Efficient large-scale replica-exchange simulations on production infrastructure.
Identifieur interne : 000248 ( Ncbi/Merge ); précédent : 000247; suivant : 000249Efficient large-scale replica-exchange simulations on production infrastructure.
Auteurs : Abhinav Thota [États-Unis] ; André Luckow ; Shantenu JhaSource :
- Philosophical transactions. Series A, Mathematical, physical, and engineering sciences [ 1364-503X ] ; 2011.
English descriptors
- KwdEn :
- MESH :
- metabolism : Hepacivirus.
- methods : Biophysics.
- virology : Hepatitis C.
- Algorithms, Humans, Models, Theoretical, Probability.
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.
DOI: 10.1098/rsta.2011.0151
PubMed: 21768142
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