Fig. 4
From: LASSIE: simulating large-scale models of biochemical systems on GPUs
Simplified scheme of LASSIE workflow. The data structures used to encode the system of ODEs are generated in phase P 1. In phase P 2, if the current simulation time t corresponds to a specified sampling time instant, then the current concentration values of all molecular species are saved; otherwise, the execution proceeds to the next phase. In phase P 3 each thread derives and solves the corresponding ODE by exploiting the RKF method, while in phase P 4 the RKF solutions are verified: (i) if the RKF solutions are rejected, then the integration step-size dt is reduced and phase P 3 is executed again; (ii) if RKF solutions are rejected but the integration step-size dt is too small, then phase P 5 is executed and the system of ODEs is solved using the BDF methods; (iii) if the RKF solutions are accepted, the termination criterion is verified during phase P 6 (all phases from P 2 on are iterated until the maximum simulation time t max is reached)