular dynamics code that is highly portable between architectures. Using OpenCL, we develop an implementation of Sandia’s miniMD benchmark that achieves good levels of performance across a wide range of hardware: CPUs, discrete GPUs and integrated GPUs.
We demonstrate that the performance bottlenecks of miniMD’s short-range force calculation kernel are the same across these architectures, and detail a number of platform- agnostic optimisations that improve its performance by at least 2x on all hardware considered. Our complete code is shown to be 1.7x faster than the original miniMD, and at most 2x slower than implementations individually hand-tuned for a specific architecture.
Item Type: | Conference Item (Paper) | ||||
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Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software | ||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science | ||||
Library of Congress Subject Headings (LCSH): | Molecular dynamics, High performance computing, OpenCL (Computer program language) | ||||
Journal or Publication Title: | 2012 SC Companion : High Performance Computing, Networking, Storage and Analysis (SCC) | ||||
Publisher: | IEEE | ||||
ISBN: | 9781467362184 | ||||
Official Date: | November 2012 | ||||
Dates: |
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Page Range: | pp. 386-395 | ||||
Status: | Peer Reviewed | ||||
Publication Status: | Published | ||||
Access rights to Published version: | Restricted or Subscription Access | ||||
Date of first compliant deposit: | 28 July 2016 | ||||
Date of first compliant Open Access: | 28 July 2016 | ||||
Funder: | Royal Society (Great Britain), Atomic Weapons Establishment (Great Britain) (AWE) | ||||
Grant number: | IF090020/AM (RS), CDK0660 (AWE), CDK0724 (AWE) | ||||
Conference Paper Type: | Paper | ||||
Title of Event: | 3rd International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computing Systems, International Conference for High Performance Computing, Networking, Storage and Analysis | ||||
Type of Event: | Conference | ||||
Location of Event: | Salt Lake City, UT | ||||
Date(s) of Event: | 10-16 Nov 2012 |
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