Installation¶
The following instructions are for Linux and Mac OS X. It should be possible to install and run PyNN on Windows, but this has not been tested.
Installing PyNN requires:
Optional dependencies are:
Installing PyNN¶
Note
if using NEURON, it is easiest if you install NEURON before you install PyNN (see below).
The easiest way to get PyNN is to use pip:
$ pip install pyNN
If you are running Debian or Ubuntu, there are binary packages available. If you would prefer to install manually, download the latest source distribution, then run the setup script, e.g.:
$ tar xzf PyNN-0.8.3.tar.gz
$ cd PyNN-0.8.3
$ python setup.py install
This will install it to your Python site-packages directory, and may
require root privileges. We strongly recommend, however, that you use a
virtualenv or a Conda environment. We assume you have already installed the
simulator(s) you wish to use it with. If this is not the case, see below for
installation instructions.
Test it using something like the following:
>>> import pyNN.nest as sim
>>> sim.setup()
>>> sim.end()
(This assumes you have NEST installed).
With NEURON as the simulator, make sure you install NEURON before you install PyNN.
The PyNN installation will then compile PyNN-specific membrane mechanisms, which are loaded when importing the neuron module:
>>> import pyNN.neuron as sim
NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
loading membrane mechanisms from /home/docker/dev/PyNN/pyNN/neuron/nmodl/x86_64/.libs/libnrnmech.so
Additional mechanisms from files
adexp.mod alphaisyn.mod alphasyn.mod expisyn.mod gap.mod gsfa_grr.mod hh_traub.mod
izhikevich.mod netstim2.mod refrac.mod reset.mod stdwa_guetig.mod stdwa_softlimits.mod
stdwa_songabbott.mod stdwa_symm.mod stdwa_vogels2011.mod tmgsyn.mod tmisyn.mod
tsodyksmarkram.mod vecstim.mod
If you installed PyNN before installing NEURON, or if you update your PyNN installation,
you will need to manually run nrnivmodl in the pyNN/neuron/nmodl directory.
Installing NEURON¶
Download the sources for the latest release of NEURON, in .tar.gz format, from http://www.neuron.yale.edu/neuron/download/getstd.
Also download Interviews from the same location.
Compile Interviews and NEURON according to the instructions given at http://www.neuron.yale.edu/neuron/static/download/compilestd_unix.html,
except that when you run configure, add the options --with-nrnpython and, optionally, --with-paranrn, i.e.:
$ ./configure --prefix=`pwd` --with-nrnpython --with-paranrn
$ 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 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
>>> import hoc
>>> import nrn
Now you can compile and install NEURON as a Python package:
$ cd src/nrnpython
$ python setup.py install
Now test everything worked:
$ python
>>> import neuron
NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015
See http://www.neuron.yale.edu/neuron/credits
If you run into problems, check out the NEURON Forum.
Installing NEST and PyNEST¶
NEST 2.12 can be downloaded from http://www.nest-simulator.org/download/. Earlier versions of NEST will not work with this version of PyNN. The full installation instructions are available in the file INSTALL, which you can find in the NEST source package, or at http://www.nest-simulator.org/installation/.
Note
NumPy must be installed before installing NEST.
Note
Make sure you have the GNU Scientific Library (GSL) installed,
otherwise some PyNN standard models (e.g. IF_cond_exp) will not be available.
On Linux, most Unix variants and Mac OS X, installation is usually as simple as:
$ ./configure --with-mpi
$ make
$ make install
This will install PyNEST to your Python site-packages directory.
If you wish to install it elsewhere, see the full installation instructions.
Now try it out:
$ cd ~
$ python
>>> import nest
-- N E S T --
Copyright (C) 2004 The NEST Initiative
Version 2.12.0 Mar 21 2016 21:29:37
...
>>> nest.Models()
(u'ac_generator', u'aeif_cond_alpha', u'aeif_cond_alpha_RK5', u'aeif_cond_alpha_multisynapse',
...
Check that 'aeif_cond_alpha' is in the list of models. If it is not, you may need to install a newer version of the GNU Scientific Library and then recompile NEST.
Installing Brian¶
Instructions for downloading and installing Brian are available from http://briansimulator.org/download/. Note that this version of PyNN works with Brian 1.4, but not with Brian 2.
