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European Conference on Parallel Processing

Euro-Par 2011: Euro-Par 2011: Parallel Processing Workshops pp 3–12Cite as

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On Parallelizing On-Line Statistics for Stochastic Biological Simulations

On Parallelizing On-Line Statistics for Stochastic Biological Simulations

  • Marco Aldinucci30,
  • Mario Coppo30,
  • Ferruccio Damiani30,
  • Maurizio Drocco30,
  • Eva Sciacca30,
  • Salvatore Spinella30,
  • Massimo Torquati31 &
  • …
  • Angelo Troina30 
  • Conference paper
  • 1118 Accesses

  • 2 Citations

Part of the Lecture Notes in Computer Science book series (LNTCS,volume 7156)

Abstract

This work concerns a general technique to enrich parallel version of stochastic simulators for biological systems with tools for on-line statistical analysis of the results. In particular, within the FastFlow parallel programming framework, we describe the methodology and the implementation of a parallel Monte Carlo simulation infrastructure extended with user-defined on-line data filtering and mining functions. The simulator and the on-line analysis were validated on large multi-core platforms and representative proof-of-concept biological systems.

Keywords

  • multi-core
  • parallel simulation
  • stochastic simulation
  • on-line clustering

This research has been funded by the BioBITs Project (Converging Technologies 2007, Biotechnology-ICT, Regione Piemonte). The authors acknowledge the HPC Advisory Council (www.hpcadvisorycouncil.com) University Award spring 2011.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Torino, Italy

    Marco Aldinucci, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella & Angelo Troina

  2. Department of Computer Science, University of Pisa, Italy

    Massimo Torquati

Authors
  1. Marco Aldinucci
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  2. Mario Coppo
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  3. Ferruccio Damiani
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  4. Maurizio Drocco
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  5. Eva Sciacca
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  6. Salvatore Spinella
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  7. Massimo Torquati
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  8. Angelo Troina
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Editor information

Editors and Affiliations

  1. Scilytics, Koellnerhofgasse 3/15A, 1010, Vienna, Austria

    Michael Alexander

  2. ICAR-CNR, Via P. Castellino, 111, 80131, Napoli, Italy

    Pasqua D’Ambra

  3. University of Amsterdam, 1090, Amsterdam, Netherlands

    Adam Belloum

  4. Innovative Computing Laboratory, The University of Tennessee, US

    George Bosilca

  5. Department of Experimental Medicine and Clinic, University Magna Græcia, 88100, Catanzaro, Italy

    Mario Cannataro

  6. Computer Science Department, University of Pisa, Italy

    Marco Danelutto

  7. Second University of Naples, Italy

    Beniamino Di Martino

  8. TUMünchen,, Boltzmannstr. 3, ,, 85748, Garching, Germany

    Michael Gerndt

  9. Equipe Runtime, INRIA Bordeaux Sud-Ouest, 33405, Talence Cedex, France

    Emmanuel Jeannot & Raymond Namyst & 

  10. Equipe HIEPACS, INRIA Bordeaux Sud-Ouest, 33405, Talence Cedex, France

    Jean Roman

  11. Computer Science and Mathematics Division, Oak Ridge National Laboratory, 37831-6164, Oak Ridge, TN, USA

    Stephen L. Scott

  12. Department of Scientific Computing, University of Vienna, Nordbergstr. 15/3C, 1090, Vienna, Austria

    Jesper Larsson Traff

  13. Computer Science and Mathematics Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA

    Geoffroy Vallée

  14. Technische Universität München, Germany

    Josef Weidendorfer

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© 2012 Springer-Verlag Berlin Heidelberg

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Cite this paper

Aldinucci, M. et al. (2012). On Parallelizing On-Line Statistics for Stochastic Biological Simulations. In: Alexander, M., et al. Euro-Par 2011: Parallel Processing Workshops. Euro-Par 2011. Lecture Notes in Computer Science, vol 7156. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-29740-3_2

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  • DOI: https://doi.org/10.1007/978-3-642-29740-3_2

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  • Print ISBN: 978-3-642-29739-7

  • Online ISBN: 978-3-642-29740-3

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