Tutorial

#Introduction

This tutorial will walk you through installing and setting up Fijee on your system.

Before you begin please read the following disclaimer

Fijee and some of the libraries required to build/run FIJEE are under development, 
as such they are considered unstable at best. It is not recommended to attempt to 
install on a mission critical system where data loss is unacceptable. This tutorial 
will walk you through installing FIJEE on a clean system, you will be asked to make 
modifications to the system that may compromise stability, including installing
unsupported or experimental software and modifying system settings. 

This tutorial is targeted for users familiar with the linux operating systems, but not necessarily familiar with programming.

#System Configuration

Before we install Fijee and its dependencies, we must make sure that the system we are using is set up to make everything as painless as possible.

The easiest way to test FIJEE on your system with minimal modification is to use a virtual machine, it is planned to distribute Fijee as a virtual machine image that can be loaded on a variety of hardware, for now however, we will assume that you either have access to a free machine or can set up a VM without our assistance.

##Operating System

This tutorial is targeted at Ubuntu 12.04 (precise), it has a good mix of support (As an LTS release it will be supported until 2017 with security and other updates) and stable software repositories.

The recomended version for this tutorial is the Ubuntu 12.04 server edition, it is also recomended to install a minimal desktop environment in order to minimize the packages that will conflict with our modifications.

Build-tools

Because Fijee is currently a source-only distribution, you must install utilities neccessary for compiling and linking the fijee executable.

Ubuntu has a convenient meta-package for installing the core set of utilities for building software. In a terminal window run the following command

$ sudo apt-get install build-essential

Fijee software is distributed via GIT, a modern Version Control System. To install git perform the following

$ sudo apt-get install git-core

Compiler Set Up

Unfortunately the version of the Gnu Compiler tools that are in the repositories for 12.04 are a little out of date. There has been considerable progress in the last few years on updating and standardizing the C++ language, and this older version of GCC does not support a number of features that is necessary to build Fijee.

Fortunately there is a considerable amount of community support for LTS releases, including "backports" or newer software versions packaged for older releases. In order to install GCC/G++ version 4.8 perform the following operations in a terminal

$ sudo apt-add-repository ppa:ubuntu-toolchain-r/test
$ sudo apt-get update
$ sudo apt-get install gcc-4.8 g++-4.8
$ sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 50

This will configure your system to pull package from a "Personal Package Archive", PPA's are used by the community and open source projects to easily distribute packages to ubuntu users. This particular PPA contains new versions of the compiler tools for us to use. update-alternatives updates system shortcuts to point to the new version of g++ in a manageable way. To verify that the right version of g++ is installed do the following

$ g++ --version

Which should show something similar to:

g++ (Ubuntu 4.8.1-2ubuntu1~12.04) 4.8.1
Copyright (C) 2013 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

OpenCL

TODO

##Instalation

##Testing

#Installing FIJEE

With our system set up we can begin the process of building FIJEE for your system

##Getting dependencies

The dependcies required to build FIJEE are packaged in a PPA, in order to install these dependcies run the following commands

$ sudo add-apt-repository ppa:akshmakov/fijee-dev-ppa
$ sudo apt-get update
$ sudo apt-get install libeigen3-dev libcgal-dev libvtk5-dev dolfin-yann-dev libviennacl-dev \
               python-vtk libnifti-dev libtrilinos-dev

##Getting Fijee

The Fijee source code is available on a publically available git repository. Downloading this source is as easy as running one command

$ git clone https://github.com/Fijee-Project/Fijee.git

##Building FIJEE

With the dependencies installed from the PPA building FIJEE is as easy as executing 5 commands:

$ cd Fijee
$ mkdir build
$ cd build
$ cmake ../
$ make

At which point you can go and relax for 30-60 minutes as the build process will take a little while (depending on system specs) if everything is in order the output should show a consitent stream of lines like the following

[  9%] Building CXX object Mesh_rendering/CMakeFiles/inrimage.dir/VTK_implicite_domain.cxx.o

##Configuring FIJEE

TODO

#Running Fijee

TODO