Warning

This is A PREVIEW for NEST 3.0 and NOT an OFFICIAL RELEASE! Some functionality may not be available and information may be incomplete!

Ubuntu/Debian Installation

Dependencies

To build NEST, you need a recent version of CMake and libtool; the latter should be available for most systems and is probably already installed.

Note

NEST requires CMake 3.12 or higher, but we recommend version 3.16. You can type cmake --version on the commandline to check your current version.

The GNU readline library is recommended if you use NEST interactively without Python. Although most Linux distributions have GNU readline installed, you still need to install its development package if you want to use GNU readline with NEST. GNU readline itself depends on libncurses (or libtermcap on older systems). Again, the development packages are needed to compile NEST.

The GNU Scientific Library is needed by several neuron models, in particular those with conductance based synapses. If you want these models, please install the GNU Scientific Library along with its development packages.

For efficient sorting algorithms the Boost library is used. Since this is an essential factor for the communication of spikes, some simulations are significantly faster when NEST is compiled with Boost.

If you want to use PyNEST, we recommend to install the following along with their development packages:

Installation from source

The following are the basic steps to compile and install NEST from source code. See the CMake Options or the High Performance Computing instructions to further adjust settings for your system.

  • If not already installed on your system, the following packages are recommended (see also the Dependencies section)

sudo apt install -y \
cython \
libgsl-dev \
libltdl-dev \
libncurses-dev \
libreadline-dev \
python3-all-dev \
python3-numpy \
python3-scipy \
python3-matplotlib \
python3-nose \
openmpi-bin \
libopenmpi-dev
  • Unpack the tarball

tar -xzvf nest-simulator-x.y.z.tar.gz
  • Create a build directory:

mkdir nest-simulator-x.y.z-build
  • Change to the build directory:

cd nest-simulator-x.y.z-build
cmake -DCMAKE_INSTALL_PREFIX:PATH=<nest_install_dir> </path/to/NEST/src>

Note

/install/path should be an absolute path

Note

Python bindings are enabled by default. Add the configuration option -Dwith-python=OFF to disable them.

  • Compile and install NEST:

make
make install
make installcheck

NEST should now be successfully installed on your system.

  • Before using NEST, make sure that all required environment variables are set correctly. In short, this can be established by sourcing the shell script nest_vars.sh, which is installed into the path for binaries selected during the CMake run. See the section Environment variables for details.

  • See the Getting started pages to find out how to get going with NEST or check out our example networks.

What gets installed where

By default, everything will be installed to the subdirectories <nest_install_dir>/{bin,lib,share}, where /install/path is the install path given to cmake:

  • Executables <nest_install_dir>/bin

  • Dynamic libraries <nest_install_dir>/lib/

  • SLI libraries <nest_install_dir>/share/nest/sli

  • Documentation <nest_install_dir>/share/doc/nest

  • Examples <nest_install_dir>/share/doc/nest/examples

  • PyNEST <nest_install_dir>/lib/pythonX.Y/site-packages/nest

  • PyNEST examples <nest_install_dir>/share/doc/nest/examples/pynest

  • Extras <nest_install_dir>/share/nest/extras/

If you want to run the nest executable or use the nest Python module without providing explicit paths, you have to add the installation directory to your search paths. Please refer to the next section section for this.

Environment variables

A number of environment variables are used to specify where the components of a NEST installation are found. In particular when installing to a custom directory, it is typically necessary to explicitly set these variables, so that your operating system can find the NEST binaries, its libraries and custom extension modules.

For your convenience, a shell script setting all required environment variables is provided in <nest_install_dir>/bin/nest_vars.sh. Setting the environment variables in your active shell session requires sourcing the script:

source <nest_install_dir>/bin/nest_vars.sh

You may want to include this line in your .bashrc file, so that the environment variables are set automatically whenever you open a new terminal.

The following variables are set in nest_vars.sh:

Variable

Description

PYTHONPATH

Search path for non-standard Python module locations. Will be newly set or prepended to the already existing variable if it is already set.

PATH

Search path for binaries. Will be newly set or prepended to the already existing variable if it is already set.

If your operating system does not find the nest executable or if Python does not find the nest module, your path variables may not be set correctly. This may also be the case if Python cannot load the nest module due to missing or incompatible libraries.