Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions
Abstract
We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.
- Authors:
-
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1165779
- DOE Contract Number:
- DE-AC52-07NA27344
- Resource Type:
- Journal Article
- Journal Name:
- Computer Physics Communications
- Additional Journal Information:
- Journal Volume: 183; Journal Issue: 12; Journal ID: ISSN 0010-4655
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; 97 MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE; MOLECULAR DYNAMICS; PARALLEL LOAD BALANCING; COMPUTATIONAL GEOMETRY
Citation Formats
Fattebert, J.-L., Richards, D.F., and Glosli, J.N. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions. United States: N. p., 2012.
Web. doi:10.1016/j.cpc.2012.07.013.
Fattebert, J.-L., Richards, D.F., & Glosli, J.N. Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions. United States. https://doi.org/10.1016/j.cpc.2012.07.013
Fattebert, J.-L., Richards, D.F., and Glosli, J.N. 2012.
"Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions". United States. https://doi.org/10.1016/j.cpc.2012.07.013. https://www.osti.gov/servlets/purl/1165779.
@article{osti_1165779,
title = {Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions},
author = {Fattebert, J.-L. and Richards, D.F. and Glosli, J.N.},
abstractNote = {We present a new algorithm for automatic parallel load balancing in classical molecular dynamics. It assumes a spatial domain decomposition of particles into Voronoi cells. It is a gradient method which attempts to minimize a cost function by displacing Voronoi sites associated with each processor/sub-domain along steepest descent directions. Excellent load balance has been obtained for quasi-2D and 3D practical applications, with up to 440·106 particles on 65,536 MPI tasks.},
doi = {10.1016/j.cpc.2012.07.013},
url = {https://www.osti.gov/biblio/1165779},
journal = {Computer Physics Communications},
issn = {0010-4655},
number = 12,
volume = 183,
place = {United States},
year = {Sat Dec 01 00:00:00 EST 2012},
month = {Sat Dec 01 00:00:00 EST 2012}
}
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