How do I get started with Jupyter Notebooks?

What is the Jupyter Notebooks service?

Jupyter Notebooks are available to all users at notebooks.msi.umn.edu. This interactive computing environment requires only a web browser, and enables data analysis and visualization on our HPC resources in a shareable, reproducible notebook format. Notebooks currently supports both the JupyterLab and Classic Notebook interfaces, computation with the Python (version 2 and 3) and R languages, and can also interoperate with user-installed Jupyter environments. MSI Python tutorial materials provide a useful overview.

This is an MSI Beta service and may receive updates at any time.

There are many excellent tutorials and videos online that explain how to use Jupyter Notebooks.

How do I connect to Notebooks at MSI?

You can connect to the Jupyter Notebooks service using any modern web browser. You do not need to install any special software. If you are off-campus you will need to connect through the University VPN.

  1. To begin, visit notebooks.msi.umn.edu in your browser. You will be prompted to log in with your University InternetID. You will be asked to select your group if you belong to more than one group.
  2. If you do not already have a running Jupyter session, you will be prompted to "Start My Server".
    If your Jupyter Notebooks server is already running, you will be redirected directly to your running session.
  3. On the "Server Options" page, select a job type (see below for additional information) and click "Start" to start your session.
  4. Please be patient. Usually your Jupyter Notebooks server will start in under a minute, but during busy periods you may have to wait up to several minutes, especially if you have selected one of the larger job types.
  5. Once your session starts, you will be redirected to the JupyterLab interface. You can start new notebooks, command line terminals, and other resources by clicking icons in the launcher. You can browse, open, and manage files via the directory view in the left sidebar.
  6. Your session is hosted by a running job, and will continue running if you close your web browser or even log out. You can reconnect to your running session by logging in to notebooks.msi.umn.edu (including from another computer or a different location).
  7. When you are done working, you should end your session to release the compute resources for other users. From the "File" menu at the top of the work area, select "Hub Control Panel" and press "Stop My Server". Unless you end your session, your server will continue running and consuming resources until the requested time runs out, even if you log out or close your web browser.

What do the "Server Options" mean?

Your session is provided by a Jupyter Notebook server running on your behalf on a scheduled HPC resource. Behind the scenes a job is created and scheduled to run for you. The "Server Options" form allows you to select the resources requested for that job. The currently supported options include:

  • Mesabi Interactive - 3 cores, 8 GB, 12 hours, 48 GB local scratch (this is the default option and will usually start very quickly)

  • Mangi AMD Medium - 2 cores, 32 GB, 4 hours, 64 GB local scratch

  • Mesabi High-mem - 12 cores, 128 GB, 4 hours, 180 GB local scratch

  • Mangi AMD wide - 24 cores, 45 GB, 4 hours, 75 GB local scratch

  • K40 GPU session - 12 cores, 60 GB, 4 hour, 100 GB local scratch, 1 K40 GPU

You can only have one Jupyter session active at a time, so in order to switch to another job type, you must stop your server (see step 7 above) and restart it with another server option selected. For larger parallel tasks, you can also start new jobs using Slurm commands from a terminal.

What happened to the old notebook interface?

MSI recently made JupyterLab the default interface for the Notebooks service. The previous interface is now called the Classic Notebook. We hope this modern interface allows a smoother and more productive experience. Some important differences include:

  • Classic Notebook opened notebooks, terminals, etc in new browser tabs. JupyterLab opens them in a unified workspace in a single tab.
  • Classic Notebook created new notebooks and other resources via a "New..." menu. JupyterLab uses a launcher panel with prominent icons.

Please see the JupyterLab documentation for more details, including a detailed tour of the interface and features. If you prefer to use the Classic Notebook interface, it is still available via the "Help" menu in the menu bar.

Category: 
interactive