INSTALL-neuron.md

Install NEURON 7.4 with Python enabled

1. Install build dependencies

   sudo apt install g++5 gcc-5 libx11-dev libxext-dev libpython2.7-dev ncurses-dev python-scipy python-matplotlib
   

2. Decide where to put NEURON, for example $HOME/nrn/7.4/, which we will call $NRNPREFIX. We can set this in the terminal:

   NRNPREFIX=$HOME/nrn/7.4/
   

3. Download (these instructions assume that you are working in the same directory as this INSTALL-neuron.md file): iv-19.tar.gz from https://neuron.yale.edu/ftp/neuron/versions/v7.4/

4. Unpack, configure and compile

   tar zxvf iv-19.tar.gz
   cd iv-19
   CC=gcc-5 CXX=g++-5 ./configure --prefix=$NRNPREFIX/iv
   make
   make install
   cd ..
   

5. Download nrn-7.4.tar.gz from https://neuron.yale.edu/ftp/neuron/versions/v7.4/

6. Unpack, configure and compile

   tar zxvf nrn-7.4.tar.gz
   

7. Patch using the patch in KappaNEURON/doc

   cd nrn-7.4
   patch -p1 ../neuron7-4-cython.patch
   

8. Compile

   
   CC=gcc-5 CXX=g++-5 ./configure --prefix=$NRNPREFIX/nrn --with-iv=$NRNPREFIX/iv --with-nrnpython=python2.7
   make
   make install
   cd ..
   

9. Set the PYTHONPATH:

   export PYTHONPATH=$HOME/nrn/7.4/nrn/lib/python/:$PYTHONPATH
   

   This should be added to your shell configuration, e.g. ~/.profile or ~/.bash_profile.

10. Test that it works by typing:

    python2.7 -m neuron
    

    The output should be:

    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
    
    /usr/bin/python: No module named neuron.__main__; 'neuron' is a package and cannot be directly executed
    

    If there is an error about not finding a library in nrn_dll(), you may need to change lib to lib64 on line 444 of PREFIX/lib64/python/neuron/__init__.py.