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Advanced NeuronetExperimenter Installation Guide 

If you do not have administrator (root-level) acccess to the system you would like to run NeuronetExperimenter on, this guide describes how to install NeuronetExperimenter in a different location than the default location that was described in the previous installation guide. This guide assumes that you have already read through the default installation guide. Once you have made these changes and built your NeuronetExperimenter binary executable, you should see no difference between the behavior of the default install and this install with regards to how the operations of the program and associated scripts are performed.

There are two critical differences between this installation and the normal installation. The first important change is to set the appropriate environment variables, so that you get the behavior expected when running through the tutorials. The second is that you should configure each of NeuronetExperimenter's dependencies to be installed in a different location, as well as NeuronetExperimenter's buildModelCode.py script to recognize this change. This is only necessary if Open-MPI and GSL are NOT already installed by the system administrator, which is probably the case if you are working through this guide.

Setting the Appropriate Environment Variables

You should set the PYTHONPATH, PATH, and NNE_BIN_PATH variables to include the directory you want to install BEFORE running './configure', 'make' and 'make install'. The environment variable topic shows how to conveniently set all three of these variables in the bash shell environment starting at the description of NNE_BIN_PATH.

Configuring the Installation of NeuronetExperimenter's Compilation Dependencies

First, pick a directory that you can install the other library dependencies. For example, a sub-directory of your home-directory such as /Users/john/NNE_deps. Now, every time you run a configure script for the dependencies (as described in the basic installation guide), append this directory similar to the following command:

> ./configure --prefix=/Users/john/NNE_deps/

Then, after typing 'make', simply type 'make install'
for each dependency (without the sudo command described in the basic installation guide).

Each of these dependencies will place files into a include/ and lib/ sub-directory of the directory you specified as the configured 
prefix. NeuronetExperimenter's configure script needs to be able to find these, so like the standard Unix configure command, you need to pass this information to the configure script in the following manner:

> ./configure --includedir=/Users/john/NNE_deps/include --libdir=/Users/john/NNE_deps/lib

The addition of these 
arguments is only necessary the first time you run the script as the options are cached for later execution of the configure script. To revert back to the default installation paths, remove the .configure.conf file, which is located in the same directory as the configure script.

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