# Jupyter Labs on Oscar ## Installing Jupyter Lab The anaconda modules provide jupyter-lab. Users can also use pip or anaconda to [install jupyter lab](https://jupyter.readthedocs.io/en/latest/install.html). ## Running Jupyter Lab on Oscar There are a couple of ways to use [Jupyter](https://jupyter.org/) Lab on Oscar. You can run a Jupyter Lab * in an [OOD Desktop App (VNC)](https://docs.ccv.brown.edu/oscar/connecting-to-oscar/open-ondemand/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. {% hint style="warning" %} Do not run Jupyter Lab on login nodes. {% endhint %} ## In a OOD Desktop App VNC Session Start an [OOD Desktop App (VNC)](https://docs.ccv.brown.edu/oscar/connecting-to-oscar/open-ondemand/desktop-app-vnc) session, and open up a terminal in the VNC session. To start a Jupyter Lab, enter ```bash jupyter-lab ``` This will start the Jupyter lab server and open up a browser with the lab. {% hint style="info" %} If you installed Jupyter Lab with pip, you may need to give the full path: `~/.local/bin/jupyter-lab` {% endhint %} ## 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 ```bash #!/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 module load anaconda/3-5.2.0 jupyter-lab --no-browser --port=$ipnport --ip=$ipnip ``` {% hint style="info" %} 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` {% endhint %} 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}`.txt`containing 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: ```console 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. ```bash ssh -N -L $ipnport:$ipnip:$ipnport user@ssh.ccv.brown.edu ``` {% hint style="info" %} If you are using Windows, follow the[ Tunneling into Jupyter with Windows](https://docs.ccv.brown.edu/oscar/jupyter-notebooks/tunneling-into-jupyter-with-windows) documentation to complete this step. {% endhint %} Enter your Oscar password. Note it will appear that nothing has happened. ### 3. Open a browser to view the lab Open a browser on your local machine to the address given in `cat jupyter-log-{jobid}.txt`. ```bash localhost:9349 (prefix w/ https:// if using password) ``` The lab will ask for a token. Copy the token from `jupyter-log-{jobid}.txt`. Then your lab will start. {% hint style="warning" %} Remember to `scancel {jobid}` when you are done with your notebook session {% endhint %} ## In an Interactive Session 1. Start Jupyter Lab in an interactive job 2. Setup an ssh tunnel to the server. 3. Open a browser to view the notebook. 4. Use `scancel` to end the batch job when you are done. ### 1.Start Jupyter Lab in in interactive job Start an [Interactive job](/oscar/submitting-jobs/interact.md) and then in your interactive session enter the following: ```bash unset XDG_RUNTIME_DIR module load anaconda/3-5.2.0 ipnport=$(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 /oscar/runtime/opt/anaconda/3-5.2.0/lib/python3.6/site-packages/jupyterlab > > \[I 13:12:03.404 LabApp] JupyterLab application directory is /oscar/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] \*\* > > \[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). ```bash ssh -N -L $ipnport:$ipnip:$ipnport user@ssh.ccv.brown.edu ``` {% hint style="info" %} If you are using Windows, follow the[ Tunneling into Jupyter with Windows](https://docs.ccv.brown.edu/oscar/jupyter-notebooks/tunneling-into-jupyter-with-windows) documentation to complete this step. {% endhint %} Enter your Oscar password. Note it will appear that nothing has happened. ### 3. Open a browser to view the notebook Open a browser on your local machine to the address: ``` localhost:$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. --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://docs.ccv.brown.edu/oscar/jupyter-notebooks/jupyter-notebooks-on-oscar.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.