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Load balancing in parallel molecular dynamics

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Solving Irregularly Structured Problems in Parallel (IRREGULAR 1998)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1457))

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Abstract

Implementing a parallel molecular dynamics as a parallel application presents some unique load balancing challenges. Non-uniform distribution of atoms in space, along with the need to avoid symmetric redundant computations, produces a highly irregular computational load. Scalability and efficiency considerations produce further irregularity. Also, as the simulation evolves, the movement of atoms causes changes in the load distributions. This paper describes the use of an object-based, measurement-based load balancing strategy for a parallel molecular dynamics application, and its impact on performance.

This work was supported in part by National Institute of Health (NIH PHS 5 P41 RR05969-04 and NIH HL 16059) and National Science Foundation (NSF/GCAG BIR 93-18159 and NSF BIR 94-23827EQ).

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Authors and Affiliations

  1. Dept. of Computer Science, and Theoretical Biophysics Group, Beckman Institute, University of Illinois, 61801, Urbana Illinois

    L. V. Kalé, Milind Bhandarkar & Robert Brunner

Authors
  1. L. V. Kalé
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  2. Milind Bhandarkar
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  3. Robert Brunner
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Alfonso Ferreira José Rolim Horst Simon Shang-Hua Teng

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© 1998 Springer-Verlag Berlin Heidelberg

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Kalé, L.V., Bhandarkar, M., Brunner, R. (1998). Load balancing in parallel molecular dynamics. In: Ferreira, A., Rolim, J., Simon, H., Teng, SH. (eds) Solving Irregularly Structured Problems in Parallel. IRREGULAR 1998. Lecture Notes in Computer Science, vol 1457. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0018544

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  • DOI: https://doi.org/10.1007/BFb0018544

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-64809-3

  • Online ISBN: 978-3-540-68533-3

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