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Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers
State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incom...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820465/ https://www.ncbi.nlm.nih.gov/pubmed/29503613 http://dx.doi.org/10.3389/fninf.2018.00002 |
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author | Jordan, Jakob Ippen, Tammo Helias, Moritz Kitayama, Itaru Sato, Mitsuhisa Igarashi, Jun Diesmann, Markus Kunkel, Susanne |
author_facet | Jordan, Jakob Ippen, Tammo Helias, Moritz Kitayama, Itaru Sato, Mitsuhisa Igarashi, Jun Diesmann, Markus Kunkel, Susanne |
author_sort | Jordan, Jakob |
collection | PubMed |
description | State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems. |
format | Online Article Text |
id | pubmed-5820465 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-58204652018-03-02 Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers Jordan, Jakob Ippen, Tammo Helias, Moritz Kitayama, Itaru Sato, Mitsuhisa Igarashi, Jun Diesmann, Markus Kunkel, Susanne Front Neuroinform Neuroscience State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems. Frontiers Media S.A. 2018-02-16 /pmc/articles/PMC5820465/ /pubmed/29503613 http://dx.doi.org/10.3389/fninf.2018.00002 Text en Copyright © 2018 Jordan, Ippen, Helias, Kitayama, Sato, Igarashi, Diesmann and Kunkel. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Neuroscience Jordan, Jakob Ippen, Tammo Helias, Moritz Kitayama, Itaru Sato, Mitsuhisa Igarashi, Jun Diesmann, Markus Kunkel, Susanne Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title | Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title_full | Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title_fullStr | Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title_full_unstemmed | Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title_short | Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers |
title_sort | extremely scalable spiking neuronal network simulation code: from laptops to exascale computers |
topic | Neuroscience |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5820465/ https://www.ncbi.nlm.nih.gov/pubmed/29503613 http://dx.doi.org/10.3389/fninf.2018.00002 |
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