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 supportpython3-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 supportThe 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:
source /usr/lib64/mpich/bin/nest_vars_mpich.sh
source /usr/lib64/openmpi/bin/nest_vars_openmpi.sh
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/
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/