qsub.sge

#$ -S /bin/bash
#$ -j y
#$ -cwd
#$ -N run_jupyter
#$ -l mem_requested=32G,tmp_requested=200G,tmpfree=200G
#$ -V

# SGE DEBUG METADATA
cat /tmp/prolog_exec_"$JOB_ID"_"$SGE_TASK_ID".log

echo "JOB: $JOB_ID TASK: $SGE_TASK_ID"
echo "$HOSTNAME $tmp_requested $TMPDIR"

#######################################
# General user to customise
#######################################
# Using my image for now... will update with required software
IMAGE_URL="docker://prismaticbunny/cellrankjupyter:latest"
IMAGE_TMP=$TMPDIR

# Unprivileged user jovyan is setup in this container. Here is to specify which
# local location is used to mount /home/jovyan inside the container for storing
# notebooks. Each RUNNING jupyter SGE session should have its own dedicated dir.
# Notebooks are saved on the local location and can be reused in the future session.
JUPYTER_DIR="$HOME/jupyter_dir/$JOB_ID"
mkdir -p $JUPYTER_DIR

# Provide a local path of your data, this location will be mounted to /data
# and expose your data inside the container.
DATA_DIR="/directflow/SCCGGroupShare/projects"

################################
# DO NOT MODIFY (Adv User ONLY)
################################

# Get the hostname of the compute node on where jupyter is running
# We'll set up an SSH tunnel to connect to the Juypter notebook server
exec_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 [ $port -lt 65535 ] ; do
  check=$( netstat -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
 
## cd ${IMAGE_TMP}

# Pull the image in a folder
#imagename=${IMAGE_URL##*/}
imagename=/directflow/SCCGGroupShare/projects/software/cellrank.sif
#singularity pull $imagename $IMAGE_URL

echo "*****************************************************"
echo "Setup SSH Tunnel - ON YOUR OWN COMPUTER macOS or Linux:"
echo ""
echo "ssh -N -f -L 8888:${exec_host}:${port} $USER@$SGE_O_HOST.garvan.unsw.edu.au"
echo ""
echo "*****************************************************"
echo ""
echo "*****************************************************"
echo "Terminate SSH Tunnel - ON YOUR OWN COMPUTER do:"
echo ""
echo "kill \$( ps x | grep 'ssh.*-L 8888:${exec_host}:${port}' | awk '{print \$1}' )"
echo ""
echo "*****************************************************"
echo ""

# Conda environment within the container
ENV_DIR=/opt/miniconda3/envs/cellrank

# 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 -C \
  -B ${JUPYTER_DIR}:$HOME \
  -B ${DATA_DIR} \
  ${imagename} \
  ${ENV_DIR}/bin/jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${HOME}