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Front Neuroinform. 2012 Nov 2;6:26. doi: 10.3389/fninf.2012.00026. eCollection 2012.

Supercomputers ready for use as discovery machines for neuroscience.

Author information

1
Institute of Neuroscience and Medicine (INM-6), Computational and Systems Neuroscience, Jülich Research Centre Jülich, Germany ; RIKEN Brain Science Institute Wako, Japan.

Abstract

NEST is a widely used tool to simulate biological spiking neural networks. Here we explain the improvements, guided by a mathematical model of memory consumption, that enable us to exploit for the first time the computational power of the K supercomputer for neuroscience. Multi-threaded components for wiring and simulation combine 8 cores per MPI process to achieve excellent scaling. K is capable of simulating networks corresponding to a brain area with 10(8) neurons and 10(12) synapses in the worst case scenario of random connectivity; for larger networks of the brain its hierarchical organization can be exploited to constrain the number of communicating computer nodes. We discuss the limits of the software technology, comparing maximum filling scaling plots for K and the JUGENE BG/P system. The usability of these machines for network simulations has become comparable to running simulations on a single PC. Turn-around times in the range of minutes even for the largest systems enable a quasi interactive working style and render simulations on this scale a practical tool for computational neuroscience.

KEYWORDS:

computational neuroscience; large-scale simulation; parallel computing; spiking neural networks; supercomputer

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