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

Research output: Contribution to journal › Article › peer-review

28 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.

Funders	Funder number
Lawrence Livermore National Laboratory
U.S. Department of Energy
Lawrence Livermore National Laboratory	DE-AC52-07NA27344

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

Abstract

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Keywords

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