Operating System Compatibility

STI-GMaS is built for, and tested against, an Ubuntu Lucid Lynx (12.04 LTS) operating system. The software should also be compatible with other linux based operating systems (including newer versions of Ubuntu) and Mac OS X, provided that they meet the the requirements of CHASTE given here, and are compatible with the software listed below.

Download & Install STI-GMaS (Linux/Mac)

Pre-requisite Software

  • Java (version 1.5 or higher). [Homepage]

     

  • CHASTE version 3.1 (and associated libraries). [Homepage]

    • To install on ubuntu, first add the CHASTE repository to your pacakage manager's configuration. Type

         sudo gedit /etc/apt/sources.list.d/chaste.list

      and add the following text

         deb http://www.cs.ox.ac.uk/chaste/ubuntu /

    • Then install the CHASTE public licence key:

         sudo apt-key adv --recv-keys --keyserver hkp://keyserver.ubuntu.com:80 422C4D99

    • Then, to install CHASTE and its dependencies:

         sudo apt-get update
         sudo apt-get install --install-recommends chaste-dependencies
         sudo apt-get install chaste-source=3.1

    • Unpack the CHASTE source as follows:
         cd $HOME
         tar -jxf /usr/src/chaste-source.tar.bz2
      This will create the directory $HOME/chaste-source

    • Set the following environment variables by typing e.g. "sudo gedit ~/.bashrc" and adding the following lines at the end of the file:
        
      export CHASTE=[location of chaste home directory]
         export CHASTE_TEST_OUTPUT=[location of chaste simulation results]
         export LD_LIBRARY_PATH=$CHASTE/lib
      Save the file and close your terminal window.

    • To check the build has been successful, in a new terminal window, type

         cd $CHASTE; scons
       

  • Paraview. [Homepage]

    • On ubuntu, install via: "sudo apt-get install paraview".

    • Ensure that the command 'paraview' is in the standard executable path.

Download & Install

  • Download the source code: STI-GMaS is available as a bolt-on project to the CHASTE software, and can be downloaded from here. New users will be required to enter their details into the form at the bottom of this page, and select

                             projects/STI-GMaS_v1.2_release_3.1_Linux.tgz

    as the file to download. Save this tarball file into the "$CHASTE/projects" folder. Unpack the tarball as follows:

    • cd $CHASTE/projects; tar -xvzf STI-GMaS_v1.1_release_3.1.tgz
       

  • Set the following environment variable by typing e.g. "sudo gedit ~/.bashrc" and adding the following line:

    • export STIGMAS=$CHASTE/projects/STI-GMaS/apps/src
       

  • To compile the CHASTE executables, in a new terminal window, run the following command:

    • cd $CHASTE; scons b=GccOptNative cl=1 exe=1 $STIGMAS
       

  • Run STI-GMaS by typing the following:

    • cd $STIGMAS; java -jar STI-GMaS.jar

© Copyright 2014 STI-GMaS Development Team. All rights reserved.