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Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C

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Abstract

The simulation of particle dynamics is an essential method to analyze and predict the behavior of molecules in a given medium. This work presents the design and implementation of a parallel simulation of Brownian dynamics with hydrodynamic interactions for shared memory systems using two approaches: (1) OpenMP directives and (2) the Partitioned Global Address Space (PGAS) paradigm with the Unified Parallel C (UPC) language. The structure of the code is described, and different techniques for work distribution are analyzed in terms of efficiency, in order to select the most suitable strategy for each part of the simulation. Additionally, performance results have been collected from two representative NUMA systems, and they are studied and compared against the original sequential code.

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Acknowledgements

This work was funded by the Ministry of Science and Innovation of Spain (Project TIN2010-16735), the Spanish network CAPAP-H3 (Project TIN2010-12011-E), and by the Galician Government (Pre-doctoral Program “María Barbeito” and Program for the Consolidation of Competitive Research Groups, ref. 2010/6).

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Authors and Affiliations

  1. Computer Architecture Group, University of A Coruña, 15071, A Coruña, Spain

    Carlos Teijeiro, Guillermo L. Taboada & Juan Touriño

  2. Jülich Supercomputing Centre (JSC), Institute for Advanced Simulation, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany

    Godehard Sutmann

  3. ICAMS, Ruhr-University Bochum, 44801, Bochum, Germany

    Godehard Sutmann

Authors
  1. Carlos Teijeiro
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  2. Godehard Sutmann
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  3. Guillermo L. Taboada
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  4. Juan Touriño
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Correspondence to Carlos Teijeiro.

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Teijeiro, C., Sutmann, G., Taboada, G.L. et al. Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C. J Supercomput 65, 1050–1062 (2013). https://doi.org/10.1007/s11227-012-0843-1

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  • DOI: https://doi.org/10.1007/s11227-012-0843-1

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