cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems
Figure 3
Pseudocode of cuTauLeaping – host side.
Host-side pseudocode of cuTauLeaping. As a first step, the stoichiometric information of the reactions is exploited to pre-calculate the data structures needed by the algorithm; all matrices are flattened during this process. Then, once the support memory areas are allocated (e.g., the chunk of global memory where the system dynamics will be stored), the four phases of cuTauLeaping begin and are repeated until all simulations are completed.