Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

J. L. Fattebert; D. F. Richards; J. N. Glosli

doi:10.1016/j.cpc.2012.07.013

Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

J. L. Fattebert, D. F. Richards, J. N. Glosli

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29 Scopus citations

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.

Original language	English
Pages (from-to)	2608-2615
Number of pages	8
Journal	Computer Physics Communications
Volume	183
Issue number	12
DOIs	https://doi.org/10.1016/j.cpc.2012.07.013
State	Published - Dec 2012
Externally published	Yes

Funding

This work was performed under the auspices of the US Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. We also acknowledge the support of the Lawrence Livermore National Laboratory Directed Research and Development Program.

Keywords

Computational geometry
Molecular dynamics
Parallel load balancing

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10.1016/j.cpc.2012.07.013

Cite this

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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.",

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AB - 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.

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KW - Molecular dynamics

KW - Parallel load balancing

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Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

Abstract

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Keywords

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