nest

The neural simulation tool.

This documentation is also provided with each nest package variant as README-Fedora.md (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

• python3-nest: PyNEST for Python 3 without MPI support

• nest-mpich: NEST simulator build with MPICH support

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

• nest-openmpi: NEST simulator build 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:

The nest_vars.sh file can be sourced:

• 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

More information on using MPI builds can be found in the NeuroFedora documentation here: https://docs.fedoraproject.org/en-US/neurofedora/mpi/

Package 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/