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.

Keywords

Computational geometry
Molecular dynamics
Parallel load balancing

Access to Document

10.1016/j.cpc.2012.07.013

Cite this

@article{92cba1fb33da4b80b1f3ee75f1c4e90e,

title = "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.",

keywords = "Computational geometry, Molecular dynamics, Parallel load balancing",

author = "Fattebert, {J. L.} and Richards, {D. F.} and Glosli, {J. N.}",

year = "2012",

month = dec,

doi = "10.1016/j.cpc.2012.07.013",

language = "English",

volume = "183",

pages = "2608--2615",

journal = "Computer Physics Communications",

issn = "0010-4655",

publisher = "Elsevier",

number = "12",

}

TY - JOUR

T1 - Dynamic load balancing algorithm for molecular dynamics based on Voronoi cells domain decompositions

AU - Fattebert, J. L.

AU - Richards, D. F.

AU - Glosli, J. N.

PY - 2012/12

Y1 - 2012/12

N2 - 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.

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.

KW - Computational geometry

KW - Molecular dynamics

KW - Parallel load balancing

UR - http://www.scopus.com/inward/record.url?scp=84865650947&partnerID=8YFLogxK

U2 - 10.1016/j.cpc.2012.07.013

DO - 10.1016/j.cpc.2012.07.013

M3 - Article

AN - SCOPUS:84865650947

SN - 0010-4655

VL - 183

SP - 2608

EP - 2615

JO - Computer Physics Communications

JF - Computer Physics Communications

IS - 12

ER -

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

Abstract

Funding

Keywords

Access to Document

Other files and links

Fingerprint

Cite this