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Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution

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Book cover Solving Irregularly Structured Problems in Parallel (IRREGULAR 1998)

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

Abstract

To achieve scalable parallel performance in Molecular Dynamics Simulation, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon Valiant's Bulk Synchronous Parallel architecture model (BSP), which describes supersteps of computation, communication, and synchronization. We have developed prototypes that estimate the differing costs of several spatial decomposition algorithms using the BSP model.

Our parallel MD implementation is not bound to the limitations of the BSP model, allowing us to extend the spatial decomposition algorithm. For an initial decomposition, we use one of the successful decomposition strategies from the BSP study, and then subsequently use performance data to adjust the decomposition, dynamically improving the load balance. We report our results here.

This work has been supported in part by the National Institutes of Health's National Center for Research Resources (grant RRO8102 to the UNC/Duke/NYU Computational Structural Biology Resource).

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Authors and Affiliations

  1. Computer Science Department, Univ. of North Carolina, 27599, Chapel Hill, NC

    Lars Nyland, Jan Prins, Hye-Chung Kum & Lei Wang

  2. Biochemistry and Biophysics Department, Univ. of North Carolina, 27599, Chapel Hill, NC

    Ru Huai Yun & Jan Hermans

Authors
  1. Lars Nyland
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  2. Jan Prins
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  3. Ru Huai Yun
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  4. Jan Hermans
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  5. Hye-Chung Kum
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  6. Lei Wang
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Editor information

Alfonso Ferreira José Rolim Horst Simon Shang-Hua Teng

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© 1998 Springer-Verlag Berlin Heidelberg

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Nyland, L., Prins, J., Yun, R.H., Hermans, J., Kum, HC., Wang, L. (1998). Modeling dynamic load balancing in molecular dynamics to achieve scalable parallel execution. 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/BFb0018552

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  • DOI: https://doi.org/10.1007/BFb0018552

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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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