Article

Analysis and Performance Results of a Molecular Modeling Application on Merrimac

Authors:

William J. Dally,

Eric DarveAuthors Info & Claims

SC '04: Proceedings of the 2004 ACM/IEEE conference on Supercomputing

Page 42

https://doi.org/10.1109/SC.2004.69

Published: 06 November 2004 Publication History

Abstract

The Merrimac supercomputer uses stream processors and a high-radix network to achieve high performance at low cost and low power. The stream architecture matches the capabilities of modem semiconductor technology with compute-intensive parallel applications. We present a detailed case study of porting the GROMACS molecular-dynamics force calculation to Merrimac. The characteristics of the architecture which stress locality, parallelism, and decoupling of memory operations and computation, allow for high performance of compiler optimized code. The rich set of hardware memory operations and the ample computation bandwidth of the Merrimac processor present a wide range of algorithmic trade-offs and optimizations which may be generalized to several scientific computing domains. We use a cycle-accurate hardware simulator to analyze the performance bottlenecks of the various implementations and to measure application run-time. A comparison with the highly optimized GROMACS code, tuned for an Intel Pentium 4, confirms Merrimacýs potential to deliver high performance.

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Cited By

Peng LTan GKalia RNakano AVashishta PFan DZhang HSong F(2013)Scalability study of molecular dynamics simulation on Godson-T many-core architectureJournal of Parallel and Distributed Computing10.1016/j.jpdc.2012.07.00773:11(1469-1482)Online publication date: 1-Nov-2013
https://dl.acm.org/doi/10.1016/j.jpdc.2012.07.007
Peng LNakano ATan GVashishta PFan DZhang HKalia RSong FCascaval CTrancoso PPrasanna V(2011)Performance analysis and optimization of molecular dynamics simulation on Godson-T many-core processorProceedings of the 8th ACM International Conference on Computing Frontiers10.1145/2016604.2016643(1-10)Online publication date: 3-May-2011
https://dl.acm.org/doi/10.1145/2016604.2016643
Li PAgrawal KBuhler JChamberlain Rauf der Heide FPhillips C(2010)Deadlock avoidance for streaming computations with filteringProceedings of the twenty-second annual ACM symposium on Parallelism in algorithms and architectures10.1145/1810479.1810526(243-252)Online publication date: 13-Jun-2010
https://dl.acm.org/doi/10.1145/1810479.1810526
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Information

Published In

cover image ACM Conferences

SC '04: Proceedings of the 2004 ACM/IEEE conference on Supercomputing

November 2004

724 pages

ISBN:0769521533

General Chair:
Jeff Huskamp

Sponsors

SIGARCH: ACM Special Interest Group on Computer Architecture
IEEE-CS: Computer Society

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IEEE Computer Society

United States

Publication History

Published: 06 November 2004

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SC '04

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SC '04: International Conference for High Performance Computing, Networking, Storage and Analysis

November 6 - 12, 2004

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SC '04 Paper Acceptance Rate 60 of 200 submissions, 30%;

Overall Acceptance Rate 1,516 of 6,373 submissions, 24%

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Cited By

Peng LTan GKalia RNakano AVashishta PFan DZhang HSong F(2013)Scalability study of molecular dynamics simulation on Godson-T many-core architectureJournal of Parallel and Distributed Computing10.1016/j.jpdc.2012.07.00773:11(1469-1482)Online publication date: 1-Nov-2013
https://dl.acm.org/doi/10.1016/j.jpdc.2012.07.007
Peng LNakano ATan GVashishta PFan DZhang HKalia RSong FCascaval CTrancoso PPrasanna V(2011)Performance analysis and optimization of molecular dynamics simulation on Godson-T many-core processorProceedings of the 8th ACM International Conference on Computing Frontiers10.1145/2016604.2016643(1-10)Online publication date: 3-May-2011
https://dl.acm.org/doi/10.1145/2016604.2016643
Li PAgrawal KBuhler JChamberlain Rauf der Heide FPhillips C(2010)Deadlock avoidance for streaming computations with filteringProceedings of the twenty-second annual ACM symposium on Parallelism in algorithms and architectures10.1145/1810479.1810526(243-252)Online publication date: 13-Jun-2010
https://dl.acm.org/doi/10.1145/1810479.1810526
Du JYang XWang GTang TZeng K(2007)Architecture-based optimization for mapping scientific applications to imagineProceedings of the 5th international conference on Parallel and Distributed Processing and Applications10.5555/2395970.2395978(32-43)Online publication date: 29-Aug-2007
https://dl.acm.org/doi/10.5555/2395970.2395978
Deng YYang XYan XZeng K(2007)Laplace transformation on the FT64 stream processorProceedings of the 12th Asia-Pacific conference on Advances in Computer Systems Architecture10.5555/2392163.2392170(52-62)Online publication date: 23-Aug-2007
https://dl.acm.org/doi/10.5555/2392163.2392170
Zhang YLi GYang X(2007)Implementing and optimizing a data-intensive hydrodynamics application on the stream processorProceedings of the 2007 international conference on Computational science and its applications - Volume Part III10.5555/1793154.1793190(353-366)Online publication date: 26-Aug-2007
https://dl.acm.org/doi/10.5555/1793154.1793190
Du JYang XYang WTang TWang G(2007)Implementation and evaluation of Jacobi iteration on the imagine stream processorProceedings of the 14th international conference on High performance computing10.5555/1782174.1782202(221-232)Online publication date: 18-Dec-2007
https://dl.acm.org/doi/10.5555/1782174.1782202
Wen MWu NZhang CWu WYang QXun C(2007)FT64Proceedings of the 14th international conference on High performance computing10.5555/1782174.1782201(209-220)Online publication date: 18-Dec-2007
https://dl.acm.org/doi/10.5555/1782174.1782201
Ahn JErez MDally WSmith B(2007)Tradeoff between data-, instruction-, and thread-level parallelism in stream processorsProceedings of the 21st annual international conference on Supercomputing10.1145/1274971.1274991(126-137)Online publication date: 17-Jun-2007
https://dl.acm.org/doi/10.1145/1274971.1274991
Ahn JErez MDally WHorner-Miller B(2006)The design space of data-parallel memory systemsProceedings of the 2006 ACM/IEEE conference on Supercomputing10.1145/1188455.1188540(80-es)Online publication date: 11-Nov-2006
https://dl.acm.org/doi/10.1145/1188455.1188540
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