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: Connect - Information Technology

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

• 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.

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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 http://ood.ris.wustl.edu .

• 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.

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Starting Up an Application in OOD

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

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• 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: /storageN/fs1/${STORAGE_ALLOCATION}/Active:/storageN/fs1/{$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 menu 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.

Navigating Your Job

• Once your job is launched you will be taken to the My Interactive Sessions part of OOD.

• Here you can see all of the sessions you have running.

• There are 3 states to a job.

  • Queued

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  • Starting

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  • Running

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• Once a job is in the Running state, you will have a launch button available. Clicking this will launch you into your chosen application.

• The interface you see will be different based on the application you use, though most will launch you into a linux desktop.

• If you wish to know more about OOD, you can find further documentation here.

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.

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• 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.

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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.

      • http://gcr.io/ris-registry-shared/matlab

      • GitHub

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Connect Using Local VNC Viewer

• Local VNC Viewer

Further Information about the Compute Platform

• If you wish to know more about using the Compute Platform and the command line interface:

  • Check out our Compute Platform FAQ.

  • Check out our workshops/seminars.

  • Check out our more technical documentation.