Installation Guide

Tip

Use virtual environments!

The scaffold framework can be installed using pip:

pip install "bsb>=4.0.0a0"

You can verify that the installation works with:

from bsb.core import Scaffold

# Create an empty scaffold network with the default configuration.
scaffold = Scaffold()

You can now head over to the get started.

Parallel support

The BSB parallelizes the network reconstruction using MPI, and translates simulator instructions to the simulator backends with it as well, for effortless parallel simulation. To use MPI from Python the mpi4py package is required, which in turn needs a working MPI implementation installed in your environment.

On your local machine you can install OpenMPI:

sudo apt-get update && sudo apt-get install -y libopenmpi-dev openmpi-bin

On Windows, install Microsoft MPI. On supercomputers it is usually installed already, otherwise contact your administrator.

To then install the BSB with MPI support:

pip install "bsb[mpi]>=4.0.0a0"

Simulator backends

If you’d like to install the scaffold builder for point neuron simulations with NEST or multicompartmental neuron simulations with NEURON use:

pip install bsb[nest]
# or
pip install bsb[neuron]
# or both
pip install bsb[nest,neuron]

Note

This does not install the simulators themselves. It installs the Python tools that the BSB needs to deal with them. Install the simulators separately according to their respective installation instructions.

Installing NEST

The BSB currently runs a fork of NEST 2.18. To install it, follow the instructions, with a virtual environment activated.

sudo apt-get update && apt-get install -y openmpi-bin libopenmpi-dev
git clone https://github.com/dbbs-lab/nest-simulator
cd nest-simulator
mkdir build
cd build
pip install cmake cython
cmake .. \
  -Dwith-mpi=ON \
  -Dwith-python=ON
make install

Confirm your installation with:

python -c "import nest; nest.test()"

Note

There might be a few failed tests related to NEST_DATA_PATH but this is OK.