Parallel and Distributed Processing Symposium, International (2006)
Rhodes Island, Greece
Apr. 25, 2006 to Apr. 29, 2006
M. Eleftheriou , IBM Thomas J. Watson Res. Center, Yorktown Heights, NY, USA
A. Rayshubski , IBM Thomas J. Watson Res. Center, Yorktown Heights, NY, USA
The replica exchange method is a popular approach for studying the folding thermodynamics of small to modest size proteins in explicit solvent, since it is easily parallelized. However, replica exchange can become computationally expensive for large-scale studies, due to the number of replicas needed as well as interprocess or communication requirements both between and within replicas. In this paper, we discuss an implementation of replica exchange molecular dynamics on Blue Gene/L for performing large scale simulation studies of systems of biological interest. The algorithm is tuned with an awareness of the physical network topology and hardware performance features of the Blue Gene/L architecture. Performance measurements for replica exchange using the blue matter molecular dynamics application are presented on Blue Gene/L hardware with up to 256 replicas simulated on 8,192 compute nodes. Both scalability and performance are achieved with this implementation.
blue matter molecular dynamics, parallel implementation, replica exchange molecular dynamics algorithm, Blue Gene/L, thermodynamics, protein, biological system, physical network topology, hardware performance feature
R. Zhou, A. Rayshubski, B. Fitch, M. Eleftheriou, R. Germain and J. Pitera, "Parallel implementation of the replica exchange molecular dynamics algorithm on Blue Gene/L," Parallel and Distributed Processing Symposium, International(IPDPS), Rhodes Island, Greece, 2006, pp. 281.