Installation of NEURON with Python

Tags: Python, NEURON

Updated 2009-01-22 for NEURON v7.0

These instructions are for NEURON v7.0. They may remain valid for future versions, and should also work for v6.1 or newer. These instructions are for Linux or Mac OS X, using the bash shell. They may well work in Cygwin, but I haven't tested them.

Binary versions of NEURON 7.0 come with Python support, and allow you to run nrniv -python (embedded Python), but they don't allow you to run Python (or IPython) and then do import neuron (NEURON as a Python module): for this you need to compile from source.

First build and install Interviews, if you don't already have it:

$ N=`pwd`
$ tar xzf iv-17.tar.gz
$ cd iv-17
$ ./configure --prefix=`pwd`
$ make
$ make install

Now build and install NEURON:

$ cd ..
$ tar xzf nrn-7.0.tar.gz
$ cd nrn-7.0
$ ./configure --prefix=`pwd` --with-iv=$N/iv-17 --with-nrnpython
$ make
$ make install

If you want to run parallel NEURON, add --with-paranrn to the configure options. On Mac OS X, I have found I need to add PYLIB=-lpython PYLIBLINK=-lpython to the configure line.

Now add the NEURON bin directory to your PATH:

$ export PATH=$N/nrn-7.0/i686/bin:$PATH

(Replace i686 with your own CPU architecture if necessary).

Now build the NEURON shared library for Python:

$ cd src/nrnpython
# python install

This command (which will probably have to be run as root or using sudo) will install the neuron package to your site-packages directory. An alternative, especially if you don't have root privileges, is:

$ python install --prefix=~

which will install the neuron package to ~/lib/python/site-packages. You will then have to add this directory to the PYTHONPATH environment variable:

$ export PYTHONPATH=$PYTHONPATH:~/lib/python/site-packages

Starting NEURON

For those who are not familiar with NEURON, it may be started without the graphical interface using nrniv or with the graphical interface using nrngui. To use Python, rather than hoc, as the interpreter, use the -python option:

$ nrniv -python
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008

>>> import neuron

If there are any NEURON extension (NMODL) mechanisms in the working directory, and they have been compiled with nrnivmodl, they will be loaded automatically.

Alternatively, you may wish to use the normal Python interpreter, or an alternative such as IPython. In this case, NEURON is started (and any NMODL mechanisms loaded) when you import neuron:

$ ipython
Python 2.4.1 (#1, May 25 2007, 17:56:29)
Type "copyright", "credits" or "license" for more information.

IPython 0.6.15 -- An enhanced Interactive Python.
?       -> Introduction to IPython's features.
%magic  -> Information about IPython's 'magic' % functions.
help    -> Python's own help system.
object? -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import neuron
NEURON -- Release 7.0 (281:80827e3cd201) 2009-01-16
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008

In [2]: