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


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

Mac OS X

  1. Prerequisites
  2. Installing StochSS

Linux

Windows

  1. Prerequisites
  2. Installing StochSS
  3. Running the Windows Launch Script
  4. Additional Info

Various StochSS introductory tutorials are provided on the Documentation page


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.
  • Starting with version 1.4, StochSS under Mac OS X requires the R language, the GNU Scientific Library (GSL)  and the FEniCS software package to be installed.

2.  Installing StochSS

  • If you have an earlier version of StochSS (1.3 or older) installed on your computer under /Applications/StochSS and in case you are planning to install the new version under the same path, we strongly suggest you to move the directory containing the old version of StochSS to another location on your computer. You can also simply rename it. This way the folders containing your model files and the output from your completed simulations will remain stored on your computer even after the installation of the new StochSS version. We are planning to automate the process of saving and transferring data (model files and output files) in a future release.
  • 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.
  • In the last two Mac OS X versions (Mountain Lion and Mavericks) the installation of software that doesn’t come from a “verified source” or from the Mac App Store is not permitted by default. This new security feature is called GateKeeper. 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. Then, right-click on the .dmg file icon and choose Open. Click the “Open” button on the next dialog warning to launch the app anyway. The installation can now start.
  • 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.
  • Keep in mind that when you launch the StochSS application for the first time, StochKit2 and the ODE wrapper are automatically installed. This installation process will take a few minutes to complete as both packages compile from source.
  • 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

  • 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.1.4.0.tgz
cd stochss.linux.1.4.0
  • StochSS requires gcc, g++, make, git, and libxml2 installed 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 installed. This installation process will take a few minutes to complete as some of those packages compile from source.
  • 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 !
Note: If you are working on a Mac and you are looking for an alternative way to download and install StochSS, you can follow these instructions. The only difference is that you have to run the script run.mac.sh from the StochSS directory to start StochSS on your Mac. 

Windows

For Windows systems we offer support for launching StochSS instances in EC2 cloud. You need to have Python installed on your Windows box.

1.  Prerequisites

  • Download the Python Windows MSI Installer from http://www.python.org/download and run it to install Python on your system.
  • Once the installation is finished, open up the Command Prompt application and type:
dir C:\py*
  • If this command outputs the name of a folder, then Python has been successfully installed on your computer. The folder name is how you will call Python. It is likely “Python27”, in which case you would call Python with the following command:
C:\Python27\python.exe

2.  Installing StochSS

  • Expand the tarball using your preferred File Decompressing Software Package.
  • Open the Command Prompt application and navigate to the StochSS folder.
  • Type in and execute the following command:
C:\Python27\python.exe run.windows.py start

3.  Running the Windows launch script

  • The Windows launch script run.windows.py works by launching a StochSS server remotely using Amazon Web Services (AWS). In order to use AWS, you need to register with Amazon and obtain some credentials. The script will look for these credentials in two places before prompting you to enter them: first in the environment variables AWS_ACCESS_KEY and AWS_SECRET_KEY, and if they are not present it will then check the configuration file that accompanies the script. The configuration file, called .ec2_config, is where the script stores all of the variables for the script, such as the AWS credentials and the instance ID of the current StochSS server. You can edit this file directly and if a valid entry exists in this file, it will be used by the script.
  • At the completion of a successful StochSS launch and installation process a web browser page opens and prompts you to log in.
  • Type in your email address and log in (password is not required).
  • Congratulations, you are now ready to use StochSS remotely via AWS !
4.  Additional Info
  • When executing the script, you must pass in the name of a command:
C:\Python27\python.exe run.windows.py command_name
  • Supported command names and their descriptions follow:

command_name = ‘start’ 

The start command launches the StochSS server remotely using AWS Elastic Compute Cloud (EC2). Upon successfully starting, the script will save the instance ID to the configuration file for future use.

command_name = ‘stop’ 

The stop command stops the remote machine that is hosting the StochSS server. The script will only stop the remote machine, meaning any of the data associated with that StochSS server will still be accessible by running the start command again with the same instance ID.

command_name = ‘terminate’

The terminate command will terminate the StochSS server with the instance ID listed in the config file. This termination implies that all of the data associated with that StochSS server will be deleted as well.