Jupyter Labs on Oscar

Installing Jupyter Lab

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

Running Jupyter Lab on Oscar

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

• in an OOD Desktop App (VNC)

• 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.

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 Lab, enter

jupyter-lab

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

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

~/.local/bin/jupyter-lab

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 lab.

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 Lab server on an Oscar compute node

#!/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 $[e-mail]
    -----------------------------------------------------------------
    Then open a browser on your local machine to the following address
    ------------------------------------------------------------------
    localhost:$ipnport  (prefix w/ https:// if using password)
    ------------------------------------------------------------------
    "
## start an ipcluster instance and launch jupyter server
module load anaconda/3-5.2.0
jupyter-lab --no-browser --port=$ipnport --ip=$ipnip

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

~/.local/bin/jupyter-lab --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 lab 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. Setup an ssh tunnel to the notebook server

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.

 ssh -N -L $ipnport:$ipnip:$ipnport [e-mail]

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 lab

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 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

In an Interactive Session

1. Start Jupyter Lab in an interactive job

2. Setup 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 Jupyter Lab in in 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 $ipnip
jupyter-lab --no-browser --port=$ipnport --ip=$ipnip

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]

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 [e-mail]

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/ http:// 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 Lab server

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.