skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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:
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 = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 1 work
Citation information provided by
Web of Science

Figures / Tables:

FIG. 1 FIG. 1: (a) Simple pseudocode description of the TAD algorithm, formulated as a recursive function. (b) The algorithm to be executed by each speculation process in SpecTAD. These processes must wait until an initial state (Xiatoms) is provided by the master process.

Save / Share:

Works referenced in this record:

Temperature-accelerated dynamics for simulation of infrequent events
journal, June 2000

  • So/rensen, Mads R.; Voter, Arthur F.
  • The Journal of Chemical Physics, Vol. 112, Issue 21
  • DOI: 10.1063/1.481576

The parallel replica dynamics method – Coming of age
journal, April 2015


The Modern Temperature-Accelerated Dynamics Approach
journal, June 2016


Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
journal, October 2016


The effects of cation–anion clustering on defect migration in MgAl 2 O 4
journal, January 2016

  • Zamora, Richard J.; Voter, Arthur F.; Perez, Danny
  • Physical Chemistry Chemical Physics, Vol. 18, Issue 29
  • DOI: 10.1039/C6CP03931F

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

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

A method for accelerating the molecular dynamics simulation of infrequent events
journal, March 1997

  • Voter, Arthur F.
  • The Journal of Chemical Physics, Vol. 106, Issue 11
  • DOI: 10.1063/1.473503

MOLECULAR DYNAMICS COMES OF AGE: 320 BILLION ATOM SIMULATION ON BlueGene/L
journal, December 2006

  • Kadau, Kai; Germann, Timothy C.; Lomdahl, Peter S.
  • International Journal of Modern Physics C, Vol. 17, Issue 12
  • DOI: 10.1142/S0129183106010182

Frequency factors and isotope effects in solid state rate processes
journal, January 1957


Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995


Parallel replica method for dynamics of infrequent events
journal, June 1998


Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
journal, June 1984


Long-Time Dynamics through Parallel Trajectory Splicing
journal, December 2015

  • Perez, Danny; Cubuk, Ekin D.; Waterland, Amos
  • Journal of Chemical Theory and Computation, Vol. 12, Issue 1
  • DOI: 10.1021/acs.jctc.5b00916

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.