Using the Oscar HPC Cluster

Long-term visitors to ICERM are provided with an exploratory account on the Oscar high performance computing cluster maintained by Brown's Center for Computation and Visualization. Oscar access may also be provided to short-term visitors on a case-by-case basis with advance notice.

Oscar can be used via SSH terminal or via the Oscar VNC client. The Oscar VNC client is preinstalled and available on the thin clients in all ICERM 10th floor offices and the graduate student workspace in the 10th floor lobby.

VNC Login Instructions

  1. On the IGEL Thin Client desktop, double click on the Oscar VNC icon to open the Oscar VNC Client.
  2. When the login screen opens, enter your CCV username and password and click Connect.
  3. A second popup window will then open asking you to select parameters for your VNC session. Select the best option for the work you plan to do. Choosing more cores and RAM will give you more computational resources but reduce the maximum session time. Once you have selected the option you prefer, click Create VNC Session.
  4. The cluster will submit your VNC session into the queue. You'll see a window similar to the screenshot below. It usually only takes a minute or two for the queue to process and the desktop to launch.
  5. Once the session has been created, the VNC desktop will launch (as seen below). You can then utilize the session just like a normal desktop.
  6. When finished with your VNC session, click the green EXIT button on the top left. You will have the option to either suspend your VNC session or kill it completely. If you plan to reconnect and resume work in a short period of time, use the disconnect option to suspend your session. If not, you can kill the session.
    ** If you choose to suspend your session, please keep in mind that it will only persist as long as the original session length.

SSH Login Instructions

  1. Open a terminal prompt. On the ICERM thin clients, enter the username user and the password icerm to log in to the terminal.
  2. In the terminal, type ssh <your ccv username>@ssh.ccv.brown.edu. If you are asked to verify the authenticity of the host 'ssh.ccv.brown.edu', type yes.
  3. You will now be prompted for your password. Enter your password (nothing will show up when you type in the terminal password prompt) and press enter.
  4. Once logged in, you should see a "Welcome to Oscar!" message. This means you're now connected to one of the login nodes, which you can use to manage your files and submit batch jobs. Please DO NOT run any computations directly on the login nodes. Use the batch system to submit your computations to the queue to be processed on the computation nodes.

Loading Modules Like Mathematica and Sage

Oscar has a large library of software available on the cluster, but only a few apps are pre-loaded in to your sessions. The commands below will allow you to list all available modules, search the list of modules, and load/unload software packages. When using Oscar over VNC, you must open the Terminal Emulator to run these commands.

  • To view all available software packages, type module avail.
  • To search the list of available packages, type module avail <package>.
    For example, to search for all available versions of mathematica: module avail mathematica. Many packages, like Mathematica, have multiple versions available. This command lets you see all available versions of the package you searched for.
  • To load a package into your session, type module load <package/version>.
    For example, module load mathematica/11.0. This will load the Mathematica 11.0 into your session and make it available for use.
  • To unload a package you are no longer using, type module unload <packagename>
Loading and Launching Mathematica
  1. Open the Terminal and use the following commands at the command line.
  2. module avail mathematica to list all the available mathematica versions.
  3. module load mathematica/11.0 to load mathematica. This command should return confirmation "module loaded".
  4. mathematica to launch the Mathematica app.
Loading and Launching Sage
  1. Open the Terminal and use the following commands at the command line.
  2. module avail sage to list all the available Sage versions.
  3. module load sage/8.2 to load Sage. This command should return confirmation "module loaded".
  4. sage to launch the Sage console within your Terminal window.
Installing Sage Packages with --user

It is possible to install most Sage packages locally to your home folder by passing the --user parameter at the end of your install command. See below for example steps to install the Sage packages "surface_dynamics" and "sage-flatsurf". In this example, we are loading both packages from git repositories, so we need to load the git module as well as Sage.

  1. module load sage/8.2
  2. module load git
  3. sage -pip install git+https://gitlab.com/videlec/surface_dynamics --user
  4. sage -pip install git+https://github.com/videlec/sage-flatsurf --user
Installing MATLAB Packages such as YALMIP

MATLAB script packages, such as YALMIP, can be installed directly by the user on their Oscar account. These instructions assume you are using Oscar via the VNC client.

  1. Open the Terminal on your VNC session.
  2. Navigate to your home folder.
    cd ~
  3. mkdir -p MATLAB
  4. wget -O yalmip.zip https://github.com/yalmip/yalmip/archive/master.zip
  5. unzip yalmip.zip
  6. In MATLAB, add the YALMIP-master directory to your path.
    1. In the MATLAB file browser, navigate to the MATLAB folder you created in your home folder.
      cd ~/MATLAB
    2. Right click on the YALMIP-master folder.
    3. Select Add to Path > Selected Folders and Subfolders. This adds the YALMIP folders to your path.
  7. To save your MATLAB path, use the savepath command in the MATLAB command prompt.
    savepath ~/MATLAB/pathdef.m

YALMIP also requires a solver like SDPT3. The steps below add SDPT3 to MATLAB.

  1. Open the Terminal.
  2. cd ~/MATLAB
  3. wget -O sdpt3.zip https://github.com/sqlp/sdpt3/archive/master.zip
  4. unzip sdpt3.zip
  5. In MATLAB, add the sdpt3 directory to your path.
    1. In the MATLAB file browser, navigate to the MATLAB folder you created in your home folder.
      cd ~/MATLAB
    2. Right click on the sdpt3-master folder.
    3. Select Add to Path > Selected Folders and Subfolders. This adds the SDPT3 folders to your path.
  6. To update/save your MATLAB path, use the savepath command in the MATLAB command prompt.
    savepath ~/MATLAB/pathdef.m

Important Notes About the Oscar Cluster

  • As mentioned above, please do not run any computations or simulations on the login nodes, as they are shared with other users. Use SLURM to submit a batch job to the queue for computations.
  • The full Oscar User Manual is available on the CCV website.
  • Oscar uses SLURM for batch job management. Detailed information on submitting jobs is available Oscar User Manual.
  • CCV has a large library of software already installed on the cluster. For a full list of available software, run the command module avail. More information about Oscar's software packages are available in the Oscar User Manual. If you require a software package that is not currently available on the Oscar cluster, please contact ICERM's IT staff and we will work with CCV to get the software installed.
  • Users can install sub-packages for some modules (like Sage and Python) to their home folders on their own by using the --user as an option in the install command. For example, with Sage, the command would be something like sage -i <package name> --user.
  • The Oscar VNC Client is a Java application that can be installed on most laptops with Java installed. If you wish to install the client on your own laptop, please make sure to download the latest version of CCV VNC Client 2.0+ to ensure proper support and compatibility.

If you have questions about these instructions or require further assistance, please contact the ICERM IT staff by dropping by the administrative offices or emailing support@icerm.brown.edu.