Using Jupyter for Classroom

OSC provide an isolated and custom Jupyter environment for each classroom project that requires Jupyter Notebook or JupyterLab. 

The instructor must apply for a classroom project that is unique for the course. More details on the classroom project can be found in our classroom project guide. Once we get the information, we will provide you a project ID and a course ID (which is commonly the course ID provided by instructor + school code, e.g. MATH_2530_OU).  The instructor can set up a Jupyter environment for the course using the information (see below). The Jupyter environment will be tied to the project ID.

Set up a Jupyter environment

Once the project space is initialized and the classroom is configured, the PI will receive a notification from OSC. Then, the instructor can proceed with the following steps to set up a Jupyter environment for the classroom.

1. Log in to class.osc.edu using the PI account associated with the classroom project.
2. Click on the Classroom Jupyter app.
3. In the Classroom dropdown list, locate and select your course ID. 
4. Click launch.

It may take a few minutes for the Jupyter environment to initialize. Once ready, you will be redirected to the JupyterLab interface, as shown below.

Manage the Jupyter environment

Install packages

Once the Jupyter environment is ready, you can open a notebook and install packages using the following command:

pip install --no-cache-dir --ignore-installed [package-name]

Note: The --no-cache-dir and --ignore-installed flags prevent pip from using cached packages stored in the user’s home directory. This helps avoid conflicts, especially if you’ve previously installed packages across multiple Python environments.

Packages installed via pip are available to all participants in the classroom environment. For this reason, participants are not permitted to install packages themselves. As a result, any commands they run that attempt to download data to a system-wide Python location will fail. To resolve this, either install the required data as the classroom owner, or instruct participants to set the download path to a location they have write access to. For example:

import os
nltk.download('stopwords', download_dir=os.environ['NOTEBOOK_ROOT'])

Install extensions

Jupyter Notebook

To enable or install nbextension, please use --sys-prefix to install into the classroom Jupyter environment, e.g.

!jupyter contrib nbextension install --sys-prefix

Please do not use --user, which install to your home directory and could mess up the Jupyter environment.

JupyterLab

To install labextension, simply click Extension Manager icon at the side bar

Enable local package access (optional)

By default this Jupyter environment is an isolated Python environment. Anyone launches python from this environment can only access packages installed inside unless PYTHONPATH is used. The instructor can change it by setting include-system-site-packages = true in /fs/ess/project_ID/course_ID/jupyter/pyvenv.cfg. This will allows students to access packages in home directory ~/.local/lib/pythonX.X/site-packages ,and install packages via pip install –user

Workspace

When a class session starts, we create a classroom workspace under the instructor's and students' home space: $HOME/osc_classes/course_ID, and launch Jupyter at the workspace. The root /  will appear in the landing page (Files) but everything can be found in $HOME/osc_classes/course_ID on OSC system.

Shared Access

Share class material

The instructor can upload class material to /fs/ess/project_ID/course_ID/materials . When a student launch a Jupyter session, the diretory will be copied to the student's worksapce $HOME/osc_classes/course_ID . The student will see the directory materials on the landing page. PI can add files to the material source directory. New files will be copied to the destination every time when a new Jupyter session starts. But If PI modifies existing files, the changes won't be copied as the files were copied before. Therefore we recommend renaming the file after the update so that it will be copied

Use data dir for large files

For large files, create a data dir to the classroom and place the large files there.

mkdir /fs/ess/project_ID/course_ID/data

Now the large data will not be copied to each user's home dir when they start a classroom job session. Make sure to reference this data properly in notebooks that will be copied to students home dirs from the /materials dir.

Access student workspace

The instructor and TAs can access a student's workspace with limited permissions. First, the instructor sends us a request with the information including the instructor's and TAs' OSC accounts. After a student launches a class session, you can access known files and directories in the student's workspace. For example, you cannot explore the student's workspace

ls /users/PZS1234/student1/osc_classes/course_ID
ls: cannot open directory /users/PZS1234/student1/osc_classes/course_ID: Permission denied

but you can access a known file or directory in the workspace

ls /users/PZS1234/student1/osc_classes/course_ID/homework