Jupyter Labs on Oscar
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The anaconda modules provide jupyter-lab. Users can also use pip or anaconda to .
There are a couple of ways to use Lab on Oscar. You can run a Jupyter Lab
in an
using a batch job
in an interactive session
With the batch job or interactive session method, you use a browser on your machine to connect to your Jupyter Lab server on Oscar.
Do not run Jupyter Lab on login nodes.
Start an session, and open up a terminal in the VNC session. To start a Jupyter Lab, enter
This will start the Jupyter lab server and open up a browser with the lab.
Submit an ssh tunnel to the server.
Set up an ssh tunnel to the server.
Open a browser to view the lab.
Use scancel to end the batch job when you are done.
Here is an example batch script to start a Jupyter Lab server on an Oscar compute node
This script can be found in ~/batch_scripts. Copy this example and submit this script with
sbatch jupyter.sh
Once your batch job is running there will be a file named jupyter-log-{jobid}.txtcontaining the information you need to connect to your Jupyter lab server on Oscar. To check if your job is running, use myq.
The output from myq will look something like this:
In this example the jobID is 7239096. To view the lab server information, use cat. For this example:
cat jupyter-log-7239096.txt
Open a terminal on your machine and copy and paste the ssh -N -L ........ line into the terminal.
Enter your Oscar password. Note it will appear that nothing has happened.
Open a browser on your local machine to the address given in cat jupyter-log-{jobid}.txt.
The lab will ask for a token. Copy the token from jupyter-log-{jobid}.txt. Then your lab will start.
Remember to scancel {jobid} when you are done with your notebook session
Start Jupyter Lab in an interactive job
Setup an ssh tunnel to the server.
Open a browser to view the notebook.
Use scancel to end the batch job when you are done.
An output similar to the one below indicates that Jupyter Lab has started:
$ jupyter-lab --no-browser --port=$ipnport --ip=$ipnip
[I 13:12:03.404 LabApp] JupyterLab beta preview extension loaded from /gpfs/runtime/opt/anaconda/3-5.2.0/lib/python3.6/site-packages/jupyterlab
[I 13:12:03.404 LabApp] JupyterLab application directory is /gpfs/runtime/opt/anaconda/3-5.2.0/share/jupyter/lab
[I 13:12:03.410 LabApp] Serving notebooks from local directory: /gpfs_home/yliu385
[I 13:12:03.410 LabApp] 0 active kernels
[I 13:12:03.410 LabApp] The Jupyter Notebook is running at:
[I 13:12:03.410 LabApp] http://172.20.209.7:9414/?token=dd9936098d03b8195fc626f017c97ca56a054887d134cb1e
[I 13:12:03.410 LabApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 13:12:03.411 LabApp]
Open a terminal on your machine and enter the following line (replace $ipnip and $ipnport with the values from the two echo commands in the previous step).
Enter your Oscar password. Note it will appear that nothing has happened.
Open a browser on your local machine to the address:
Again, you need to replace $ipnport with the value from the first echo command in Step 1. The notebook will ask for a token. You can copy the token from the output from Step 2.
Once you finish and no longer need the Jupyter Lab server, you can kill the server by pressing Ctrl+C twice in your interactive session.
If you are using Windows, follow the documentation to complete this step.
Start an and then in your interactive session enter the following:
If you are using Windows, follow the documentation to complete this step.