Journal Article

FZJ-2020-01876

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Efficient Communication in Distributed Simulations of Spiking Neuronal Networks With Gap Junctions

Jordan, J. (Corresponding author)FZJ* ; Helias, M.FZJ* ; Diesmann, M.FZJ* ; Kunkel, S.

2020
Frontiers Research Foundation Lausanne

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Please use a persistent id in citations: http://hdl.handle.net/2128/24781  doi:10.3389/fninf.2020.00012

Abstract: Investigating the dynamics and function of large-scale spiking neuronal networks with realistic numbers of synapses is made possible today by state-of-the-art simulation code that scales to the largest contemporary supercomputers. However, simulations that involve electrical interactions, also called gap junctions, besides chemical synapses scale only poorly due to a communication scheme that collects global data on each compute node. In comparison to chemical synapses, gap junctions are far less abundant. To improve scalability we exploit this sparsity by integrating an existing framework for continuous interactions with a recently proposed directed communication scheme for spikes. Using a reference implementation in the NEST simulator we demonstrate excellent scalability of the integrated framework, accelerating large-scale simulations with gap junctions by more than an order of magnitude. This allows, for the first time, the efficient exploration of the interactions of chemical and electrical coupling in large-scale neuronal networks models with natural synapse density distributed across thousands of compute nodes.

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Contributing Institute(s):

1. Computational and Systems Neuroscience (INM-6)
2. Theoretical Neuroscience (IAS-6)
3. Jara-Institut Brain structure-function relationships (INM-10)

Research Program(s):

1. 574 - Theory, modelling and simulation (POF3-574) (POF3-574)
2. MSNN - Theory of multi-scale neuronal networks (HGF-SMHB-2014-2018) (HGF-SMHB-2014-2018)
3. HBP - The Human Brain Project (604102) (604102)
4. HBP SGA1 - Human Brain Project Specific Grant Agreement 1 (720270) (720270)
5. HBP SGA2 - Human Brain Project Specific Grant Agreement 2 (785907) (785907)
6. DEEP-EST - DEEP - Extreme Scale Technologies (754304) (754304)
7. Advanced Computing Architectures (aca_20190115) (aca_20190115)
8. Brain-Scale Simulations (jinb33_20121101) (jinb33_20121101)

Appears in the scientific report 2020

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Database coverage:
; ; ; ; BIOSIS Previews ; Clarivate Analytics Master Journal List ; DOAJ Seal ; IF < 5 ; JCR ; PubMed Central ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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