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.

Parallel Fast Multipole Method for Molecular Dynamics

We report on a parallel version of the Fast Multipole Method (FMM) implemented in the classical molecular dynamics code, NAMD (Not Another Molecular Dynamics program). This novel implementation of FMM aims to minimize interprocessor communication through the modification of the FMM grid to match the hybrid force and spatial decomposition scheme already present in NAMD. This new implementation has the benefit of replacing all-to-all communications broadcasts with direct communications between nearest neighbors. This results in a significant reduction in the amount of communication compared to earlier attempts to integrate FMM into common molecular dynamics programs. The early performance of FMM is similar to the existing electrostatics methods already in NAMD. In addition, tests of the stability and accuracy of the FMM algorithm in molecular dynamics as applied to several common solvated protein structures are discussed