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NEST

Neural Simulation Tool by the NEST Initiative

Scientific area

Large-scale simulations of biological neuronal networks.

Short description

The Neural Simulation Tool (NEST) is an open-source software tool designed for the simulation of large-scale neuronal networks at the resolution of individual neurons and synapses. It is developed and maintained by the NEST initiative under the GNU General Public License, version 2 and can be freely downloaded from the website of the NEST simulator. The collaborative development of NEST follows an iterative, incremental strategy derived from the requirements and constraints given by the community. Users can control simulations either via a built-in scripting language (SLI) or a Python module (PyNEST). While the definition of the network in terms of the specification of neuronal populations and connections can be performed in procedural form in an interpreted language, all compute-intensive tasks such as the actual generation of connectivity or the propagation of neuron dynamics are executed by the simulation kernel implemented in C++. NEST supports a variety of computing platforms, from laptops to moderately-sized clusters and supercomputers using a common codebase. To optimally use the available compute resources, NEST supports hybrid parallelization employing MPI for inter-node communication and multi-threading via OpenMP within each MPI process.
The weak scaling performance of NEST exploits the full JUQUEEN system to simulate up to 0.65 billion neurons connected via 7.26 trillion synapses.

Scalability

  • 458,752 cores on BlueGene/Q (JUQUEEN)
  • 663,552 cores on SPARC64 VIIIfx (K computer)

Performance of NEST on JUQUEENWeak scaling of an archetypal neural network simulation. Runtime and memory usage per compute node with 1 MPI process and 64 threads per node. Each compute node hosts 22,500 neurons with 11,250 incoming synapses per neuron. (A) Simulation time. Gray triangles and dashed line show the total network size N (right vertical axis). (B) Cumulative memory usage for a single MPI process after construction of neurons (dotted; < 140 MB), after construction of connections (dashed), and after simulation (solid).

Programming language and model

  • Python, C++
  • MPI, OpenMP

Tested on platforms

  • BlueGene/Q (JUQUEEN)
  • SPARC64 VIIIfx (K computer)
  • x86

Application developers and contact

  • The NEST Initiative
  • Institute of Neuroscience and Medicine (INM-6),
    Computational and Systems Neuroscience
    & Institute for Advanced Simulation (IAS-6),
    Theoretical Neuroscience
    Forschungszentrum Jülich GmbH
    52425 Jülich
  • Simulation Laboratory Neuroscience
    Jülich Supercomputing Centre
    Forschungszentrum Jülich GmbH
    52425 Jülich


(Text and images provided by the developers)


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