Communications of the ACM
The Timed Asynchronous Distributed System Model
IEEE Transactions on Parallel and Distributed Systems
Chord: A scalable peer-to-peer lookup service for internet applications
Proceedings of the 2001 conference on Applications, technologies, architectures, and protocols for computer communications
Analysis of the Clustering Properties of the Hilbert Space-Filling Curve
IEEE Transactions on Knowledge and Data Engineering
Parallel Programming: Techniques and Applications Using Networked Workstations and Parallel Computers (2nd Edition)
Enabling Flexible Queries with Guarantees in P2P Systems
IEEE Internet Computing
Flexible information discovery with guarantees in decentralized distributed systems
Flexible information discovery with guarantees in decentralized distributed systems
Salsa: Scalable Asynchronous Replica Exchange for Parallel Molecular Dynamics Applications
ICPP '06 Proceedings of the 2006 International Conference on Parallel Processing
Parallel implementation of the replica exchange molecular dynamics algorithm on blue gene/L
IPDPS'06 Proceedings of the 20th international conference on Parallel and distributed processing
Enabling autonomic computing on federated advanced cyberinfrastructures
Proceedings of the 2013 ACM Cloud and Autonomic Computing Conference
| Hi-index | 0.00 |
Replica exchange is a powerful sampling algorithm and can be effectively used for applications such as simulating the structure, function, folding, and dynamics of proteins and drug design. However, Grid-based implementations of the algorithm present significant challenges due to its synchronization and communication requirements. This paper presents an asynchronous formulation of the replica exchange algorithm and the design and implementation of a Grid-based asynchronous replica exchange engine (GARE). GARE is based on CometG, a decentralized computational infrastructure for Desktop Grid environments that provides a scalable communication and interaction substrate and presents a virtual semantically specialized shared space abstraction. It enables the dynamic and asynchronous interactions required by the algorithm to be simply expressed and efficiently implemented. The design and implementation of GARE/CometG and the replica exchange simulations that it enables are presented. Experimental evaluations using the PlanetLab [1] wide-area test bed as well as a campus Grid environment are presented.