Runtime Construction of Large-Scale Spiking Neuronal Network Models on GPU Devices

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Simulation speed matters for neuroscientific research: this includes not only how quickly the simulated model time of a large-scale spiking neuronal network progresses but also how long it takes to instantiate the network model in computer memory. On the hardware side, acceleration via highly parallel GPUs is being increasingly utilized. On the software side, code generation approaches ensure highly optimized code at the expense of repeated code regeneration and recompilation after modifications to the network model. Aiming for a greater flexibility with respect to iterative model changes, here we propose a new method for creating network connections interactively, dynamically, and directly in GPU memory through a set of commonly used high-level connection rules. We validate the simulation performance with both consumer and data center GPUs on two neuroscientifically relevant models: a cortical microcircuit of about 77,000 leaky-integrate-and-fire neuron models and 300 million static synapses, and a two-population network recurrently connected using a variety of connection rules. With our proposed ad hoc network instantiation, both network construction and simulation times are comparable or shorter than those obtained with other state-of-the-art simulation technologies while still meeting the flexibility demands of explorative network modeling.

Authors 9

1. Bruno Golosio

   University of Cagliari · Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari

   Affiliation as printed

   Department of Physics, University of Cagliari, 09042 Monserrato, Italy and Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari, 09042 Monserrato, Italy

2. José Villamar

   Forschungszentrum Jülich · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany

3. Gianmarco Tiddia

   University of Cagliari · Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari

   Affiliation as printed

   Department of Physics, University of Cagliari, 09042 Monserrato, Italy and Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari, 09042 Monserrato, Italy

4. Elena Pastorelli

   Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare, Sezione di Roma, 00185 Roma, Italy

5. Jonas Stapmanns

   Forschungszentrum Jülich · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany

6. Viviana Fanti

   University of Cagliari · Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari

   Affiliation as printed

   Department of Physics, University of Cagliari, 09042 Monserrato, Italy and Istituto Nazionale di Fisica Nucleare, Sezione di Cagliari, 09042 Monserrato, Italy

7. Pier Stanislao Paolucci

   Istituto Nazionale di Fisica Nucleare · Istituto Nazionale di Fisica Nucleare, Sezione di Roma I

   Affiliation as printed

   Istituto Nazionale di Fisica Nucleare, Sezione di Roma, 00185 Roma, Italy

8. Abigail Morrison Aachen Institute of Neuroscience and Medicine (INM-9) Institute for Advanced Simulation (IAS-5) JARA Institute Brain Structure-Function Relationships (INM-10)

   Forschungszentrum Jülich · Jülich Aachen Research Alliance · RWTH Aachen University

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany and Department of Computer Science 3, Software Engineering, RWTH Aachen University, 52062 Aachen, Germany

9. Johanna Senk

   Forschungszentrum Jülich · Jülich Aachen Research Alliance

   Affiliation as printed

   Institute of Neuroscience and Medicine (INM-6), Institute for Advanced Simulation (IAS-6), JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, 52428 Jülich, Germany