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A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

Authors:

Charles A. Rendleman,

David W. Borhani,

Justin Gullingsrud,

Morten Ø. Jensen,

John L. Klepeis,

Paul Maragakis,

Patrick Miller,

Kate A. Stafford,

David E. ShawAuthors Info & Claims

SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing

Article No.: 56, Pages 1 - 12

Published: 15 November 2008 Publication History

Abstract

As parallel algorithms and architectures drive the longest molecular dynamics (MD) simulations towards the millisecond scale, traditional sequential post-simulation data analysis methods are becoming increasingly untenable. Inspired by the programming interface of Google's MapReduce, we have built a new parallel analysis framework called HiMach, which allows users to write trajectory analysis programs sequentially, and carries out the parallel execution of the programs automatically. We introduce (1) a new MD trajectory data analysis model that is amenable to parallel processing, (2) a new interface for defining trajectories to be analyzed, (3) a novel method to make use of an existing sequential analysis tool called VMD, and (4) an extension to the original MapReduce model to support multiple rounds of analysis. Performance evaluations on up to 512 cores demonstrate the efficiency and scalability of the HiMach framework on a Linux cluster.

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Cited By

Asmussen NRoitzsch MHärtig HDan TDahlia M(2019)M3XProceedings of the 2019 USENIX Conference on Usenix Annual Technical Conference10.5555/3358807.3358859(617-631)Online publication date: 10-Jul-2019
https://dl.acm.org/doi/10.5555/3358807.3358859
Dongarra JTourancheau BAupy GGoglin BHonoré VRaffin B(2019)Modeling high-throughput applications for in situ analyticsInternational Journal of High Performance Computing Applications10.1177/109434201984726333:6(1185-1200)Online publication date: 1-Nov-2019
https://dl.acm.org/doi/10.1177/1094342019847263
Chen XBenson JPeterson MTaufer MEstrada T(2018)KeyBin2Proceedings of the 47th International Conference on Parallel Processing10.1145/3225058.3225149(1-10)Online publication date: 13-Aug-2018
https://dl.acm.org/doi/10.1145/3225058.3225149
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Index Terms

A scalable parallel framework for analyzing terascale molecular dynamics simulation trajectories

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Published In

cover image ACM Conferences

SC '08: Proceedings of the 2008 ACM/IEEE conference on Supercomputing

November 2008

739 pages

ISBN:9781424428359

Conference Chair:
Patricia Teller

Sponsors

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

Publisher

IEEE Press

Publication History

Published: 15 November 2008

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SC '08

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SIGARCH
IEEE-CS

SC '08: International Conference for High Performance Computing, Networking, Storage and Analysis

November 15 - 21, 2008

Texas, Austin

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SC '08 Paper Acceptance Rate 59 of 277 submissions, 21%;

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

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Cited By

Asmussen NRoitzsch MHärtig HDan TDahlia M(2019)M3XProceedings of the 2019 USENIX Conference on Usenix Annual Technical Conference10.5555/3358807.3358859(617-631)Online publication date: 10-Jul-2019
https://dl.acm.org/doi/10.5555/3358807.3358859
Dongarra JTourancheau BAupy GGoglin BHonoré VRaffin B(2019)Modeling high-throughput applications for in situ analyticsInternational Journal of High Performance Computing Applications10.1177/109434201984726333:6(1185-1200)Online publication date: 1-Nov-2019
https://dl.acm.org/doi/10.1177/1094342019847263
Chen XBenson JPeterson MTaufer MEstrada T(2018)KeyBin2Proceedings of the 47th International Conference on Parallel Processing10.1145/3225058.3225149(1-10)Online publication date: 13-Aug-2018
https://dl.acm.org/doi/10.1145/3225058.3225149
Paraskevakos ILuckow AKhoshlessan MChantzialexiou GCheatham TBeckstein OFox GJha S(2018)Task-parallel Analysis of Molecular Dynamics TrajectoriesProceedings of the 47th International Conference on Parallel Processing10.1145/3225058.3225128(1-10)Online publication date: 13-Aug-2018
https://dl.acm.org/doi/10.1145/3225058.3225128
Scharnowski KFrey SRaffin BErtl TPeytavie ABosch C(2017)Spline-based decomposition of streamed particle trajectories for efficient transfer and analysisProceedings of the European Association for Computer Graphics: Short Papers10.2312/egsh.20171010(41-44)Online publication date: 24-Apr-2017
https://dl.acm.org/doi/10.2312/egsh.20171010
Terraz TRibes AFournier YIooss BRaffin BMohr BRaghavan P(2017)MelissaProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/3126908.3126922(1-14)Online publication date: 12-Nov-2017
https://dl.acm.org/doi/10.1145/3126908.3126922
Wang YAgrawal GBicer TJiang WKern JVetter J(2015)SmartProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/2807591.2807650(1-12)Online publication date: 15-Nov-2015
https://dl.acm.org/doi/10.1145/2807591.2807650
Phillips JStone JVandivort KArmstrong TWozniak JWilde MSchulten KChen JEdelman AShen WTerrel A(2014)Petascale Tcl with NAMD, VMD, and Swift/TProceedings of the 1st First Workshop for High Performance Technical Computing in Dynamic Languages10.1109/HPTCDL.2014.7(6-17)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/HPTCDL.2014.7
Dreher MRaffin BReed DSun XFoster I(2014)A flexible framework for asynchronous in situ and in transit analytics for scientific simulationsProceedings of the 14th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing10.1109/CCGrid.2014.92(277-286)Online publication date: 26-May-2014
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Kendall WWang JAllen MPeterka THuang JErickson DLathrop SCosta JKramer W(2011)Simplified parallel domain traversalProceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis10.1145/2063384.2063397(1-11)Online publication date: 12-Nov-2011
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