Title :
Trading Computation Time for Synchronization Time in Spatial Distributed Simulation
Author_Institution :
Dipt. di Ing. e Scienza dell´´Inf., Univ. di Trento, Trento, Italy
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;
Conference_Titel :
Principles of Advanced and Distributed Simulation (PADS), 2011 IEEE Workshop on
Conference_Location :
Nice
Print_ISBN :
978-1-4577-1363-7
Electronic_ISBN :
1087-4097
DOI :
10.1109/PADS.2011.5936766