Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics. (December 2016)

• Record Type: Journal Article
• Authors: Zamora, Richard J; Voter, Arthur F; Perez, Danny; Santhi, Nandakishore; Mniszewski, Susan M; Thulasidasan, Sunil; Eidenbenz, Stephan J
• Is Part Of: Simulation. Volume 92:Number 12(2016:Dec.)
• Page Start: 1065
• Page End: 1086
• Publication Date: 2016-12
• Subjects: Discrete-event simulation -- performance prediction -- accelerated molecular dynamics -- temperature-accelerated dynamics -- distributed computing; Computer simulation -- Periodicals; 003.3
• DOI: 10.1177/0037549716674806
• Languages: English
• ISSNs: 0037-5497

Abstract

Due to its unrivaled ability to predict the dynamical evolution of interacting atoms, molecular dynamics (MD) is a widely used computational method in theoretical chemistry, physics, biology, and engineering. Despite its success, MD is only capable of modeling timescales within several orders of magnitude of thermal vibrations, leaving out many important phenomena that occur at slower rates. The temperature-accelerated dynamics (TAD) method overcomes this limitation by thermally accelerating the state-to-state evolution captured by MD. Due to the algorithmically complex nature of the serial TAD procedure, implementations have yet to improve performance by parallelizing the concurrent exploration of multiple states. Here we utilize a discrete-event-based application simulator to introduce and explore a new speculatively parallel TAD (SpecTAD) method. We investigate the SpecTAD algorithm, without a full-scale implementation, by constructing an application simulator proxy (SpecTADSim). Following this method, we discover that a non-trivial relationship exists between the optimal SpecTAD parameter set and the number of CPU cores available at run-time. Furthermore, we find that a majority of the available SpecTAD boost can be achieved within an existing TAD application using relatively simple algorithm modifications.