nest

The neural simulation tool.

Note: Nest 2.16 does not support 32 bit hardware.

Note: it is not yet built with libneurosim support, so all models may not be available in PyNN.

This documentation is also provided with each nest package variant as README.Fedora (nest, nest-mpich, nest-openmpi):

The Fedora packages of the NEST simulator are built to cover various configurations and installs their files in the standard locations:

  • nest: NEST simulator without MPI support
  • python2-nest: PyNEST for Python 2 without MPI support
  • python3-nest: PyNEST for Python 3 without MPI support

  • nest-mpich: NEST simulator build with MPICH support

  • python2-nest-mpich: PyNEST for Python 2 with MPICH support
  • python3-nest-mpich: PyNEST for Python 3 with MPICH support

  • nest-openmpi: NEST simulator build with OpenMPI support

  • python2-nest-openmpi: PyNEST for Python 2 with OpenMPI support
  • python3-nest-openmpi: PyNEST for Python 3 with OpenMPI support

Usage

The nest_vars.sh must be sourced to set up the environment correctly for NEST, which makes use of a few environment variables:

  • NEST_INSTALL_DIR
  • NEST_DATA_DIR
  • NEST_MODULE_PATH
  • NEST_PYTHON_PREFIX
  • NEST_DOC_DIR

The nest_vars.sh file is located in:

For MPICH builds:

source /usr/lib64/mpich/bin/nest_vars_mpich.sh

For OpenMPI builds: source /usr/lib64/openmpi/bin/nest_vars_openmpi.sh

For non MPI builds: source /usr/bin/nest_vars.sh

To use an MPI build of NEST, one must also load the appropriate module. For MPICH builds:

module load mpi/mpich-$arch # $arch is the architecture, for example x86_64

For OpenMPI builds:

module load mpi/openmpi-$arch # $arch is the architecture, for example x86_64

It is generally easier to add these lines to the ~/.bashrc file (for bash users) so that these commands are automatically run on each login.

The binaries for each MPI build are suffixed to distinguish them from each other:

For MPICH builds, they would be:

nest_mpich
nest_vars_mpich.sh
nest_config_mpich
nest_serial_mpich
nest_indirect_mpich
sli_mpich

For OpenMPI builds:

nest_openmpi
nest_vars_openmpi.sh
nest_config_openmpi
nest_serial_openmpi
nest_indirect_openmpi
sli_openmpi

Documentation

The generated documentation is provided in the nest-doc package, and is common for all builds.

Official documentation can be found at http://nest-simulator.org/

For issues with this package, please contact the NeuroFedora SIG.