Fig. 9: The MPI implementation and Blender extension module.
From: Vesicle and reaction-diffusion hybrid modeling with STEPS
a Schematic of the MPI splitting solution, in which n-1 RDEF ranks carry out reaction-diffusion and voltage calculations on partitioned mesh space, and on a slower clock the VesRaft rank (rank 0) calculates vesicle and raft diffusion and some other vesicle-related processes over all space, communicating new positions to the RDEF ranks (Note: for clear illustration purposes and to show how vesicles can change partition during simulation, a relatively large diffusion step of approximately one diameter is shown, although vesicles will often diffuse shorter distances in real simulations). b Detailed description of the parallel algorithm timeline. c Example parallel performance of a realistic synaptic bouton model of Gallimore et al.35. d Screenshot of the Blender extension model applied to the same synaptic bouton model.
