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Jupyter Notebooks on Oscar

Installing Jupyter Notebook

The anaconda modules provide jupyter-notebook. Users can also use pip or anaconda to install jupyter notebook.

Running Jupyter Notebook on Oscar

There are a couple of ways to use Jupyter Notebook on Oscar. You can run Jupyter Notebook

With the batch job or interactive session method, you use a browser on your machine to connect to your Jupyter Notebook server on Oscar.

Start by going to the directory you want to access when using Jupyter Notebook, and then start Jupyter Notebook. The directory where a Jupyter Notebook is started is the working directory for the Notebook.

Do not run Jupyter Notebook on login nodes.

In a OOD Desktop App VNC Session

Start an OOD Desktop App (VNC) session, and open up a terminal in the VNC session. To start a Jupyter Notebook, enter

jupyter-notebook

This will start the Jupyter Notebook server and open up a browser with the notebook.

If you installed Jupyter Notebook with pip, you may need to give the full path:

~/.local/bin/jupyter-notebook

Using a Batch Job

  1. Submit an ssh tunnel to the server.

  2. Set up an ssh tunnel to the server.

  3. Open a browser to view the notebook.

  4. Use scancel to end the batch job when you are done.

1. Submit batch script

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.

#!/bin/bash
#SBATCH --nodes 1
#SBATCH -c 6
#SBATCH --time 04:00:00
#SBATCH --mem-per-cpu 3G
#SBATCH --job-name tunnel
#SBATCH --output jupyter-log-%J.txt
## get tunneling info
XDG_RUNTIME_DIR=""
ipnport=$(shuf -i8000-9999 -n1)
ipnip=$(hostname -i)
## print tunneling instructions to jupyter-log-{jobid}.txt
echo -e "
    Copy/Paste this in your local terminal to ssh tunnel with remote
    -----------------------------------------------------------------
    ssh -N -L $ipnport:$ipnip:$ipnport $USER@ssh.ccv.brown.edu
    -----------------------------------------------------------------
    Then open a browser on your local machine to the following address
    ------------------------------------------------------------------
    localhost:$ipnport  (prefix w/ https:// if using password)
    ------------------------------------------------------------------
    "
## start an ipcluster instance and launch jupyter server

jupyter-notebook --no-browser --port=$ipnport --ip=$ipnip

If you installed Jupyter notebook with pip you may need to give the full path:

~/.local/bin/jupyter-notebook --no-browser --port-$ipnport --ip=$ipnip

If you are using a Conda environment, replace the last two lines with thes lines:

module purge
module load miniconda3/23.11.0s-odstpk5 
source /oscar/runtime/software/external/miniconda3/23.11.0/etc/profile.d/conda.sh
jupyter-notebook --no-browser --port=$ipnport --ip=$ipnip

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:

Jobs for user mhamilton

Running:
ID       NAME    PART.  QOS          CPU  WALLTIME  REMAIN   NODES
7239096  tunnel  batch  pri-mhamilt  6    4:00:00   3:57:33  node1036

Pending:
(none)

2. Set up an ssh tunnel to the notebook server

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.

 ssh -N -L $ipnport:$ipnip:$ipnport user@ssh.ccv.brown.edu

If you are using Windows, follow the Tunneling into Jupyter with Windows documentation to complete this step.

Enter your Oscar password. Note it will appear that nothing has happened.

3. Open a browser to view the notebook

Open a browser on your local machine to the address given in cat jupyter-log-{jobid}.txt.

localhost:9349  (prefix w/ https:// if using password)

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.

In an Interactive Session

  1. Start Jupyter Notebook in an interactive job.

  2. Set up an ssh tunnel to the server.

  3. Open a browser to view the notebook.

  4. Use scancel to end the batch job when you are done.

1. Start a Jupyter Notebook in an interactive job

Start an Interactive job and then in your interactive session enter the following:

unset XDG_RUNTIME_DIR
module load anaconda/3-5.2.0
ipnport=$(shuf -i8000-9999 -n1)
echo $ipnport
ipnip=$(hostname -i)
echo $ipnip
jupyter-notebook --no-browser --port=$ipnport --ip=$ipnip

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

2. Setup an ssh tunnel to the server

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).

 ssh -N -L $ipnport:$ipnip:$ipnport user@ssh.ccv.brown.edu

If you are using Windows, follow the Tunneling into Jupyter with Windows documentation to complete this step.

Enter your Oscar password. Note it will appear that nothing has happened.

3. Open a browser to view the notebook

Open a browser on your local machine to the address:

localhost:$ipnport  (prefix w/ https:// if using password)

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.

4. Press Ctrl+C twice to kill your Jupyter Notebook server

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.

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