== Compiling LibRoadRunner for CC3D on Linux (tested on Ubuntu distributions) ==
CC3D git repository contains a copy of a RoadRunner Library which has been customized to work with CC3D. You can find it in ''<CC3D_Git_root>/RoadRunner''. In my case the location is ''/home/m/CODE_TGIT/RoadRunner''.

The compilation of RoadRunner is a two step process. First we build ThirdParty libraries located in ''/home/m/CODE_TGIT/RoadRunner/ThirdParty'' folder and then we build actual RoadRunner library located in ''/home/m/CODE_TGIT/RoadRunner''.

=== Building ThirdParty libraries: ===
==== Cmake Configuration and Makefile generation ====
Open Cmake and point it to source (''/home/m/CODE_TGIT/RoadRunner/ThirdParty'') and build (''/home/m/CODE_TGIT_build/ThirdPartyBuild'') directories:

{{attachment:rrl01.jpg}}

Click configure button at the bottom and Unix Makefiles from pull down menu in the dialog box that pops up, click Finish:

{{attachment:rrl02.jpg}}

After Cmake finishes initial configuration you should get the following screen:

{{attachment:rrl03.jpg}}

Notice, I have changed CMAKE_INSTALL _PREFIX to point to ''/home/m/install_projects/RR_linux''. It is a good idea to change it in your Cmake configuration as well to a directory where you will install RoadRunner.

'''Be careful here''': Next thing we will do is to change build CMAKE_BUILD_TYPE variable from Debug to Release:

__'''IMPORTANT'''__:

You need to determine what type of linux installation you are dealing with because configuration options will depend on it. To check 
linux distribution simply type:

{{{
cat /etc/*-release
}}}

in my case I get
{{{
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=12.04
DISTRIB_CODENAME=precise
DISTRIB_DESCRIPTION="Ubuntu 12.04.2 LTS"
NAME="Ubuntu"
VERSION="12.04.2 LTS, Precise Pangolin"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu precise (12.04.2 LTS)"
VERSION_ID="12.04"
}}}

which tells me that I am on 32 bit machine (I don't see anywhere in the above printout phrases like x86_64 or 64 bit)


If you are on 64 bit linux all you need to do is to change Debug To Release as shown in figure below

{{attachment:rrl04_32bit.jpg}}

If you are on 32 bit linux installation you have to decrease optimization of the C code by changing CMAKE_C_FLAGS_RELEASE to ''-O0 -DNDEBUG'' as shown below:

{{attachment:rrl04_32bit.jpg}}

After clicking Configure and then Generate you will generate Makefiles project for ThirdParty libraries.

==== Compilation of ThirdParty project using command line tools: ====
Open terminal on luinux and go to the directory where the Makefiles are generated - in my case they are in ''/home/m/CODE_TGIT_build/ThirdPartyBuild'' so I type 

{{{
cd /home/m/CODE_TGIT_build/ThirdPartyBuild
}}}

{{attachment:rrl05.jpg}}

To start compilation I type 
{{{

make
}}}

{{attachment:rrl06.jpg}}

After compilation is finished and there are no errors

I type

{{{
make install
}}}

{{attachment:rrl07.jpg}}

and this installs ThirdParty libraries to ''/home/m/install_projects/RR_linux''

=== Building RoadRunner for CC3D on linux (tested on Ubuntu systems) ===
==== Cmake Configuration and Makefile generation ====
Open Cmake and point it to source (''/home/m/CODE_TGIT/RoadRunner'') and build (''/home/m/CODE_TGIT_build/RoadRunnerBuild'') directories:

{{attachment:rrl08.jpg}}

Click configure button at the bottom and Choose Unix Makefiles from pull down menu in the dialog box that pops up, click Finish. You should get the following screen

{{attachment:rrl09.jpg}}

Here we have to change few things:

a) THIRD_PARTY_INSTALL_FOLDER gets changed to ''/home/m/install_projects/RR_linux'' - remember , this is where ThirdParty Libraries were installed

b) CMAKE_INSTALL_PREFIX gets changed to ''/home/m/install_projects/RR_linux'' - we  will be installing core RoadRunnerLibrary there

c) CMAKE_BUILD_TYPE gets changed to ''Release''

d) Click  BUILD_CC3D_EXTENSION option at the top

{{attachment:rrl10.jpg}}

Then click Configure and you should get the following screen:

{{attachment:rrl11.jpg}}

Here we will change CC3D_INSTALL_PREFIX (see the top option in the above screenshot) to /home/m/install_projects/CompuCell3D (I am assuming your base CC3D is in this directory)

{{attachment:rrl12.jpg}}

==== Compilation of RoadRunner project: ====
This is identical to the compilation of ThirdParty libraries:

1) Open terminal and go to ''/home/m/CODE_TGIT_build/RoadRunnerBuild''

{{{
cd /home/m/CODE_TGIT_build/RoadRunnerBuild
}}}

2) type
{{{
make
}}}

to start compilation

3) type

{{{
make install
}}}

to install RoadRunner


Now your CC3D installtion should have RoadRunner installed and all SBMLSolver based simulations should run