Achieving strong scaling with NAMD on blue Gene/L

Authors:
Sameer Kumar;Chao Huang;Gheorghe Almasi;Laxmikant V. Kalé
Affiliations:
IBM T.J. Watson Research Center, Yorktown Heights, NY;University of Illinois at Urbana-Champaign, Urbana, IL;IBM T.J. Watson Research Center, Yorktown Heights, NY;University of Illinois at Urbana-Champaign, Urbana, IL
Venue:
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Year:
2006

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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.