• DocumentCode
    1973889
  • Title

    Trading Computation Time for Synchronization Time in Spatial Distributed Simulation

  • Author

    Zunino, Roberto

  • Author_Institution
    Dipt. di Ing. e Scienza dell´´Inf., Univ. di Trento, Trento, Italy
  • fYear
    2011
  • fDate
    14-17 June 2011
  • Firstpage
    1
  • Lastpage
    8
  • Abstract
    We consider a class of models describing generic agents (e.g. macromolecules, small organisms) which are able to travel in space, can sense the surrounding environment, and can react accordingly. In these models, we focus on individual-based simulation. We start with defining a simple centralized simulation algorithm, which we then improve so to develop a distributed algorithm producing the same output. An analytical model is given to estimate the expected speedup of our distributed algorithm depending on several parameters. A main aspect of our approach is that it trades computation time for synchronization time. That is, we allow each node to perform apparently redundant computation whenever this reduces the amount of needed synchronization in such a way that the overall performance improves.
  • Keywords
    biology computing; digital simulation; distributed algorithms; macromolecules; reaction-diffusion systems; centralized simulation algorithm; computation time; distributed algorithm; generic agents; macromolecules; molecular crowding; reaction-diffusion individual-based simulation; redundant computation; small organisms; spatial distributed simulation; synchronization time; Adaptation model; Biological system modeling; Computational modeling; Distributed algorithms; Silicon; Solid modeling; Synchronization;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Principles of Advanced and Distributed Simulation (PADS), 2011 IEEE Workshop on
  • Conference_Location
    Nice
  • ISSN
    1087-4097
  • Print_ISBN
    978-1-4577-1363-7
  • Electronic_ISBN
    1087-4097
  • Type

    conf

  • DOI
    10.1109/PADS.2011.5936766
  • Filename
    5936766