TY - GEN
T1 - Achieving strong scaling with NAMD on Blue Gene/L
AU - Kumar, Sameer
AU - Huang, Chao
AU - Almasi, Gheorghe
AU - Kalé, Laxmikant V.
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
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U2 - 10.1109/IPDPS.2006.1639298
DO - 10.1109/IPDPS.2006.1639298
M3 - Conference contribution
AN - SCOPUS:33847130594
SN - 1424400546
SN - 9781424400546
T3 - 20th International Parallel and Distributed Processing Symposium, IPDPS 2006
BT - 20th International Parallel and Distributed Processing Symposium, IPDPS 2006
PB - IEEE Computer Society
T2 - 20th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2006
Y2 - 25 April 2006 through 29 April 2006
ER -