Compute Quick Start

Compute Resources

Connecting via SSH

  • If you are off campus, you will need to use a VPN to access compute1.

  • Instructions for accessing the WashU VPNs can be found here:

  • If you run into issues using the VPN, you will need to follow the directions in the previous link to contact WashU IT proper.


  • WashU has several VPNs. compute1 can be accessed from the following VPNs:


  • If you are not familiar with a command line interface or would prefer a GUI, you only need to connect via SSH once.

  • You can use SSH to connect to the compute platform with your WUSTL Key (single sign on) and password.

  • E.g.


Where to SSH From

  • If you are using Windows, you can use SSH from either the command prompt or powershell if you have Windows 10 or 11.

  • Or you can use a software like PuTTY or MobaXterm .

  • If you use a Mac or Linux, you can use the built in terminal to connect via SSH.

Connecting to Open On Demand (OOD)

  • OOD is a web browser based interface that connects to compute resources, in this case, the RIS Compute Platform.

  • If you have logged in via SSH at least once, you can point your browser to .

  • Once you’re logged into OOD you can:
    • Start up one of the applications installed (Jupyter, Matlab, Rstudio, Relion3,Stata)

    • Use one of the RIS noVNC created Docker images (found here) via the Custom noVNC Image application.

    • Start up the Compute RIS Desktop to use a more traditional HPC environment via the module load system. You can find more on the THPC here.


Starting Up an Application in OOD

  • All of the applications, including the Compute RIS Desktop and Custome noVNC image, have the same base fields.

../../_images/application-fields-1.png ../../_images/application-fields-2.png
  • The base fields are as follows:
    • Mounts
      • This is where you input your storage allocation information.

      • The format for this is based of the linux format and looks like: /storage1/fs1/${STORAGE_ALLOCATION}/Active:/storage1/fs1/{$STORAGE_ALLOCATION}/Active

      • ${STORAGE_ALLOCATION should be replaced with the name of your storage allocation.

      • The name before the colon is the full path of your storage allocation.

      • The name after the colon is what you would like the path to be named in the application. (We recommend leaving it the same.)

      • More information on storage allocation can be found here.

    • Job Group
      • The default Job Group should be something like wustlkey/ood

      • This field should be automatically filled in and does not need to be changed.

      • If you wish to know more about job groups, you can find the information here.

    • User Group
      • This is a drop down menu of the compute groups a user is part of.

      • This does not need to be changed if the user is a member of a single group.

    • Queue
      • This is a field where the user can input which queue they would like to use.

      • Only queues that the user is part of are valid. If you are not part of a queue, you job will error.

      • All restrictions on a queue are still in effect, even if the job is launched through OOD.

    • SLA Name
      • This field is for users who are part of a subscription tier and can be ignored by general and condo users.

      • More information about subscriptions and SLA can be found here.

    • Memory (GB)
      • This is the amount of memory or RAM you want to give the job.

      • This is constrained by the selected queue and the amount of physical memory available on hosts in that queue.

    • Number of hours
      • This is the number of hours you want your job to run.

      • This is limited by the queue chosen.
        • general queue limit is 28 days or 672 hours

        • general-interactive queue limit is 24 hours

    • GPUs to Allocate
      • This is the number of GPUs you wish to have available for your job.

      • This is limited by the number of GPUs available to GPU hosts in the chosen queue (typically 4).

      • You can find more information about GPUs here.

    • Number of processors
      • This is the number of processors or CPUS you wish to have available for you job.

      • This is limited by the number of CPUs available to hosts in the chosen queue (varies).

      • You can find more information about CPUs here.

    • Font Size
      • This is a drop down menue that you can use to select how big you want the font in your job.

  • Some applications have fields that are specific to them. They will have a description of what’s required for that field.

  • Once you have filled in the appropriate fields, you click on the launch button and your job will be launched.

Using the Compute RIS Desktop to Access the THPC Environment

  • The THPC environment uses Lmod to dynamically control the environment through use of module files.

  • Here are the official docs for guidance beyond these basic commands.

  • Shorthand exists for these module commands as well. Use ml -h in a job session.

  • Loading modules without specifying a version will result in the default module being loaded.

  • Default module versions are denoted with (D) in the listing if more than one version is available.

  • To view what modules are available you use module avail via the terminal.

  • To list what modules are currently loaded you use module list.

  • To load a module you use module load package where package is the name of the module.

  • To unload a module you use module unload package.


Using the Custom noVNC Image to Load Additional or Personalized Software

  • This application does not have a preset Docker image, the user supplies one.

  • The list for software developed to be used this way, can be found here.

  • If you create a Docker image using these images as a base, you can use that container here as well.

  • There are two additional fields in this application that are important.
    • Environment Variables
      • This is where you put environment variables that the image needs to run.

      • E.g.
        • PASSWORD=password

        • PATH=/opt/conda/bin/:$PATH

      • Necessary variables for an image are included in their individual documentation pages.

    • Docker Image
      • This is where you put in the name of the Docker image you wish to use, including any tags.

      • E.g.



Further Information about the Compute Platform