Achieving Strong Scaling with NAMD on Blue Gene/L

NAMD is a scalable molecular dynamics application, which has demonstrated its performance on several paral-lel 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 in-teresting biological phenomenon. The Blue Gene/L ma-chine is a massive source of compute power. It consists of tens of thousands of embedded Power PC 440 proces-sors. 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 communi-cation. We were able to achieve 1.2 TF of peak performance for cutoff simulations and 0.99 TF with PME.