This section about the use of Jupiter notebooks with GPUs is currently being updated to work with AMD GPUs on Setonix. The existing information at this point in time is not accurate and should not be considered as useful until this warning is removed.

#!/bin/bash -l
# This example is for GPUs on Setonix
# Allocate slurm resources, edit as necessary
#SBATCH --account=[your-project-name]
# Here we request the appropriate GPU partition on a system
#SBATCH --partition=gpu
# Be aware that the request for GPU resources may change in later versions of slurm
#SBATCH --nodes=1
#SBATCH --gres=gpu:1  #Asking for a single GPU-pack (Read documentation about running GPU jobs)
#SBATCH --time=02:00:00
#SBATCH --job-name=jupyter_notebook
#SBATCH --export=NONE

# Set our working directory
# This is the directory we'll mount to /home/jovyan in the container
# Should be in a writable path with some space, like /scratch
jupyterDir="${MYSCRATCH}/jupyter-dir"

# Set the image and tag we want to use
image="docker://jupyter/datascience-notebook:latest"

# You should not need to edit the lines below

# Prepare the working directory
mkdir -p ${jupyterDir}
cd ${jupyterDir}

# Get the image filename
imagename=${image##*/}
imagename=${imagename/:/_}.sif

# Get the hostname
# We'll set up an SSH tunnel to connect to the Juypter notebook server
host=$(hostname)

# Set the port for the SSH tunnel
# This part of the script uses a loop to search for available ports on the node;
# this will allow multiple instances of GUI servers to be run from the same host node
port="8888"
pfound="0"
while [ $port -lt 65535 ] ; do
  check=$( ss -tuna | awk '{print $4}' | grep ":$port *" )
  if [ "$check" == "" ] ; then
    pfound="1"
    break
  fi
  : $((++port))
done
if [ $pfound -eq 0 ] ; then
  echo "No available communication port found to establish the SSH tunnel."
  echo "Try again later. Exiting."
  exit
else
  echo "Port to use is port=${port}"
fi

# Load Singularity
module load singularity/4.1.0-nompi

# Load ROCm and set environment variable for Singularity
module load rocm/5.7.3
export SINGULARITYENV_ROCM_PATH=$ROCM_PATH

# Pull our image in a folder
singularity pull $imagename $image

echo "*****************************************************"
echo "Setup - from your laptop do:"
echo "ssh -N -f -L ${port}:${host}:${port} $USER@$PAWSEY_CLUSTER.pawsey.org.au"
echo "*****"
echo "The launch directory is: $jupyterDir"
echo "*****************************************************"
echo ""
echo "*****************************************************"
echo "Terminate - from your laptop do:"
echo "kill \$( ps x | grep 'ssh.*-L *${port}:${host}:${port}' | awk '{print \$1}' )"
echo "*****************************************************"
echo ""
 
# Launch our container
# and mount our working directory to /home/jovyan in the container
# and bind the run time directory to our home directory
singularity exec --rocm -C \
  -B ${jupyterDir}:/home/joyvan \
  -B ${jupyterDir}:$HOME \
  ${imagename} \
  jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${jupyterDir}