Topics

Web-based Computing

Web-based computing is now available on the Yen servers with JupyterHub!. JupyterHub is a platform designed to allow multiple users to launch their own Jupyter notebook servers on a shared system with minimal user effort. Our implementation of JupyterHub currently features several language kernels including Python 3, R, and SAS.

Getting Started

To get started, open a web browser and visit one of the following links for each server:

You will need to login with your SUNet credentials, and then Launch Server. From there, you will have access to the web-based computing services available.

If you are a non-GSB collaborator and don’t have a SUNet, you must request full sponsorship to access Jupyter. You can learn more about SUNet ID sponsorship here.

Features of JupyterHub

We recommend taking a look at the official documentation for JupyterHub if you have any questions on the features below!

Notebooks

Notebooks allow you to write code and execute it within a web browser. Code is written into cells, which can be run in any order, on demand. You can also include text, images, and plots to make your code read like a lab notebook. As of March 2020, the above coding languages are supported. Contact the DARC team if you have a language you would like installed

RStudio

RStudio is also available! Clicking this link will bring up a new tab with a web-based RStudio on the Yens.

SAS

There are a few preliminary steps that need to be taken before SAS can be used on Yens/notebooks.

  • Log into the Yens
  • Install the SAS kernel for Jupyter by running pip3 install sas_kernel
  • Confirm that you see the newly installed SAS kernel by running jupyter kernelspec list
  • Find the location where this new kernel is installed by running pip3 show saspy (it will probably be something like /home/users/{SUNetID}/.local/lib/python3.6/site-packages/saspy)
  • Edit the default SAS path in the sascfg.py file within that directory to be /software/non-free/SAS-langsup/SAS9.4/software/SASFoundation/9.4/sas
  • Restart JupyterHub and start a new notebook with the SAS kernel. After running your first cell, the output should show a successful connection to SAS.

I don’t see Julia on my JupyterHub!

See our FAQ page on how to install it!

Consoles and Terminal

You can also launch interactive consoles from JupyterHub. These will behave very similar to the versions on the Yen servers.

You can also launch a bash terminal from JupyterHub. This provides access to commands you would normally run on the Yens, but through the web browser.

File Upload and Download

One very useful feature of JupyterHub is the ability to upload and download files from ZFS/AFS. First, make sure you are in the proper directory. Then, to upload, click the up arrow on the top left of your screen to select a file.

To download, right click the file you would like, and click “Download”.

Technical Details

File Access and Storage

The JupyterHub instances will automatically launch from your home directory on the Yens. Use the afs-home and zfs directories in your home directory to navigate to your normal file systems.

Installing Packages

JupyterHub will load packages found in your ~/.local/ directory. If you wish to install Python packages from a JupyterHub notebook, run !pip3 install --user <package_name> in a cell. We recommend using similar user-based installs for other package managers.

Technical Limits

The following limits will be imposed on JupyterHub servers:

JupyterHub instance will shut down after 3 hours idle (no notebooks actively running code).

If your processes require more than these limits, reach out to the DARC team for support.