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
Set up a Jupyter environment
The instructor can set up a Jupyter environment for the course once the project space is initialized:
- Login to Owens or Pitzer as PI account of the classroom project.
- Run setup script with the
~support/classroom/tools/setup_jupyter_classroom /fs/ess/project_ID course_ID
If the Jupyter environment is created successfully, please inform us so we can update you when your class is ready at class.osc.edu.
Upgrade a Jupyter environment
You may need to upgrade Jupyter kernels to the latest stable version for a security vulnerability or trying out new features. Please run upgrade script with the
project ID and
~support/classroom/tools/upgrade_jupyter_classroom /fs/ess/project_ID course_ID
Manage the Jupyter environment
When your class is ready, launch your class session at class.osc.edu. Then, open a notebook and use the following command to install packages:
pip install --no-cache-dir --ignore-installed [package-name]
Please note that using the
--ignore-installed flags can skip using the caches in the home directory, which may cause conflicts when installing classroom packages if you have previously used pip to install packages in multiple Python environments.
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.
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
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.
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.
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