Jupyterhub on II2

create_python_kernel-ii2.sh

#!/bin/bash

MODULES=(
	ipython/.5.3.0-foss-2017a-python-2.7.13 \
	ipywidgets/7.2.1-foss-2017a-python-2.7.13 \
	matplotlib/2.2.2-foss-2017a-python-2.7.13 \
	pillow/5.1.0-foss-2017a-python-2.7.13 \
	av/6.0.0-foss-2017a-python-2.7.13 \
	scipy/1.0.1-foss-2017a-python-2.7.13 \
	scikit-learn/0.19.1-foss-2017a-python-2.7.13 \
	scikit-image/0.14.0-foss-2017a-python-2.7.13 \
	tifffile/0.12.1-foss-2017a-python-2.7.13 \
	h5py/2.7.1-foss-2017a-python-2.7.13 \
	pyyaml/3.12-foss-2017a-python-2.7.13 \
	lap/0.3.0-foss-2017a-python-2.7.13 \
	psutil/5.4.1-foss-2017a-python-2.7.13 \
	keras/2.1.4-foss-2017a-python-2.7.13 \
	tensorflow/1.5.0-foss-2017a-python-2.7.13 \
	opencv/3.4.1-foss-2017a-python-2.7.13 \
	numba/0.37.0-foss-2017a-python-2.7.13 \
	gcccore/6.3.0 \
)

KERNEL_BASE_DIR=~/.local/share/jupyter/kernels/ 
mkdir -p $KERNEL_BASE_DIR 2>/dev/null || true
TIMESTAMP=$(date +%Y%m%d%H%M%S)
KERNEL_NAME=analysis-$TIMESTAMP
shift

command pushd $KERNEL_BASE_DIR >/dev/null

if ! mkdir "$KERNEL_NAME" 2>/dev/null; then
	echo 2>&2 "Error: Kernel with name \"$KERNEL_NAME\" already exists in $KERNEL_BASE_DIR"
	exit 1
fi

cd "$KERNEL_NAME"

cat > "setup-$KERNEL_NAME.sh" <<XXX
#!/bin/bash
#
# Automatically generated script to setup kernel $KERNEL_NAME.
#

ml reset
ml use /groups/pauli/software/171020-ii2/modules/all/
cd $KERNEL_BASE_DIR
mkdir $KERNEL_NAME 2>/dev/null || true
cd $KERNEL_NAME
for module in ${MODULES[@]}; do
	echo "Loading module \$module"
	module --ignore-cache load "\$module"
done
echo

PYTHON=\$(which python)
PY_DIR=\$(dirname \$(dirname \$(which python)))
PY_VER_SHORT=\$(python -V 2>&1 | cut -d\  -f2 | cut -f-2 -d.)

echo "Setting up kernel $KERNEL_NAME"
cat > "kernel.json" <<YYY
{
 "display_name": "$KERNEL_NAME",
 "language": "python",
 "argv": [
  "\$PYTHON",
  "-m",
  "ipykernel",
  "-f",
  "{connection_file}"
 ],
 "env": {
  "PATH": "\$PATH",
  "LD_LIBRARY_PATH": "\$LD_LIBRARY_PATH",
  "PYTHONPATH": "\$PYTHONPATH",
  "PYTHON_LIBRARY_DIR": "\$PY_DIR/lib",
  "PYTHON_LIBRARY": "\$PY_DIR/lib/libpython\$PY_VER_SHORT.so"
  }
}
YYY
XXX
chmod +x setup-$KERNEL_NAME.sh

./setup-$KERNEL_NAME.sh

command popd >/dev/null

jupyterhub-ii2.sh

#!/bin/bash
#
# Run jupyterhub instance inside the current directory.  This can be connected
# to through a browser and used to edit and run IPython notebooks (.ipynb).
#

set -eu -o pipefail

IP=$(dig +short $(hostname).ii2.imp.ac.at A)
if [ -z "$IP" ]; then
	echo >&2 "Failed to detect local IP address."
	exit 1
fi

function check_port () {
	IP=$1
	PORT=$2
	bash -c "echo >/dev/tcp/$IP/$PORT" 2>/dev/null
	return $?
}

PORT=61616
while check_port $IP $PORT && check_port $IP $(expr $PORT + 2); do
	echo "Port $PORT or $(expr $PORT + 2) are not available" 
	# FIXME: dont know the exact range that is allowed
	PORT=$(shuf -i 60000-65500 -n1)
	echo $PORT...
done
echo "Using ports $PORT and $(expr $PORT + 2)"

GRP=pauli
WORK_DIR="$(pwd)"
JH_MODULE=jupyterhub/0.8.1-foss-2017a-python-3.6.4
JH_DIR="$JH_MODULE"
mkdir -p "$JH_DIR"

ml reset
ml use /groups/$GRP/software/171020-ii2/modules/all
ml $JH_MODULE
ml widgetsnbextension/3.2.1-foss-2017a-python-3.6.4
jupyter nbextension install widgetsnbextension --user --py
jupyter nbextension enable widgetsnbextension --user --py

IP_KEY="$JH_DIR/$IP.key"
IP_CERT="$JH_DIR/$IP.cert"
CONFIG="$JH_DIR/$IP-config.py"
if [ ! -e "$IP_KEY" ]; then
	echo "No key for this IP ($IP) and this version of Python, generating..."
	openssl genrsa -out "$IP_KEY" 2048  \
	&& openssl req -new -x509 -key "$IP_KEY" -out "$IP_CERT" -days 3650 -subj "/CN=$IP" \
	&& echo "Done."
fi
cat >"$CONFIG" <<-HERE
c.Authenticator.admin_users = {'$USER'}
c.Authenticator.whitelist = {'$USER'}
c.JupyterHub.cookie_secret_file = '$JH_DIR/cookie_secret'
c.JupyterHub.db_url = '$JH_DIR/sqlite'
c.JupyterHub.extra_log_file = '$JH_DIR/extra_log'
c.JupyterHub.pid_file = '$JH_DIR/pid'
c.JupyterHub.hub_port = $(expr $PORT + 2)
c.ConfigurableHTTPProxy.api_url = 'http://127.0.0.1:$(expr $PORT + 1)'
c.Spawner.notebook_dir = '$WORK_DIR'
c.Spawner.env_keep = ['PATH', 'PYTHONPATH', 'LD_LIBRARY_PATH', 'VIRTUAL_ENV', 'LANG', 'LC_ALL', 'JAVA_HOME']
HERE
cd $WORK_DIR
export CONFIGPROXY_AUTH_TOKEN=`openssl rand -hex 32`
jupyterhub --ip "$IP" --port "$PORT" --ssl-key "$IP_KEY" --ssl-cert "$IP_CERT" --config "$CONFIG"