Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

Zamora, Richard James; Voter, Arthur F.; Perez, Danny; Santhi, Nandakishore; Mniszewski, Susan M.; Thulasidasan, Sunil; Eidenbenz, Stephan J.

doi:10.1177/0037549716674806

Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics

Journal Article · Thu Dec 01 00:00:00 EST 2016 · Simulation

DOI:https://doi.org/10.1177/0037549716674806· OSTI ID:1335595

Zamora, Richard James ^[1]; Voter, Arthur F. ^[1]; Perez, Danny ^[1]; Santhi, Nandakishore ^[2]; Mniszewski, Susan M. ^[2]; Thulasidasan, Sunil ^[2]; Eidenbenz, Stephan J. ^[2]

Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Computer, Computational & Statistical Sciences Division

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 time scales 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). Finally, following this method, we discover that a nontrivial 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.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1335595

Report Number(s):: LA-UR-15-23844

Journal Information:: Simulation, Journal Name: Simulation Journal Issue: 12 Vol. 92; ISSN 0037-5497

Publisher:: SAGECopyright Statement

Country of Publication:: United States

Language:: English

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