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Title: Speculation and replication in temperature accelerated dynamics

Abstract

Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similar to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.

Authors:
ORCiD logo [1];  [1];  [1]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Publication Date:
Research Org.:
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1441309
Report Number(s):
LA-UR-17-28909
Journal ID: ISSN 0884-2914
Grant/Contract Number:  
AC52-06NA25396
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Journal of Materials Research
Additional Journal Information:
Journal Volume: 33; Journal Issue: 7; Journal ID: ISSN 0884-2914
Publisher:
Materials Research Society
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 36 MATERIALS SCIENCE; Computer Science; Material Science

Citation Formats

Zamora, Richard J., Perez, Danny, and Voter, Arthur F. Speculation and replication in temperature accelerated dynamics. United States: N. p., 2018. Web. doi:10.1557/jmr.2018.17.
Zamora, Richard J., Perez, Danny, & Voter, Arthur F. Speculation and replication in temperature accelerated dynamics. United States. doi:10.1557/jmr.2018.17.
Zamora, Richard J., Perez, Danny, and Voter, Arthur F. Mon . "Speculation and replication in temperature accelerated dynamics". United States. doi:10.1557/jmr.2018.17. https://www.osti.gov/servlets/purl/1441309.
@article{osti_1441309,
title = {Speculation and replication in temperature accelerated dynamics},
author = {Zamora, Richard J. and Perez, Danny and Voter, Arthur F.},
abstractNote = {Accelerated Molecular Dynamics (AMD) is a class of MD-based algorithms for the long-time scale simulation of atomistic systems that are characterized by rare-event transitions. Temperature-Accelerated Dynamics (TAD), a traditional AMD approach, hastens state-to-state transitions by performing MD at an elevated temperature. Recently, Speculatively-Parallel TAD (SpecTAD) was introduced, allowing the TAD procedure to exploit parallel computing systems by concurrently executing in a dynamically generated list of speculative future states. Although speculation can be very powerful, it is not always the most efficient use of parallel resources. In this paper, we compare the performance of speculative parallelism with a replica-based technique, similar to the Parallel Replica Dynamics method. A hybrid SpecTAD approach is also presented, in which each speculation process is further accelerated by a local set of replicas. Finally and overall, this work motivates the use of hybrid parallelism whenever possible, as some combination of speculation and replication is typically most efficient.},
doi = {10.1557/jmr.2018.17},
journal = {Journal of Materials Research},
number = 7,
volume = 33,
place = {United States},
year = {Mon Feb 12 00:00:00 EST 2018},
month = {Mon Feb 12 00:00:00 EST 2018}
}

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Works referenced in this record:

A climbing image nudged elastic band method for finding saddle points and minimum energy paths
journal, December 2000

  • Henkelman, Graeme; Uberuaga, Blas P.; J�nsson, Hannes
  • The Journal of Chemical Physics, Vol. 113, Issue 22, p. 9901-9904
  • DOI: 10.1063/1.1329672