title: Real-time simulation of a spiking neural network model of the basal ganglia circuitry using general purpose computing on graphics processing units.
abstract: Real-time simulation of a biologically realistic spiking neural network is necessary for evaluation of its capacity to interact with real environments. However, the real-time simulation of such a neural network is difficult due to its high computational costs that arise from two factors: (1) vast network size and (2) the complicated dynamics of biologically realistic neurons. In order to address these problems, mainly the latter, we chose to use general purpose computing on graphics processing units (GPGPUs) for simulation of such a neural network, taking advantage of the powerful computational capability of a graphics processing unit (GPU). As a target for real-time simulation, we used a model of the basal ganglia that has been developed according to electrophysiological and anatomical knowledge. The model consists of heterogeneous populations of 370 spiking model neurons, including computationally heavy conductance-based models, connected by 11,002 synapses. Simulation of the model has not yet been performed in real-time using a general computing server. By parallelization of the model on the NVIDIA Geforce GTX 280 GPU in data-parallel and task-parallel fashion, faster-than-real-time simulation was robustly realized with only one-third of the GPU's total computational resources. Furthermore, we used the GPU's full computational resources to perform faster-than-real-time simulation of three instances of the basal ganglia model; these instances consisted of 1100 neurons and 33,006 synapses and were synchronized at each calculation step. Finally, we developed software for simultaneous visualization of faster-than-real-time simulation output. These results suggest the potential power of GPGPU techniques in real-time simulation of realistic neural networks.
authors.affiliation: Computational Science Research Program, RIKEN, Japan. igarashi@brain.riken.jp
authors.forename: Jun
authors.initials: J
authors.lastname: Igarashi
authors.forename: Osamu
authors.initials: O
authors.lastname: Shouno
authors.forename: Tomoki
authors.initials: T
authors.lastname: Fukai
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Tsujino
mesh_terms: D000465:Algorithms; D001479:Basal Ganglia / Q000166:cytology / Q000502:physiology*; D003196:Computer Graphics; D003198:Computer Simulation; D003199:Computer Systems; D003201:Computers; D008838:Microcomputers; D009415:Nerve Net / Q000166:cytology / Q000502:physiology; D009431:Neural Conduction / Q000502:physiology; D016571:Neural Networks, Computer; D013569:Synapses / Q000502:physiology