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$ cd $MYSOFTWARE # This path defaults to /software/projects/<user_project>/<username>/ 

# Load the required modules. Note that the specific version numbers may change
$ module load python/3.10.810
$ module load py-pip/2223.21.2-py3.10.810

# Create and activate the virtual environment 
$ python -m venv pangeo
$ source ${MYSOFTWARE}/pangeo/bin/activate

# Install Pangeo, Dask, and dependencies
$ pip install dask-mpi dask distributed mpi4py jupyter-server-proxy jupyterlab ipywidgets xarray zarr numcodecs hvplot geoviews datashader widgetsnbextension dask-jobqueue dask-labextension notebook wheel netCDF4 pyFFTW basemap geos nodejs-bin

# Clean your pip cache to prevent exceeding your file count quota on the /software partition
$ pip cache purge

#!/bin/bash -l
# Allocate slurm resources, edit as necessary
#SBATCH --account=your_pawsey_account
#SBATCH --partition=work
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=2
#SBATCH --mem=8GB
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --job-name=jupyter_notebook
#SBATCH --export=NONE
 
# Set our working directory
# Should be in a writable path with some space, like /scratch
dir="${MYSCRATCH}/jupyter"
 
# Load dependencies for pangeo
module load python/3.10.810
source ${MYSOFTWARE}/pangeo/bin/activate

# You should not need to edit the lines below
 
# Prepare the working directory
mkdir -p ${dir}
cd ${dir}

# 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
fi

 
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: $dir"
echo "*****************************************************"
echo ""
echo "*****************************************************"
echo "Terminate - from your laptop do:"
echo "kill \$( ps x | grep 'ssh.*-L *${port}:${host}:${port}' | awk '{print \$1}' )"
echo "*****************************************************"
echo ""
  
#Launch the notebook 
srun -N $SLURM_JOB_NUM_NODES -n $SLURM_NTASKS -c $SLURM_CPUS_PER_TASK \
	jupyter lab \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${dir}