title: Efficient large-scale replica-exchange simulations on production infrastructure.
abstract: Replica-exchange (RE) algorithms are used to understand physical phenomena--ranging from protein folding dynamics to binding affinity calculations. They represent a class of algorithms that involve a large number of loosely coupled ensembles, and are thus amenable to using distributed resources. We develop a framework for RE that supports different replica pairing (synchronous versus asynchronous) and exchange coordination mechanisms (centralized versus decentralized) and which can use a range of production cyberinfrastructures concurrently. We characterize the performance of both RE algorithms at an unprecedented number of cores employed--the number of replicas and the typical number of cores per replica--on the production distributed infrastructure. We find that the asynchronous algorithms outperform the synchronous algorithms, even though details of the specific implementations are important determinants of performance.
authors.affiliation: Centre for Computation and Technology, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Thota
authors.forename: André
authors.initials: A
authors.lastname: Luckow
authors.forename: Shantenu
authors.initials: S
authors.lastname: Jha
mesh_terms: D000465:Algorithms; D001703:Biophysics / Q000379:methods*; D016174:Hepacivirus / Q000378:metabolism; D006526:Hepatitis C / Q000821:virology; D006801:Humans; D008962:Models, Theoretical; D011336:Probability