S. Kumar, C. Huang, G. Zheng, E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, and
L. V. Kale.
Scalable molecular dynamics with NAMD on the IBM Blue
Gene/L system.
IBM Journal of Research and Development, 52:177-188, 2008.
KUMA2008-LK
NAMD (nanoscale molecular dynamics) is a production molecular
dynamics (MD) application for biomolecular simulations that
include assemblages of proteins, cell membranes, and water
molecules. In a biomolecular simulation, the problem size is fixed
and a large number of iterations must be executed in order to
understand interesting biological phenomena. Hence, we need MD
applications to scale to thousands of processors, even though the
individual timestep on one processor is quite small. NAMD has
demonstrated its performance on several parallel computer
architectures. In this paper, we present various compiler
optimization techniques that use single-instruction, multiple-data
(SIMD) instructions to obtain good sequential performance with
NAMD on the embedded IBM PowerPCt 440 processor core. We
also present several techniques to scale the NAMD application to
20,480 nodes of the IBM Blue Gene/Le (BG/L) system. These
techniques include topology-specific optimizations to localize
communication, new messaging protocols that are optimized for the
BG/L torus, topology-aware load balancing, and overlap of
computation and communication. We also present performance
results of various molecular systems with sizes ranging from 5,570
to 327,506 atoms.
