Journal Article

Spiking network simulation code for petascale computers

Plesser, Hans E., Fukai, Tomoki, Igarashi, Jun, Morrison, Abigail, Eppler, Jochen M., Ishii, Shin, Masumoto, Gen, Helias, Moritz, Kunkel, Susanne, Schmidt, Maximilian, Diesmann, Markus

2014

Overview

Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and synapses and over the past decade researchers have learned to manage the heterogeneity of neurons and synapses with efficient data structures. Already early parallel simulation codes stored synapses in a distributed fashion such that a synapse solely consumes memory on the compute node harboring the target neuron. As petaflop computers with some 100,000 nodes become increasingly available for neuroscience, new challenges arise for neuronal network simulation software: Each neuron contacts on the order of 10,000 other neurons and thus has targets only on a fraction of all compute nodes; furthermore, for any given source neuron, at most a single synapse is typically created on any compute node. From the viewpoint of an individual compute node, the heterogeneity in the synaptic target lists thus collapses along two dimensions: the dimension of the types of synapses and the dimension of the number of synapses of a given type. Here we present a data structure taking advantage of this double collapse using metaprogramming techniques. After introducing the relevant scaling scenario for brain-scale simulations, we quantitatively discuss the performance on two supercomputers. We show that the novel architecture scales to the largest petascale supercomputers available today.

• Publisher: Frontiers Research Foundation,Frontiers Media S.A
• Subject: Brain research / computational neuroscience / Computers / Distributed processing / Laboratories / large-scale simulation / Memory / memory footprint / memory management / Nervous system / Neurons / Neuroscience / Neurosciences / Parallel Computing / Science / supercomputer / Supercomputers