Run Jupyter Notebooks in an Interactive Session

Overview:

  • Teaching: 0 min
  • Exercises: 0 min

Questions

  • How can I run my code using Jupyter notebooks on Balena

Objectives

  • Understand how to set-up and access Jupyter notebooks from an batch session on Balena

Login to Balena

First of all you will need to login to Balena.

You will need to submit a jobscript to launch the session. You can download and copy this example jobscript to Balena, or just create a file along the lines of the following.

#!/bin/bash

#SBATCH --partition=batch
#SBATCH --job-name="notebook"
#SBATCH --output=job.notebook.%j

#SBATCH --nodes=1


## 30 mintues
#SBATCH --time=30

module load python3/2019.x

echo "URL to CONNECT for JOB $SLURM_JOB_ID is http://$(host $(hostname) | awk 'NF>1{print $NF}')"

jupyter notebook --ip="*" --no-browser

The jobscript interacts with the scheduler in exactly the same way as any other job so if you wanted to run longer jobs or use a premium account you just need to modify/enter the appropriate #SBATCH instructions in the file.

The Jupyter Notebook output that printed to screen in the interactive case printed to screen will now be output to the file job.notebook.%j where %j is the jobid in the scheduler. If you do not use the provided jobscript, and do not specify the name of the output #SBATCH --output=output_file then the output will default to slurm-<jobid>.out.

You should search the file for the IP address and the port with e.g.:

grep "CONNECT\|http" job.notebook.<jobid>

which will give output similar to:

URL to CONNECT for JOB 2454254 is http://172.30.4.165
[I 10:27:03.417 NotebookApp] http://[all ip addresses on your system]:8888/

when the job has started and the Jupyter notebook server has launched successfully.

You can now access the notebook server by opening a web browser on your local machine and, in this case above entering the address:

http://172.30.4.165:8888

If you have follwed the tutorial successfully you should be prompted for the password you entered in the previous episode, running interactively , and be launched into the familar Jupyter notebooks environment.

Key Points:

  • You can run Jupyter notebooks from a batch session on Balena
  • You can then access the notebook server from a browser on your local machine
  • You will need to wait until the job launches.

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