Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON

Abstract

Large multiscale neuronal network simulations are of increasing value as more big data are gathered about brain wiring and organization under the auspices of a current major research initiative, such as Brain Research through Advancing Innovative Neurotechnologies. The development of these models requires new simulation technologies. We describe here the current use of the NEURON simulator with message passing interface (MPI) for simulation in the domain of moderately large networks on commonly available high-performance computers (HPCs). We discuss the basic layout of such simulations, including the methods of simulation setup, the run-time spike-passing paradigm, and postsimulation data storage and data management approaches. Using the Neuroscience Gateway, a portal for computational neuroscience that provides access to large HPCs, we benchmark simulations of neuronal networks of different sizes (500-100,000 cells), and using different numbers of nodes (1-256). We compare three types of networks, composed of either Izhikevich integrate-and-fire neurons (I&F), single-compartment Hodgkin-Huxley (HH) cells, or a hybrid network with half of each. Results show simulation run time increased approximately linearly with network size and decreased almost linearly with the number of nodes. Networks with I&F neurons were faster than HH networks, although differences were small since all tested cells were point neurons with a single compartment.

Figure 1

Main steps required to build and simulate a parallel network model, and NEURON ParallelContext functions employed at each stage.

Figure 2

Raster plot for a 500 cell network. The same sequence of spikes was produced with HH, I&F or hybrid networks.

Figure 3

Simulation run time as a function of number of cells and number of nodes in log-log plots. A. HH network, B. I&F network, C. Hybid network. (black: linear reference)

Figure 4

Comparison of saving time and disk space to store the output of the 50,000 cell network simulation for 6 common file formats. 473,879 spikes were saved with saving of spike times and gids (cell global identifiers) for each.