Universität zu Köln

Tiddia, Gianmarco ORCID: 0000-0001-7524-0285, Golosio, Bruno, Albers, Jasper, Senk, Johanna, Simula, Francesco, Pronold, Jari, Fanti, Viviana, Pastorelli, Elena, Paolucci, Pier Stanislao ORCID: 0000-0003-1937-6086 and van Albada, Sacha J. (2022). Fast Simulation of a Multi-Area Spiking Network Model of Macaque Cortex on an MPI-GPU Cluster. Front. Neuroinformatics, 16. LAUSANNE: FRONTIERS MEDIA SA. ISSN 1662-5196

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Abstract

Spiking neural network models are increasingly establishing themselves as an effective tool for simulating the dynamics of neuronal populations and for understanding the relationship between these dynamics and brain function. Furthermore, the continuous development of parallel computing technologies and the growing availability of computational resources are leading to an era of large-scale simulations capable of describing regions of the brain of ever larger dimensions at increasing detail. Recently, the possibility to use MPI-based parallel codes on GPU-equipped clusters to run such complex simulations has emerged, opening up novel paths to further speed-ups. NEST GPU is a GPU library written in CUDA-C/C++ for large-scale simulations of spiking neural networks, which was recently extended with a novel algorithm for remote spike communication through MPI on a GPU cluster. In this work we evaluate its performance on the simulation of a multi-area model of macaque vision-related cortex, made up of about 4 million neurons and 24 billion synapses and representing 32 mm(2) surface area of the macaque cortex. The outcome of the simulations is compared against that obtained using the well-known CPU-based spiking neural network simulator NEST on a high-performance computing cluster. The results show not only an optimal match with the NEST statistical measures of the neural activity in terms of three informative distributions, but also remarkable achievements in terms of simulation time per second of biological activity. Indeed, NEST GPU was able to simulate a second of biological time of the full-scale macaque cortex model in its metastable state 3.1x faster than NEST using 32 compute nodes equipped with an NVIDIA V100 GPU each. Using the same configuration, the ground state of the full-scale macaque cortex model was simulated 2.4x faster than NEST.

Item Type:	Journal Article
Creators:	Creators Email ORCID ORCID Put Code Tiddia, Gianmarco UNSPECIFIED orcid.org/0000-0001-7524-0285 UNSPECIFIED Golosio, Bruno UNSPECIFIED UNSPECIFIED UNSPECIFIED Albers, Jasper UNSPECIFIED UNSPECIFIED UNSPECIFIED Senk, Johanna UNSPECIFIED UNSPECIFIED UNSPECIFIED Simula, Francesco UNSPECIFIED UNSPECIFIED UNSPECIFIED Pronold, Jari UNSPECIFIED UNSPECIFIED UNSPECIFIED Fanti, Viviana UNSPECIFIED UNSPECIFIED UNSPECIFIED Pastorelli, Elena UNSPECIFIED UNSPECIFIED UNSPECIFIED Paolucci, Pier Stanislao UNSPECIFIED orcid.org/0000-0003-1937-6086 UNSPECIFIED van Albada, Sacha J. UNSPECIFIED UNSPECIFIED UNSPECIFIED
URN:	urn:nbn:de:hbz:38-684221
DOI:	10.3389/fninf.2022.883333
Journal or Publication Title:	Front. Neuroinformatics
Volume:	16
Date:	2022
Publisher:	FRONTIERS MEDIA SA
Place of Publication:	LAUSANNE
ISSN:	1662-5196
Language:	English
Faculty:	Unspecified
Divisions:	Unspecified
Subjects:	no entry
Uncontrolled Keywords:	Keywords Language DENSITY; SPINNAKER; BRAIN; CODE Multiple languages Mathematical & Computational Biology; Neurosciences Multiple languages
URI:	http://kups.ub.uni-koeln.de/id/eprint/68422