Instructions for installing Neuron

Last Update 2019-01-10 by Adam Lu

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• Install make (needed for NEURON’s nrnivmodl to work):

    sudo apt-get install make
  

• Install the GNU C Compiler (needed for NEURON’s nrnivmodl to work):

    sudo apt-get install gcc
  

• Install the new curses library (needed for NEURON’s nrnivmodl to work):

    sudo apt-get install libncurses5-dev
    sudo apt-get install libncurses5-dbg
    sudo apt-get install ncurses-doc
    sudo apt-get install ncurses-examples
    sudo apt-get install libncursesw5-dev
    sudo apt-get install libncursesw5-dbg
  

• Download the .deb package from the NEURON download page, then applied the command:

    sudo dpkg -i nrn-7.5.x86_64.deb
  

• Tested what is needed to set up the python environment: (NOT DONE for chalkboard yet)

    nrnpyenv.sh
  

  Output:

    # find /usr/lib/python2.7 -name libpython2.7\*.so
    # ['/usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so']
    # items in sys.path = 9
    # beginning with sys.prefix = 8
    # site-3 same as sys.prefix
    # in neither location ['.']
    # sys.prefix = /usr
    # site-3 = /usr
      
    # if launch nrniv, then likely need:
    export PYTHONHOME="/usr"
    export NRN_PYLIB="/usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so"
  

  Therefore, added these lines to the file /etc/bash.bashrc:

    # Needed for nrniv -python to work:
    export PYTHONHOME="/usr"
    export NRN_PYLIB="/usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so"
  

• Updated to newer versions by applying the commands: (REVERTED)

    sudo dpkg --remove nrn
    sudo dpkg -i nrn-7.6.x86_64-linux.deb
  

  Note: there were issues with nrn-7.6.x86_64-linux.deb so this was reverted