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2012 ACM/IEEE/SCS 26th Workshop on Principles of Advanced and Distributed Simulation (2008)
June 3, 2008 to June 6, 2008
ISSN: 1087-4097
ISBN: 978-0-7695-3159-5
pp: 51-59
ABSTRACT
The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cell-biological simulations, a field that has emerged as data and knowledge concerning these systems increases and??biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a??model's validity. We describe an optimistic, parallel and distributed variant of??the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system Aurora are shown.
INDEX TERMS
optimistic time management, parallel distributed simulation, Aurora
CITATION
Richard Fujimoto, Adelinde M. Uhrmacher, Alfred Park, Roland Ewald, Matthias Jeschke, "Parallel and Distributed Spatial Simulation of Chemical Reactions", 2012 ACM/IEEE/SCS 26th Workshop on Principles of Advanced and Distributed Simulation, vol. 00, no. , pp. 51-59, 2008, doi:10.1109/PADS.2008.20
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