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NeuronetExperimenter Installation Guide 

Since NeuronetExperimenter generates optimized C++ code from your models, you need to be able to generate an excutable binary on your system. This requires several free development tools. Most of these tools should be accessible on any Unix-compatible system (i.e., Linux, OS X, *BSD, Solaris, etc.).

Required Tools:
GCC 4.X+ - The Gnu Compiler Collection
Python 2.5.X+ - The Python Programming Language Interpreter
NeuronetExperimenter

Optional Libraries:

GSL - The Gnu Scientific Library for random number generation
OpenMPI - A library for parallel processing communication

Installing GCC

Linux, Solaris, and *BSD:

GCC is typically installed by default on most Linux distributions or can be selected as an additional package to include during installation. 

OS X:

GCC is usually NOT installed by default on OS X. However, GCC is usually included in the Developer Tools package of the OS X CD that comes with your Mac. This is the best place to install GCC from.

Leopard:

If that does not work, you can download the XCode 3.0 Developer Tools from http://developer.apple.com/technology/xcode.html. This requires you to sign up (for free) as an Apple Developer (ADC membership).

Tiger:

For Tiger, you can download the XCode 2.5 Developer Tools from http://connect.apple.com/. This requires you to sign up (for free) as an Apple Developer (ADC membership). Sign in, then click Downloads and then on the right-side, click on Developer Tools. Then scroll down to find the Xcode 2.5 Developer Tools (Disk Image)

Finally, if none of those approaches work, you can download pre-built binaries from the High Performance Computing for OS X website. That website has instructions for installing their distributions of the software.

Installing Python

A Python interpreter should already be installed on most Unix-compatible systems. You can confirm this by typing,

>python -V

at a command terminal. This will return the Python version that is installed. If the command is not recognized, you can download and install the package from http://www.python.org.

Installing GSL

Download the latest stable version of GSL from the developer's website: http://www.gnu.org/software/gsl/. For example, http://ftp.gnu.org/pub/gnu/gsl/gsl-1.11.tar.gz.

Unpack the source code and build the code as follows (note the comment in blue):


>tar zxvf gsl-1.11.tar.gz
>cd
gsl-1.11
>./configure
>make
>sudo make install               # or if that does not work, use 'su; make install'

The last line requires that you type in your administrator (root) password to complete installation.

Installing Open MPI

Download the latest stable version of Open MPI from the developer's website: http://www.open-mpi.org/. For example, http://www.open-mpi.org/software/ompi/v1.2/downloads/openmpi-1.2.6.tar.gz.

Unpack the source code and build the code as follows (note the comment in blue):


>tar zxvf openmpi-1.2.6.tar.gz
>cd
openmpi-1.2.6
>./configure
>make
>sudo make install               # or if that does not work, use 'su; make install'

The last line requires that you type in your administrator (root) password to complete installation.

Installing NeuronetExperimenter

Download the latest stable version of NeuronetExperimenter from website: http://people.wm.edu/~cadeln/code.htm. For example, http://people.wm.edu/~cadeln/code/NeuronetExperimenter-3.10.tar.gz.

If you have not already, unpack the NeuronetExperimenter source code as follows:

>tar zxvf NeuronetExperimenter-3.10.tar.gz
>cd
NeuronetExperimenter-3.10

After developing a model to use by NeuronetExperimenter, you will routinely need to perform the following operations.

>./configure                     
>make                            # this builds an excutable binary of the core simulator w/o the models included
>sudo make install               # this makes the binary accessible from anywhere on your file system

After that, you should be able to type the following to enter the NeuronetExperimenter's interactive mode:

NeuronetExperimenter interactive mode
>NeuronetExperimenter

Welcome to NeuronetExperimenter v3.10
Copyright (C) 2006-2009, J. A. Hayes and J. L. Mendenhall

Neurons this binary supports:

Select one from the following menu:
-1. Enter manually
0. Use the same setup and network file as last time
1. ../
2. docs/
3. include/
4. models/
5. scripts/
6. src/

Ctrl-C to exit

Now if everything is installed, you should be able to go through the tutorials without any problems.


>>Tutorial #1. Building and Running a Simple Single-Neuron Simulation

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