Blue Matter, an application framework for molecular simulation on blue gene
Journal of Parallel and Distributed Computing - High-performance computational biology
Blue matter on blue gene/L: massively parallel computation for biomolecular simulation
CODES+ISSS '05 Proceedings of the 3rd IEEE/ACM/IFIP international conference on Hardware/software codesign and system synthesis
Optimization of MPI collective communication on BlueGene/L systems
Proceedings of the 19th annual international conference on Supercomputing
Overview of the Blue Gene/L system architecture
IBM Journal of Research and Development
Early performance data on the blue matter molecular simulation framework
IBM Journal of Research and Development
IBM Journal of Research and Development
Performance measurements of the 3D FFT on the blue gene/l supercomputer
Euro-Par'05 Proceedings of the 11th international Euro-Par conference on Parallel Processing
Blue matter: scaling of N-body simulations to one atom per node
IBM Journal of Research and Development
Grid-based asynchronous replica exchange
GRID '07 Proceedings of the 8th IEEE/ACM International Conference on Grid Computing
A decentralized parallel implementation for parallel tempering algorithm
Parallel Computing
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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 interprocessor 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.