StochSS Installation Instructions

Before you start
StochSS will not work if its installation path contains spaces. For example, the following will not work: 

/home/myhome/my applications folder/StochSS

The path below represents a viable alternative. Note that the spaces have been replaced with the underscore character.

/home/myhome/my_applications_folder/StochSS

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Obtaining and Installing StochSS under Mac OS X, Linux and Windows
Mac OS X

1. Prerequisites
2. Installing StochSS

Linux

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Various StochSS introductory tutorials are provided on the Documentation page

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Mac OS X
If the last version of Xcode is already installed on your Mac, skip to Installing StochSS.
1.  Prerequisites

• Running StochSS under Mac OS X requires you to have the the latest version of Xcode installed on your computer. Xcode can be downloaded from the Mac App Store.

• Download and install R following the instructions at http://cran.r-project.org/bin/macosx/

• Download and install GSL following the instructions at http://www.gnu.org/software/gsl/.  As an alternative you can install GSL using Homebrew.

• Download and install FEniCS following the instructions at http://fenicsproject.org

2.  Installing StochSS

• Download the latest version of StochSS

• Once the download has completed, the disk image (.dmg file) should mount and a new window should appear on your desktop. If the .dmg file does not mount automatically you should be able to find it in your default download folder (typically ‘/Users/yourhomefolder/Downloads’). Double click on the file to expand and mount.

• Newer Mac operating systems may prevent StochSS from launching. If the following alert dialog appears on your screen: “StochSSserver can’t be opened because it is from an unidentified developer”, just click on the OK button to close it. This error is caused by Apple’s Gatekeeper which by default prevents users from using applications from anywhere but the App Store. Disable Gatekeeper for StochSS to proceed.

• Drag the StochSS folder to the Applications folder.

• Navigate to the Applications folder and double click on the StochSS folder icon to open it. This folder contains the StochSS application (StochSSserver.app) and a subfolder named ‘examples’ where a number of StochKit2 example model files are stored.

• Double click on the StochSS application to launch. A log window showing the details of the launching process will appear on your screen. Note: Apple’s Gatekeeper can cause problems here too. If it does, bypass it again.

• Keep in mind that when you launch the StochSS application for the first time, a number of additional software packages are automatically built inside StochSS. This installation process will take a few minutes to complete.

• At the completion of a successful StochSS launch and installation a web browser page opens and prompts you to log in.

• Congratulations, you are now ready to use StochSS on your Mac !

Linux

• Download the StochSS Linux tarball

• Move the StochSS tarball to a directory of your choice. Make sure that the full path of that directory does not contain any spaces.

• Use the terminal to navigate to the directory containing the StochSS tarball and    type in the following two command lines:

tar -xzf stochss.linux.1.6.1.tgz
cd stochss.linux.1.6.1

• StochSS requires gcc, g++, Make, Git, and libXML2 along with the Python libraries h5py, Numpy, Scipy, Matplotlib, and FEniCS to run. If you wish to, install these packages manually and then execute ./run.generic.sh to launch StochSS. However, for Ubuntu the special runscripts ./run.ubuntu.sh can be used to install the required packages automatically before running (requires sudo).

• Keep in mind that when you launch the StochSS application for the first time, a number of additional software packages are automatically built inside StochSS. This installation process will take a few minutes to complete.

• At the completion of a successful StochSS launch and installation process a web browser page opens and prompts you to log in.

• Congratulations, you are now ready to use StochSS on your Linux box !