Please use this identifier to cite or link to this item: https://zone.biblio.laurentian.ca/handle/10219/2700
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dc.contributor.authorMeyer, Ralf-
dc.date.accessioned2017-02-10T18:57:34Z-
dc.date.available2017-02-10T18:57:34Z-
dc.date.issued2013-11-
dc.identifier.citationR. Meyer, Efficient parallelization of short-range molecular dynamics simulations on many-core systems, Phys. Rev. E 88, 053309 (2013).en_CA
dc.identifier.issn1539-3755-
dc.identifier.urihttps://doi.org/10.1103/PhysRevE.88.053309-
dc.identifier.urihttps://zone.biblio.laurentian.ca/handle/10219/2700-
dc.description© 2013 American Physical Societyen_CA
dc.description.abstractThis article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly inhomogeneous systems like nanodevices or nanostructured materials. In the proposed scheme the calculation of the forces and the generation of neighbor lists are divided into small tasks. The tasks are then executed by a thread pool according to a dependent task schedule. This schedule is constructed in such a way that a particle is never accessed by two threads at the same time. Benchmark simulations on a typical 12-core machine show that the described algorithm achieves excellent parallel efficiencies above 80% for different kinds of systems and all numbers of cores. For inhomogeneous systems the speedups are strongly superior to those obtained with spatial decomposition. Further benchmarks were performed on an Intel Xeon Phi coprocessor. These simulations demonstrate that the algorithm scales well to large numbers of cores.en_CA
dc.description.sponsorshipNatural Sciences and Engineering Research Council of Canada (NSERC) [grant number 371446-11] , Laurentian Universityen_CA
dc.language.isoenen_CA
dc.publisherAmerican Physical Societyen_CA
dc.subjectmolecular dynamics simulationsen_CA
dc.subjectparallel computingen_CA
dc.titleEfficient parallelization of short-range molecular dynamics simulations on many-core systemsen_CA
dc.typeArticleen_CA
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