UC Santa Barbara
EFFICIENT PARALLELIZATION OF STOCHASTIC SIMULATION ALGORITHM FOR CHEMICALLY REACTING SYSTEMS ON THE GRAPHICS PROCESSING UNIT
- Author(s): Li, Hong
- Petzold, Linda
- et al.
Published Web Locationhttp://hpc.sagepub.com/cgi/rapidpdf/1094342009106066v1
The small number of some reactant molecules in biological systems formed by living cells can result in dynamical behavior which cannot be captured by traditional deterministic models. In such a problem, a more accurate simulation can be obtained with discrete stochastic simulation (Gillespie's stochastic simulation algorithm – SSA). Many stochastic realizations are required to capture accurate statistical information of the solution. This carries a very high computational cost. The current generation of graphics processing units (GPU) is well-suited to this task. In this paper we describe our implementation and present some computational experiments illustrating the power of this technology for this important and challenging class of problems.