Wiki Navigation

Installation

Use of PyNN requires that you have Python and the numpy package installed, plus at least one of the supported simulators: NEURON, NEST or PCSIM.

Installing NEURON

Download the sources for the latest release of NEURON, in .tar.gz format, from http://www.neuron.yale.edu/neuron/install/install.html. Also download Interviews from the same location.

Compile Interviews and NEURON according to the instructions given at http://www.neuron.yale.edu/neuron/install/compile_unix.html#fullinstall, except that when you run configure, add the options --with-nrnpython and, optionally, --with-mpi (the latter assumes you have the MPICH library installed on your machine), i.e.:

$ ./configure --prefix=`pwd` --with-nrnpython --with-mpi
$ make
$ make install

Make sure that you add the Interviews and NEURON bin directories to your path. Test that the Python support has been enabled by running:

$ nrniv -python
NEURON -- Release 6.1.2 (1927) 2007-12-30
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html

>>> import hoc
>>> import nrn

Now you can compile and install NEURON as a Python package:

$ cd src/nrnpython
# python setup.py install

Note that the latter step requires running as root and will install to your global python site-packages directory. If you would prefer to install it locally, replace the last step with:

$ python setup.py install --prefix=~

which will install into ~/lib/python2.5/site-packages/ (or the equivalent for other Python versions; for more fine-grained control over where the package is installed, see the distutils documentation), then add this directory to your PYTHONPATH:

$ export PYTHONPATH=$PYTHONPATH:~/lib/python2.5/site-packages

Now test everything worked:

$ python
>>> import neuron
NEURON -- Release 6.1.1 (1894) 2007-11-24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html

>>>

Installing NEST and PyNEST

NEST can be downloaded from http://www.nest-initiative.org/?page=Software&subpage=Download. Installation instructions are available in the file INSTALL, which you can find in the source package.

Checkout PyNEST from the following Subversion repository (contact the NEST developers for access):

$ svn co svn+ssh://facets@www.nest-initiative.uni-freiburg.de/facets/trunk pynest
$ cd pynest

Set the SLIHOME environment variable to your NEST source installation and SLIBUILD to your NEST build directory, e.g. (for bash):

$ export SLIHOME=/usr/src/nest-1.0.13
$ export SLIBUILD=$SLIHOME/build

Finally, build and install PyNEST:

$ python setup.py install

This will install it to your python site-packages directory, and may require root privileges. If you wish to install it elsewhere:

$ python setup.py install --prefix=/where/to/install/pynest

and then set the PYTHONPATH environment variable appropriately, e.g.:

$ export PYTHONPATH=$PYTHONPATH:/where/to/install/pynest/lib/python2.4/site-packages/

Now try it out:

$ cd ~
$ python
>>> import pynest
>>> pynest.sps([1,2,3])
>>> pynest.spp()
[1, 2, 3]

Installing PCSIM

PCSIM is available by svn as follows:

$ svn co https://pcsim.svn.sourceforge.net/svnroot/pcsim pcsim

For compilation instructions, see the files in the HowTos directory.

Installing PyNN

The easiest way to get PyNN is to download the latest source distribution from the PyNN download page, then run the setup script, e.g.:

$ tar xzf PyNN-0.4.0.tar.gz
$ cd PyNN-0.4.0
$ python setup.py install

This will install it to your python site-packages directory, and may require root privileges. If you wish to install it elsewhere use the --prefix or --home option, and set the PYTHONPATH environment variable accordingly (see above).

Test it using something like the following:

>>> from pyNN.nest1 import *
>>> setup()
>>> end()

(This assumes you have PyNEST installed).

With NEURON as the simulator, PyNN-specific membrane mechanisms are loaded on setup():

>>> from pyNN.neuron import *
NEURON -- Release 6.1.1 (1894) 2007-11-24
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html

>>> setup()
loading membrane mechanisms from /usr/lib/python/site-packages/pyNN/hoc/i686/.libs/libnrnmech.so
Additional mechanisms from files
 alphaisyn.mod alphasyn.mod expisyn.mod refrac.mod reset.mod stdwa_softlimits.mod
 stdwa_songabbott.mod stdwa_symm.mod vecstim.mod