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Implementation of a Non-bonded Interaction Calculation Algorithm for the Cell Architecture

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Parallel Computing Technologies (PaCT 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5698))

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Abstract

Calculation of non-bonded interactions takes up to 80% of the total execution time of a molecular dynamics program. It can be accelerated by porting the algorithm to the Cell architecture. A simple method of such porting has been applied to the MOLKERN program, which simulates the structure and dynamics of biomolecular models. A 32-fold speedup was achieved for calculation of short-range non-bonded interactions, and threefold, for long-range Coulomb interactions. The overall program speedup proved to be more than 4.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, Siberian Branch of the Rusian Academy of Science, 10 Lavrentiev Ave., 630090, Novosibirsk, Russia

    Eduard Fomin & Nikolay Alemasov

Authors
  1. Eduard Fomin
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  2. Nikolay Alemasov
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Editor information

Editors and Affiliations

  1. Institute of Computational Mathematics and Mathematical Geophysics, Supercomputer Department, Pr. Lavrentieva, ICM&MG RAS, Russian Academy of Sciences, 630090, Novosibirsk, Russia

    Victor Malyshkin

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© 2009 Springer-Verlag Berlin Heidelberg

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Fomin, E., Alemasov, N. (2009). Implementation of a Non-bonded Interaction Calculation Algorithm for the Cell Architecture. In: Malyshkin, V. (eds) Parallel Computing Technologies. PaCT 2009. Lecture Notes in Computer Science, vol 5698. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03275-2_39

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  • DOI: https://doi.org/10.1007/978-3-642-03275-2_39

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-03274-5

  • Online ISBN: 978-3-642-03275-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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