On computation and synchronization costs in spatial distributed simulation

We consider the problem of simulating spatially distributed entities which can move, see each other, and react accordingly. We provide centralized reference algorithms for both time-stepped and discrete-event simulation. Under reasonable assumptions, we then proceed to distribute the simulation among several nodes by assigning each node a subregion of the simulation space. A main characteristic of our approach is that the subregions do not form a partitioning, but a covering. That is, they partially overlap, hence causing some duplicated computation, which is apparently redundant. The amount of overlapping is a tunable parameter of our algorithms, which affects the overall performance in a non-trivial way. Through an analytical model as well as experimental results we discover a trade-off. Choosing a small overlapping requires to perform frequent synchronizations, which negatively affect performance. However, a large overlapping leads to more duplicated work, which also decreases performance. Balancing the amount of overlapping is then required to optimize performance.

[1]  Sergei Gorlatch,et al.  Conclusions and Related Work , 2009 .

[2]  J. Banks,et al.  Discrete-Event System Simulation , 1995 .

[3]  Adelinde M. Uhrmacher,et al.  Parallel and Distributed Spatial Simulation of Chemical Reactions , 2008, 2008 22nd Workshop on Principles of Advanced and Distributed Simulation.

[4]  Pieter Retief Kasselman,et al.  Analysis and design of cryptographic hash functions , 1999 .

[5]  Chih Jeng Kenneth Tan,et al.  On Parallel Pseudo-Random Number Generation , 2001, International Conference on Computational Science.

[6]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[7]  Jack Dongarra,et al.  Computational Science — ICCS 2001 , 2001, Lecture Notes in Computer Science.

[8]  Corrado Priami,et al.  Beta-binders for Biological Quantitative Experiments , 2006, QAPL.

[9]  Jaap A. Kaandorp,et al.  Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli , 2006, Bioinform..

[10]  Bart Preneel,et al.  Cryptographic hash functions , 2010, Eur. Trans. Telecommun..

[11]  Corrado Priami,et al.  A Bounded-Optimistic, Parallel Beta-Binders Simulator , 2008, 2008 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications.

[12]  Wentong Cai,et al.  Collaborative Interest Management for Peer-to-Peer Networked Virtual Environment , 2011, 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation.

[13]  Mathias John,et al.  A Spatial Extension to the pi Calculus , 2008, Electron. Notes Theor. Comput. Sci..

[14]  David R. Jefferson,et al.  Virtual time , 1985, ICPP.

[15]  Adelinde M. Uhrmacher,et al.  Spatial modeling in cell biology at multiple levels , 2010, Proceedings of the 2010 Winter Simulation Conference.

[16]  Michael Hunter,et al.  On the Accuracy of Ad Hoc Distributed Simulations for Open Queueing Network , 2011, 2011 IEEE Workshop on Principles of Advanced and Distributed Simulation.

[17]  Masaru Tomita,et al.  Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico , 2005, FEBS letters.

[18]  Alan Bundy,et al.  Constructing Induction Rules for Deductive Synthesis Proofs , 2006, CLASE.

[19]  Ezio Bartocci,et al.  Shape Calculus. A Spatial Mobile Calculus for 3D Shapes , 2010, Sci. Ann. Comput. Sci..

[20]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[21]  Krzysztof Pawlikowski,et al.  Distributed stochastic discrete-event simulation in parallel time streams , 1994, WSC '94.

[22]  Michael Mascagni,et al.  Testing parallel random number generators , 2003, Parallel Comput..

[23]  J. Elf,et al.  Spontaneous separation of bi-stable biochemical systems into spatial domains of opposite phases. , 2004, Systems biology.