This README contains instruction how to install NEURON and solve some troubles with Ubuntu and CentOS. The repository also contains file to test the installation on all operating systems.

NEURON should work with: most Linux distributions, Windows and OSX, however prerequisites installations and trouble solving concentrate here on Ubuntu.

NEURON Documentation

https://www.neuron.yale.edu/neuron/docs

Prerequisites

Python

• Works with Python: 3.5 and 3.6

• It is recommended to work with Python 3.6

• Python > 3.6 may work but it also may have different issues, eg:

  • Python 3.7 have problem with libpython3.7 and pycairo on Ubuntu.
  • It is possible to work with 3.7 but running from PyCharm may be error prone

Ubuntu

NEURON > 7.5 requires the following additional libraries:

• Ubuntu 16.04 install: sudo apt install libreadline5 python-lxml

• Ubuntu 18.04 install: sudo apt install libreadline-gplv2-dev python-lxml

• Ubuntu 20.04: sudo apt-get install libtinfo5 libreadline-gplv2-dev python-lxml

CentOS

Follow those procedures:

• module load common/mpi/openmpi/3.1.4_gnu-7.3
• module load common/compilers/gcc/7.3.1
• rpm -q ncurses
• wget http://download-ib01.fedoraproject.org/pub/epel/7/x86_64/Packages/p/python36-Cython-0.28.5-1.el7.x86_64.rpm

Anadonda

• It is recommended to install Anaconda: https://www.anaconda.com/products/individual

• Then create a new env:

  • conda create --name neuron python=3.6
  • conda activate neuron
  • cd neuron_netpyne_get_started
  • pip install -r requirements.txt

NEURON Installation

Ubuntu

Python-only installation

• pip install neuron

Full Neuron installation

• Allows to use nrngui, nrnivmodl as well as run HOC files from the console
• Download *.deb from https://www.neuron.yale.edu/neuron/download
• dpkg -i neuron.deb
• add to ~/.bashrc: export PYTHONPATH="$PYTHONPATH:/usr/local/nrn/lib/python/"

CentOS

Python-only installation

• pip install neuron

Full Neuron installation

• Download nrn*.tar.gz from https://neuron.yale.edu/ftp/neuron/versions/

• extract to nrn_source

• Download iv*.tar.gz from https://neuron.yale.edu/ftp/neuron/versions/

• extract to iv_source

• cd iv_source

• ./configure --prefix=$HOME/iv

• make -j

• sudo make install -j

• cd ..

• cd nrn_source

• ./configure --prefix=$HOME/nrn --with-iv=/where/is/iv --with-nrnpython=python --with-paranrn

• make

• make install

• add to ~/.bashrc: export PYTHONPATH="$PYTHONPATH:$HOME/nrn/lib/python/" export PATH="$PATH:$HOME/nrn/x86_64/bin/"

Test NEURON installation for all OS:

• run python neuron_example.py
• if you see no errors - it works fine

Using NEURON with PyCharm

• For Python-only installation it should work out-of-the-box
• For full NEURON installation - follow steps below:

The image above shows where you need to go through settings, you can also follow the instruction below:

• Setting -> Project Interpreter
• click on interpreter list and select "Show All"
• Add or select your interpreter
• click "Show paths for the selected interpreter"
• add the path: /usr/local/nrn/lib/python

Known issues

CentOS

Refer to: https://www.neuron.yale.edu/neuron/download/compile_linux

libreadline5 issue:

• during compiling *.mod file you have an error: /usr/bin/ld: cannot find -lreadline
• during nrngui run from console you have an error: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory
• during Python from neuron import h you have an error:

Traceback (most recent call last):
  File "/usr/local/nrn/lib/python/neuron/__init__.py", line 110, in <module>
    import neuron.hoc
ImportError: libreadline.so.5: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/nrn/lib/python/neuron/__init__.py", line 112, in <module>
    exec("import neuron.hoc%d%d as hoc" % (sys.version_info[0], sys.version_info[1]))
  File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'neuron.hoc37'

Install in bash console:

sudo apt-get install libreadline5

Ubuntu: X11 error

• After compiling MOD files with nrnivmodl you encounter the error:

/usr/bin/ld: cannot find -lX11

• check linker:

ld -lX11 --verbose

• Install:

sudo apt-get install libx11-dev:i386 libx11-dev

Helvetica warning

• During each NEURON run you may face error such as:

nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"

• To solve it you must install helvetica font specified in the warning

Solving Helvetica warning in Ubuntu:

sudo apt-get install xfonts-100dpi

• Then logout and login again