Abstract Next Subvolume Method: A logical process-based approach for spatial stochastic simulation of chemical reactions

作者：Wang, Bing^*; Hou, Bonan; Xing, Fei; Yao, Yiping

来源：Computational Biology and Chemistry, 2011, 35(3): 193-198.

DOI：10.1016/j.compbiolchem.2011.05.001

• Stochastic simulation algorithm
• Next subvolume Method
• Spatial stochastic simulation
• Parallel discrete-event simulation

The spatial stochastic simulation of biochemical systems requires significant calculation efforts. Parallel discrete-event simulation is a promising approach to accelerate the execution of simulation runs. However, achievable speedup depends on the parallelism inherent in the model. One of our goals is to explore this degree of parallelism in the Next Subvolume Method type simulations. Therefore we introduce the Abstract Next Subvolume Method, in which we decouple the model representation from the sequential simulation algorithms, and prove that state trajectories generated by its executions statistically accord with those generated by the Next Subvolume Method. The experimental performance analysis shows that optimistic synchronization algorithms, together with careful controls over the speculative execution, are necessary to achieve considerable speedup and scalability in parallel spatial stochastic simulation of chemical reactions. Our proposed method facilitates a flexible incorporation of different synchronization algorithms, and can be used to select the proper synchronization algorithm to achieve the efficient parallel simulation of chemical reactions.

• 出版日期2011-6
• 单位中国人民解放军国防科学技术大学