Setup and Apptainer

Initial setup

Before we get started with running notebooks on Sockeye, we have to pull the requisite container images, and set up some scripts.

Parameter	Description
<allocation>	Sockeye allocation
<CWL>	Your CWL

Pulling the container

[!NOTE]

• We'll be storing all of our container images inside /arc/project/<allocation>/jupyter as per UBC Confluence convention. They can be stored elsewhere, but this document uses the UBC Confluence convention, so you will have to adapt the paths if you store them elsewhere.

Instructions

1. Create the directory in /arc/project/<allocation> to store your images.

   mkdir /arc/project/<allocation>/jupyter

2. Pull the jupyter/datascience-notebook container from quay.io into your image folder.

    module load gcc apptainer
    cd /arc/project/<allocation>/jupyter
    apptainer pull --name jupyter-datascience.sif docker://quay.io/jupyter/datascience-notebook

   Updating your container

   Many times, containers have to be updated to bring in the latest Python/R/compiler versions. You can overwrite the current file with a new version by running:

   apptainer pull --force --name jupyter-datascience.sif docker://quay.io/datascience-notebook

3. Set up the Slurm job.

   First, create a job directory in /scratch for your personal Jupyter Notebooks to use as scratch space - ARC Sockeye has a file count quota on top of a file size quota, and files produced by Jupyter can cause you to hit this limit. Run this command to do so:

   mkdir -p /scratch/<allocation>/<cwl>/jupyter

   Now, put this script wherever you would like. A good spot could be in your home folder, but in this guide, we'll use /arc/project/<allocation>/<cwl>/jupyter-datascience.sh.

Job script

```bash
#!/bin/bash

#SBATCH --job-name=my_jupyter_notebook
#SBATCH --account=st-lknelson-1
#SBATCH --time=03:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --mem=10G
#SBATCH --partition=interactive_cpu

################################################################################

# Change directory into the job dir
cd $SLURM_SUBMIT_DIR

# Load software environment
module load gcc
module load apptainer

# Set RANDFILE location to writeable dir
export RANDFILE=$TMPDIR/.rnd

# Generate a unique token (password) for Jupyter Notebooks
export APPTAINERENV_JUPYTER_TOKEN=password

# Find a unique port for Jupyter Notebooks to listen on
readonly PORT=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()')

# Print connection details to file
cat > connection.txt <<END

1. Create an SSH tunnel to Jupyter Notebooks from your local workstation using the following command:

ssh -N -L 8888:${HOSTNAME}:${PORT} ${USER}@sockeye.arc.ubc.ca

2. Point your web browser to http://localhost:8888

3. Login to Jupyter Notebooks using the following token (password):

${APPTAINERENV_JUPYTER_TOKEN}

When done using Jupyter Notebooks, terminate the job by:

4. Quit or Logout of Jupyter Notebooks
5. Issue the following command on the login node (if you did Logout instead of Quit):

scancel ${SLURM_JOB_ID}

END

# Execute jupyter within the Apptainer container
apptainer exec --home /scratch/st-lknelson-1/iberez01/my_jupyter --env XDG_CACHE_HOME=/scratch/st-lknelson-1/iberez01/my_jupyter /arc/project/st-lknelson-1/jupyter/jupyter-datascience.sif jupyter notebook --no-browser --port=${PORT} --ip=0.0.0.0 --notebook-dir=$SLURM_SUBMIT_DIR
```

Next steps

Now that you're "done" setting up, here are some next steps.

Happy with packages

If you are happy with the packages that are installed in the jupyter-datascience image, then you can proceed to Initializing a Jupyter Notebook Instance.

Need GPUs?

See Adding GPU Support. Do this before you create new environments.

Need more packages?

If you (suspect) you require more packages in your notebook's environment, have a look at Creating Custom Environments.