Jupyter Notebooks on Oscar
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The anaconda modules provide jupyter-notebook. Users can also use pip or anaconda to .
There are a couple of ways to use Notebook on Oscar. You can run Jupyter Notebook
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 Notebook server on Oscar.
Do not run Jupyter Notebook on login nodes.
Start an session, and open up a terminal in the VNC session. To start a Jupyter Notebook, enter
This will start the Jupyter Notebook server and open up a browser with the notebook.
Submit an ssh tunnel to the server.
Set up an ssh tunnel to the server.
Open a browser to view the notebook.
Use scancel to end the batch job when you are done.
Here is an example batch script to start a Jupyter notebook server on an Oscar compute node. This script assumes that you are not using a Conda or a virtual environment.
If you are using a Conda environment, replace the last two lines with thes lines:
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 notebook 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 notebook 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 notebook will ask for a token. Copy the token from jupyter-log-{jobid}.txt. Then your notebook will start.
Remember to scancel {jobid} when you are done with your notebook session.
Start Jupyter Notebook in an interactive job.
Set up 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 Notebook has started:
$ jupyter-notebook --no-browser --port=$ipnport --ip=$ipnip
[I 13:35:25.948 NotebookApp] JupyterLab beta preview extension loaded from /gpfs/runtime/opt/anaconda/3-5.2.0/lib/python3.6/site-packages/jupyterlab
[I 13:35:25.948 NotebookApp] JupyterLab application directory is /gpfs/runtime/opt/anaconda/3-5.2.0/share/jupyter/lab
[I 13:35:25.975 NotebookApp] Serving notebooks from local directory: /gpfs_home/yliu385
[I 13:35:25.975 NotebookApp] 0 active kernels
[I 13:35:25.975 NotebookApp] The Jupyter Notebook is running at:
[I 13:35:25.975 NotebookApp] http://172.20.207.61:8855/?token=c58d7877cfcf1547dd8e6153123568f58dc6d5ce3f4c9d98
[I 13:35:25.975 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 13:35:25.994 NotebookApp]
Copy/paste this URL into your browser when you connect for the first time,
to login with a token:
http://172.20.207.61:8855/?token=c58d7877cfcf1547dd8e6153123568f58dc6d5ce3f4c9d98&token=c58d7877cfcf1547dd8e6153123568f58dc6d5ce3f4c9d98
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 Notebook 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.