NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons.
Support mailing list: http://mail.nest-initiative.org/cgi-bin/mailman/listinfo/nest_user.
Bug tracker: https://github.com/nest/nest-simulator/issues.
Fedora package information: https://apps.fedoraproject.org/packages/nest/overview/.
NeuroFedora currently includes the two most recent versions of NEST:
|Modularity allows for parallel availability, but not parralel installability. So, only one version of NEST can be installed at one time.|
NEST can be installed on Fedora using the DNF package manager. NEST supports the use of MPI (Message passing interface) for use on clusters and super computers. Fedora includes MPICH and OpenMPI implementations of MPI. NEST can be used with either of these, or without any MPI support. NEST in Fedora is:
nest: NEST simulator without MPI support.
python2-nest: PyNEST for Python 2 without MPI support (Fedora 28/29 only).
python3-nest: PyNEST for Python 3 without MPI support.
nest-mpich: NEST simulator built with MPICH support.
python2-nest-mpich: PyNEST for Python 2 with MPICH support (Fedora 28/29 only).
python3-nest-mpich: PyNEST for Python 3 with MPICH support.
nest-openmpi: NEST simulator built with OpenMPI support.
python2-nest-openmpi: PyNEST for Python 2 with OpenMPI support (Fedora 28/29 only).
python3-nest-openmpi: PyNEST for Python 3 with OpenMPI support.
nest-doc: Generated documentation.
Since NEST 2.18.0 is made available in the standard Fedora platform repositories, it can be installed simply by using
dnf without any additional configuration.
sudo dnf install python3-nest
NEST 2.16.0 is provided using a module stream.
It can also be installed using
dnf but requires the use of the
module sub command:
sudo dnf module install nest:2.16.0
This installs the
default profile for the stream.
default profile is the non-MPI build of NEST.
openmpi are the other provided profiles:
sudo dnf module list .. .. nest 2.16.0 [x] default [d], mpich, openmpi The neural simulation tool
To install a profile, use:
sudo dnf module install nest:2.16.0/mpich # for the mpich profile
More information on modules, their design, their creation, and their usage can be found on the Modularity documentation.
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
For non MPI (serial) builds:
For MPICH builds:
For OpenMPI builds:
To use an MPI build of NEST, the appropriate environment version must be loaded as documented here.
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