Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics
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 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.
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1335595
- Report Number(s):
- LA-UR-15-23844
Journal ID: ISSN 0037-5497
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Simulation
- Additional Journal Information:
- Journal Volume: 92; Journal Issue: 12; Journal ID: ISSN 0037-5497
- Publisher:
- SAGE
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 97 MATHEMATICS AND COMPUTING; Computer Science; Material Science
Citation Formats
Zamora, Richard James, Voter, Arthur F., Perez, Danny, Santhi, Nandakishore, Mniszewski, Susan M., Thulasidasan, Sunil, and Eidenbenz, Stephan J. Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics. United States: N. p., 2016.
Web. doi:10.1177/0037549716674806.
Zamora, Richard James, Voter, Arthur F., Perez, Danny, Santhi, Nandakishore, Mniszewski, Susan M., Thulasidasan, Sunil, & Eidenbenz, Stephan J. Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics. United States. https://doi.org/10.1177/0037549716674806
Zamora, Richard James, Voter, Arthur F., Perez, Danny, Santhi, Nandakishore, Mniszewski, Susan M., Thulasidasan, Sunil, and Eidenbenz, Stephan J. Thu .
"Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics". United States. https://doi.org/10.1177/0037549716674806. https://www.osti.gov/servlets/purl/1335595.
@article{osti_1335595,
title = {Discrete event performance prediction of speculatively parallel temperature-accelerated dynamics},
author = {Zamora, Richard James and Voter, Arthur F. and Perez, Danny and Santhi, Nandakishore and Mniszewski, Susan M. and Thulasidasan, Sunil and Eidenbenz, Stephan J.},
abstractNote = {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.},
doi = {10.1177/0037549716674806},
journal = {Simulation},
number = 12,
volume = 92,
place = {United States},
year = {Thu Dec 01 00:00:00 EST 2016},
month = {Thu Dec 01 00:00:00 EST 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 10 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
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
Extending the Time Scale in Atomistic Simulation of Materials
journal, August 2002
- Voter, Arthur F.; Montalenti, Francesco; Germann, Timothy C.
- Annual Review of Materials Research, Vol. 32, Issue 1
Exploiting past visits or minimum-barrier knowledge to gain further boost in the temperature-accelerated dynamics method
journal, January 2002
- Montalenti, F.; Voter, A. F.
- The Journal of Chemical Physics, Vol. 116, Issue 12
Exploring the performance of spatial stochastic simulation algorithms
journal, April 2011
- Jeschke, Matthias; Ewald, Roland; Uhrmacher, Adelinde M.
- Journal of Computational Physics, Vol. 230, Issue 7
TADSim: Discrete Event-Based Performance Prediction for Temperature-Accelerated Dynamics
journal, May 2015
- Mniszewski, Susan M.; Junghans, Christoph; Voter, Arthur F.
- ACM Transactions on Modeling and Computer Simulation, Vol. 25, Issue 3
The parallel replica dynamics method – Coming of age
journal, April 2015
- Perez, Danny; Uberuaga, Blas P.; Voter, Arthur F.
- Computational Materials Science, Vol. 100
The Modern Temperature-Accelerated Dynamics Approach
journal, June 2016
- Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny
- Annual Review of Chemical and Biomolecular Engineering, Vol. 7, Issue 1
Speed Dependence of Atomic Stick-Slip Friction in Optimally Matched Experiments and Molecular Dynamics Simulations
journal, March 2011
- Li, Qunyang; Dong, Yalin; Perez, Danny
- Physical Review Letters, Vol. 106, Issue 12
Efficient Annealing of Radiation Damage Near Grain Boundaries via Interstitial Emission
journal, March 2010
- Bai, X. M.; Voter, A. F.; Hoagland, R. G.
- Science, Vol. 327, Issue 5973
A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
journal, October 1999
- Henkelman, Graeme; Jónsson, Hannes
- The Journal of Chemical Physics, Vol. 111, Issue 15
Adaptive temperature-accelerated dynamics
journal, February 2011
- Shim, Yunsic; Amar, Jacques G.
- The Journal of Chemical Physics, Vol. 134, Issue 5
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
Extended temperature-accelerated dynamics: Enabling long-time full-scale modeling of large rare-event systems
journal, September 2014
- Bochenkov, Vladimir; Suetin, Nikolay; Shankar, Sadasivan
- The Journal of Chemical Physics, Vol. 141, Issue 9
A Review of Computational Methods in Materials Science: Examples from Shock-Wave and Polymer Physics
journal, December 2009
- Steinhauser, Martin; Hiermaier, Stefan
- International Journal of Molecular Sciences, Vol. 10, Issue 12
Spontaneous atomic shuffle in flat terraces: Ag(100)
journal, November 2002
- Montalenti, F.; Voter, A. F.; Ferrando, R.
- Physical Review B, Vol. 66, Issue 20
Frequency factors and isotope effects in solid state rate processes
journal, January 1957
- Vineyard, George H.
- Journal of Physics and Chemistry of Solids, Vol. 3, Issue 1-2
Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals
journal, June 1984
- Daw, Murray S.; Baskes, M. I.
- Physical Review B, Vol. 29, Issue 12
A bridging model for parallel computation
journal, August 1990
- Valiant, Leslie G.
- Communications of the ACM, Vol. 33, Issue 8
Reaching extended length scales and time scales in atomistic simulations via spatially parallel temperature-accelerated dynamics
journal, November 2007
- Shim, Yunsic; Amar, Jacques G.; Uberuaga, B. P.
- Physical Review B, Vol. 76, Issue 20
Works referencing / citing this record:
Algorithmic developments of the kinetic activation-relaxation technique: Accessing long-time kinetics of larger and more complex systems
journal, October 2017
- Trochet, Mickaël; Sauvé-Lacoursière, Alecsandre; Mousseau, Normand
- The Journal of Chemical Physics, Vol. 147, Issue 15
Speculation and replication in temperature accelerated dynamics
journal, February 2018
- Zamora, Richard J.; Perez, Danny; Voter, Arthur F.
- Journal of Materials Research, Vol. 33, Issue 7