Tag Archives: Simulation

The Virtual Brain (TVB-HPC)

TVBThe Virtual Brain (TVB) is a large-scale brain simulator. With a community of thousands of users around the world, TVB has become a validated, popular and standard choice for the simulation of whole brain activity. TVB users can create simulations using neural mass models which can produce outputs for different analysis and modalities. TVB allows scientists to explore and analyze both simulated and experimental data. It contains analytic tools for evaluating relevant scientific parameters in light of that data. The current implementation of TVB is written in Python, with limited large-scale parallelization over different parameters. The objective of TVB-HPC is to enable large-scale parallelization of TVB simulations by making use of high performance computing to explore large parameter spaces for the models. With this approach, neuroscientists can define their models in a domain specific language based on NeuroML and automatically generate code which can run either on GPUs or on CPUs with different architectures and optimizations. The result is a framework that hides the complexity of writing robust parallel code and offers neuroscientists a fast and efficient access to high performance computing. TVB-HPC is publicly available on GitHub and, at the end of HBP project phase SGA2, it will be possible to launch large parameter simulations using code automatically generated with this framework via the HBP Collaboratory.

Date of release30.04.2019 (continuous minor releases since then)
Version of softwarev0.1-alpha
Version of documentationv0.1-alpha
Software availablehttps://github.com/the-virtual-brain/tvb-hpc
ResponsibleSandra Diaz (JUELICH): s.diaz@fz-juelich.de
Requirements & dependencies
Target system(s)HPC systems


ArborArbor is a software library designed from the ground up for simulators of large networks of multi-compartment neurons on hybrid/accelerated/many core computer architectures.

Performance portability was completed for the three main target HPC architectures available through the HBP: Intel x86 CPUs (AVX2 and AVX512), Intel KNL (AVX512) and NVIDIA GPUs (CUDA).

Optimized kernels are automatically generated to target each architecture, and the system used in Arbor can be extended to new architectures in the future.

The other enhancements and features implemented in Arbor are:

  • Fully parallelized event generation and queuing from spikes.
  • Efficient sampling of model state on CPU and GPU implementations, e.g. voltage and current.
  • Significant refactoring to prepare the code for general release.
  • A Python interface for users.

The source code was released publicly on GitHub with an open source BSD license, along with documentation on Read the Docs, and automatic testing was set up on Travis CI.

Date of releaseAugust 2019
Version of software0.2.1
Version of documentation0.2.1
Software availablehttps://github.com/eth-cscs/arbor
ResponsibleBenjamin Cumming (ETHZ): bcumming@cscs.ch
Alexander Peyser (JUELICH): a.peyser@fz-juelich.de
Requirements & dependencies
Target system(s)

NEST: The Neural Simulation Tool

Science has driven the development of the NEST simulator for the past 20 years. Originally created to simulate the propagation of synfire chains using single-processor workstations, we have pushed NEST’s capabilities continuously to address new scientific questions and computer architectures. Prominent examples include studies on spike-timing dependent plasticity in large simulations of cortical networks, the verification of mean-field models, models of Alzheimer’s and Parkinson’s disease and tinnitus. Recent developments include a significant reduction in memory requirements, as demonstrated by a record-breaking simulation of 1.86 billion neurons connected by 11.1 trillion synapses on the Japanese K supercomputer, paving the way for brain-scale simulations.

Running on everything from laptops to the world’s largest supercomputers, NEST is configured and controlled by high-level Python scripts, while harnessing the power of C++ under the hood. An extensive testsuite and systematic quality assurance ensure the reliability of NEST.

The development of NEST is driven by the demands of neuroscience and carried out in a collaborative fashion at many institutions around the world, coordinated by the non-profit member-based NEST Initiative. NEST is released under GNU Public License version 2 or later.

How NEST has been improved in HBP

Continuous dynamics

The continuous dynamics code in NEST enables simulations of rate- based model neurons in the event-based simulation scheme of the spiking simulator NEST. The technology was included and released with NEST 2.14.0.

Furthermore, additional rate-based models for the Co-Design Project “Visuo-Motor Integration” (CDP4) have been implemented and scheduled for NEST release 2.16.0.

Related publication:
Hahne et al. (2017) Front. Neuroinform. 11,34. doi:10.3389/fninf.2017.00034


NESTML is a domain-specific language that supports the specification of neuron models in a precise and concise syntax, based on the syntax of Python. Model equations can either be given as a simple string of mathematical notation or as an algorithm written in the built-in procedural language. The equations are analyzed by NESTML to compute an exact solution if possible, or use an appropriate numeric solver otherwise.

Link to this release (2018): https://github.com/nest/nestml

Related Publications:

Plotnikov et al. (2016) NESTML: a modeling language for spiking neurons.

Simulator-simulator interfaces

This technology couples the simulation software NEST and UG4 by means of the MUSIC library. NEST can only send spike trains where spiking occurs; UG4 receives those in form of events arriving at synapses (timestamps). The time course of the extracellular potential in a cube (representing a piece of tissue) is simulated based on the arriving spike data.The evolution of the membrane potential in space and time is described by the Xylouris-Wittum model.

Link to this release (2017): https://github.com/UG4

Related publications:
Vogel et al. (2014) Comput Vis Sci. 16,4. doi: 10.1007/s00791-014-0232-9Xylouris, K., Wittum, G. (2015) Front Comput Neurosci. doi: 10.3389/fncom.2015.00094

More information

NEST – A brain simulator (short movie)

NEST::documented (long movie)

NEST brochure:


Date of releaseJuly 2019
Version of softwarev2.18.0
Version of documentationv2.18.0
Software availableNEST can be run directly from a Jupyter notebook inside a Collab in the HBP Collaboratory.
Download & Information: https://www.nest-simulator.org
Latest code version: https://github.com/nest/nest-simulator
ResponsibleNEST Initiative (http://www.nest-initiative.org/)
General Contact: NEST User Mailing List (http://www.nest-simulator.org/community/)

Contact for HBP Partners:
Hans Ekkehard Plesser (NMBU/JUELICH): hans.ekkehard.plesser@nmbu.no
Dennis Terhorst (JUELICH): d.terhorst@fz-juelich.de
Requirements & dependenciesAny Unix-like operating system and basic development tools
GNU Science Library
Target system(s)All Unix-like systems
Laptop to Supercomputer; has been ported to Raspberry Pi, too