Achieving strong scaling with NAMD on Blue Gene/L

Sameer Kumar, Chao Huang, Gheorghe Almasi, Laxmikant V Kale

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

NAMD is a scalable molecular dynamics application, which has demonstrated its performance on several parallel computer architectures. Strong scaling is necessary for molecular dynamics as problem size is fixed, and a large number of iterations need to be executed to understand interesting biological phenomenon. The Blue Gene/L machine is a massive source of compute power. It consists of tens of thousands of embedded Power PC 440 processors. In this paper, we present several techniques to scale NAMD to 8192 processors of Blue Gene/L These include topology specific optimizations, new messaging protocols, load-balancing, and overlap of computation and communication. We were able to achieve 1.2 TF of peak performance for cutoff simulations and 0.99 TF with PME.

Original languageEnglish (US)
Title of host publication20th International Parallel and Distributed Processing Symposium, IPDPS 2006
PublisherIEEE Computer Society
ISBN (Print)1424400546, 9781424400546
DOIs
StatePublished - Jan 1 2006
Event20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006 - Rhodes Island, Greece
Duration: Apr 25 2006Apr 29 2006

Publication series

Name20th International Parallel and Distributed Processing Symposium, IPDPS 2006
Volume2006

Other

Other20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006
CountryGreece
CityRhodes Island
Period4/25/064/29/06

Fingerprint

Molecular dynamics
Genes
Computer architecture
Resource allocation
Topology
Network protocols
Communication

ASJC Scopus subject areas

  • Engineering(all)

Cite this

Kumar, S., Huang, C., Almasi, G., & Kale, L. V. (2006). Achieving strong scaling with NAMD on Blue Gene/L. In 20th International Parallel and Distributed Processing Symposium, IPDPS 2006 [1639298] (20th International Parallel and Distributed Processing Symposium, IPDPS 2006; Vol. 2006). IEEE Computer Society. https://doi.org/10.1109/IPDPS.2006.1639298

Achieving strong scaling with NAMD on Blue Gene/L. / Kumar, Sameer; Huang, Chao; Almasi, Gheorghe; Kale, Laxmikant V.

20th International Parallel and Distributed Processing Symposium, IPDPS 2006. IEEE Computer Society, 2006. 1639298 (20th International Parallel and Distributed Processing Symposium, IPDPS 2006; Vol. 2006).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Kumar, S, Huang, C, Almasi, G & Kale, LV 2006, Achieving strong scaling with NAMD on Blue Gene/L. in 20th International Parallel and Distributed Processing Symposium, IPDPS 2006., 1639298, 20th International Parallel and Distributed Processing Symposium, IPDPS 2006, vol. 2006, IEEE Computer Society, 20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006, Rhodes Island, Greece, 4/25/06. https://doi.org/10.1109/IPDPS.2006.1639298
Kumar S, Huang C, Almasi G, Kale LV. Achieving strong scaling with NAMD on Blue Gene/L. In 20th International Parallel and Distributed Processing Symposium, IPDPS 2006. IEEE Computer Society. 2006. 1639298. (20th International Parallel and Distributed Processing Symposium, IPDPS 2006). https://doi.org/10.1109/IPDPS.2006.1639298
Kumar, Sameer ; Huang, Chao ; Almasi, Gheorghe ; Kale, Laxmikant V. / Achieving strong scaling with NAMD on Blue Gene/L. 20th International Parallel and Distributed Processing Symposium, IPDPS 2006. IEEE Computer Society, 2006. (20th International Parallel and Distributed Processing Symposium, IPDPS 2006).
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