research-article

Adapting a message-driven parallel application to GPU-accelerated clusters

Authors:

James C. Phillips,

Klaus SchultenAuthors Info & Claims

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

Article No.: 8, Pages 1 - 9

Published: 15 November 2008 Publication History

Abstract

Graphics processing units (GPUs) have become an attractive option for accelerating scientific computations as a result of advances in the performance and flexibility of GPU hardware, and due to the availability of GPU software development tools targeting general purpose and scientific computation. However, effective use of GPUs in clusters presents a number of application development and system integration challenges. We describe strategies for the decomposition and scheduling of computation among CPU cores and GPUs, and techniques for overlapping communication and CPU computation with GPU kernel execution. We report the adaptation of these techniques to NAMD, a widely-used parallel molecular dynamics simulation package, and present performance results for a 64-core 64-GPU cluster.

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Cited By

De Supinski BCasalino LDommer AGaieb ZBarros ESztain TAhn STrifan ABrace ABogetti AClyde AMa HLee HTurilli MKhalid SChong LSimmerling CHardy DMaia JPhillips JKurth TStern AHuang LMcCalpin JTatineni MGibbs TStone JJha SRamanathan AAmaro R(2021)AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamicsInternational Journal of High Performance Computing Applications10.1177/1094342021100645235:5(432-451)Online publication date: 1-Sep-2021
https://dl.acm.org/doi/10.1177/10943420211006452
Liu JRobson MQuinn TKulkarni MEigenmann RDing CMcKee S(2019)Efficient GPU tree walks for effective distributed n-body simulationsProceedings of the ACM International Conference on Supercomputing10.1145/3330345.3330348(24-34)Online publication date: 26-Jun-2019
https://dl.acm.org/doi/10.1145/3330345.3330348
Acun BHardy DKale LLi KPhillips JStone J(2018)Scalable molecular dynamics with NAMD on the Summit systemIBM Journal of Research and Development10.1147/JRD.2018.288898662:6(4:1-4:9)Online publication date: 1-Nov-2018
https://dl.acm.org/doi/10.1147/JRD.2018.2888986
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Adapting a message-driven parallel application to GPU-accelerated clusters

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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

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

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IEEE Press

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Published: 15 November 2008

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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

De Supinski BCasalino LDommer AGaieb ZBarros ESztain TAhn STrifan ABrace ABogetti AClyde AMa HLee HTurilli MKhalid SChong LSimmerling CHardy DMaia JPhillips JKurth TStern AHuang LMcCalpin JTatineni MGibbs TStone JJha SRamanathan AAmaro R(2021)AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamicsInternational Journal of High Performance Computing Applications10.1177/1094342021100645235:5(432-451)Online publication date: 1-Sep-2021
https://dl.acm.org/doi/10.1177/10943420211006452
Liu JRobson MQuinn TKulkarni MEigenmann RDing CMcKee S(2019)Efficient GPU tree walks for effective distributed n-body simulationsProceedings of the ACM International Conference on Supercomputing10.1145/3330345.3330348(24-34)Online publication date: 26-Jun-2019
https://dl.acm.org/doi/10.1145/3330345.3330348
Acun BHardy DKale LLi KPhillips JStone J(2018)Scalable molecular dynamics with NAMD on the Summit systemIBM Journal of Research and Development10.1147/JRD.2018.288898662:6(4:1-4:9)Online publication date: 1-Nov-2018
https://dl.acm.org/doi/10.1147/JRD.2018.2888986
Phillips JSanielevici S(2018)What You Should Know About NAMD and Charm++ But Were Hoping to IgnoreProceedings of the Practice and Experience on Advanced Research Computing: Seamless Creativity10.1145/3219104.3219134(1-6)Online publication date: 22-Jul-2018
https://dl.acm.org/doi/10.1145/3219104.3219134
Gysi TBär JHoefler TWest J(2016)dCUDAProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.5555/3014904.3014974(1-12)Online publication date: 13-Nov-2016
https://dl.acm.org/doi/10.5555/3014904.3014974
Bleuse RKedad-Sidhoum SMonna FMounié GTrystram D(2015)Scheduling independent tasks on multi-cores with GPU acceleratorsConcurrency and Computation: Practice & Experience10.1002/cpe.335927:6(1625-1638)Online publication date: 25-Apr-2015
https://dl.acm.org/doi/10.1002/cpe.3359
Choi JChandramowlishwaran AMadduri KVuduc RCavazos JGong XKaeli D(2014)A CPUProceedings of Workshop on General Purpose Processing Using GPUs10.1145/2588768.2576787(64-71)Online publication date: 1-Mar-2014
https://dl.acm.org/doi/10.1145/2588768.2576787
Phillips JSun YJain NBohm EKalé LDamkroger TDongarra J(2014)Mapping to irregular torus topologies and other techniques for petascale biomolecular simulationProceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis10.1109/SC.2014.12(81-91)Online publication date: 16-Nov-2014
https://dl.acm.org/doi/10.1109/SC.2014.12
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
Vasudevan RVadhiyar SKalé LMalony ANemirovsky MMidkiff S(2013)G-CharmProceedings of the 27th international ACM conference on International conference on supercomputing10.1145/2464996.2465444(349-358)Online publication date: 10-Jun-2013
https://dl.acm.org/doi/10.1145/2464996.2465444
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