How to Run JupyterLab via Container

This page describes how to run JupyterLab in a container on Pawsey systems with Slurm. This involves launching JupyterLab and then connecting to the Jupyter server.

On this page:

Overview

The first step in using JupyterLab is to make it available on the supercomputer. Given the possibly long list of dependencies, it is better to use a container rather than installing it in the traditional way. The first section shows how you can get the container image of JupyterLab. Then, you will need to prepare a batch script to execute the JupyterLab server on a compute node. Finally, when you are finished, you will need to clean up the session.

Getting the container images

There are a number of good resources for prebuilt Jupyter and RStudio Docker images:

  • Jupyter Docker Stacks (external site) provides prebuilt Jupyter images designed for Tensforflow, Spark, and data science workflows, which are available on DockerHub.
  • Rocker has prebuilt RStudio images available on DockerHub.

You can use these as base images to install additional packages if needed. Once you have your desired image built we can submit a batch script that launches the container.

For this example, we're going to be using the jupyter/datascience-notebook (external site) Docker image. It provides a Conda environment with a large collection of common Python packages (including NumPy, SciPy, Pandas, Scikit-learn, Bokeh and Matplotlib), an R environment (with the tidyverse (external site) packages), and a Julia environment. All of these are accessible via a Jupyter notebook server.

This Docker image ships with a startup script that allows for a number of runtime options to be specified. Most of these are specific to running a container using Docker; we will focus on how to run this container using  Singularity.

The datascience-notebook image has a default user, jovyan, and it assumes that you will be able to write to /home/jovyan. When you run a Docker container via Singularity, you will be running as your Pawsey username inside the container, so we won't be able to write to /home/jovyan. Instead, we can mount a specific directory (on Pawsey's filesystems) into the container at /home/jovyan. This will allow our Jupyter server to do things like save notebooks and write checkpoint files, and those will persist on Pawsey's filesystem after the container has stopped.

Setting up the batch script

The following script launches a Jupyter notebook on a compute node. The first step is to enter a writable directory with some space, such as /scratch, to launch the notebook. Create a directory where you will start our Jupyter notebook container and put any relevant data or Jupyter notebooks in this directory. This is also the directory that will be mounted to /home/jovyan.

Listing 1. Slurm script for running JupyterHub in a container
#!/bin/bash -l
# Allocate slurm resources, edit as necessary
#SBATCH --account=[your-project-name]
# Here we request the appropriate partition for the system
#SBATCH --partition=work
# Since jupyterlab is not mpi enabled, we just use one task 
#SBATCH --ntasks=1
#SBATCH --mem=20GB
#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
fi

# Load Singularity
module load singularity/3.11.4-nompi

# 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 -C \
  -B ${jupyterDir}:/home/joyvan \
  -B ${jupyterDir}:${HOME} \
  ${imagename} \
  jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${jupyterDir}

Run your Jupyter notebook server

To start, submit the SLURM jobscript. It will take a few minutes to start (depending on how busy the queue and how large of an image you're downloading). Once the job starts you will have a SLURM output file in your directory, which will have instructions on how to connect at the end. 

Terminal 1. Launching JupyterHub and extracting connection information
$ sbatch jupyter-notebook-one-singularity.slm
Submitted batch job 3528476
$ cat slurm-3528476.out
.
.
.
Writing manifest to image destination
Storing signatures
[34mINFO:   [0m Creating SIF file...
[34mINFO:   [0m Build complete: /scratch/pawsey0002/matilda/jupyter-dir/singularity-cache/cache/oci-tmp/18ef2702c6a25bd26b81e7b6dc831adb2bc294ae7bc9b011150b8f4573c41d4a/datascience-notebook_latest.sif

*****************************************************
Setup - from your laptop do:
ssh -N -f -L 8888:z123:8888 <user>@setonix.pawsey.org.au
*****
The launch directory is: /scratch/pawsey0001/...
*****************************************************

*****************************************************
Terminate - from your laptop do:
kill $( ps x | grep 'ssh.*-L *8888:z123:8888' | awk '{print $1}' )
*****************************************************

[I 04:38:34.503 NotebookApp] Writing notebook server cookie secret to /home/matilda/.local/share/jupyter/runtime/notebook_cookie_secret
[I 04:38:36.677 NotebookApp] JupyterLab extension loaded from /opt/conda/lib/python3.7/site-packages/jupyterlab
[I 04:38:36.677 NotebookApp] JupyterLab application directory is /opt/conda/share/jupyter/lab
[I 04:38:37.605 NotebookApp] Serving notebooks from local directory: /group/pawsey0002/matilda/jupyter-dir
[I 04:38:37.605 NotebookApp] The Jupyter Notebook is running at:
[I 04:38:37.605 NotebookApp] http://z123:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
[I 04:38:37.605 NotebookApp]  or http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
[I 04:38:37.605 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 04:38:37.616 NotebookApp] 
    
    To access the notebook, open this file in a browser:
        file:///home/matilda/.local/share/jupyter/runtime/nbserver-17-open.html
    Or copy and paste one of these URLs:
        http://z123:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242
     or http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242

In a separate local terminal window, run SSH based on the command listed in the output file:

ssh -N -f -L 8888:z123:8888 <username>@setonix.pawsey.org.au 

After this step, you can open up a web browser and use the address displayed in the output file to access your Jupyter notebook. In this example the address is:

http://127.0.0.1:8888/?token=3291a7b1e6ce7791f020df84a7ce3c4d2f3759b5aaaa4242

Alternatively, you could go to the web address http://27.0.0.1:8888 or http://localhost:8888, and then when prompted insert the token string that comes after "?token=" above. (Note that your port number might differ from "8888".)


Figure 1. Jupyter authentication page

Note:

The information above is a notebook launched on zeus.pawsey.org.au. Ensure that you look at your output to select the correct machine.

Clean up when you are finished

Once you have finished:

  • Cancel your job with scancel.
  • Kill the SSH tunnel, based on the command displayed in the output file:

kill $( ps x | grep 'ssh.*-L *8888:z123:8888' | awk '{print $1}' )

Run a GPU-enabled Jupyter notebook

This section is being updated for AMD GPUs

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.

Running a GPU-enabled container on GPU Pawsey systems with Slurm is very similar to running a standard Jupyter notebook. The main differences are:

  • Use of the gpu partition on Setonix
  • Request a GPU to Slurm
  • Pass the environment variable CUDA_HOME to Singularity
  • Run the container using the flag  --nv, to enable the GPU support from Singularity


Listing 2. Slurm script for running JupyterHub in a GPU-enabled container
#!/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 --gpus-per-node=1
#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
fi

# Load Singularity
module load singularity/3.11.4-nompi

# Load ROCm and set environment variable for Singularity
module load rocm/5.2.3
export SINGULARITYENV_CUDA_HOME=$CUDA_HOME

# 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 --nv -C \
  -B ${jupyterDir}:/home/joyvan \
  -B ${jupyterDir}:$HOME \
  ${imagename} \
  jupyter notebook \
  --no-browser \
  --port=${port} --ip=0.0.0.0 \
  --notebook-dir=${jupyterDir}

Testing your notebook with a simple example GPU code

Try copying and pasting the following snippet inside a Jupyter cell. This python code uses the numba python library to run some calculations with a Nvidia GPU. 

Listing 3. Simple GPU-enabled Python code snippet
# key GPU library
from numba import cuda
import numpy as np

# define some kernels
@cuda.jit
def add_kernel(x, y, out):
    idx = cuda.grid(1)
    out[idx] = x[idx] + y[idx]

n = 4096
x = np.arange(n).astype(np.int32) # [0...4095] on the host
y = np.ones_like(x)               # [1...1] on the host
out = np.zeros_like(x)

# cuda commands to copy memory to the device 
d_x = cuda.to_device(x)
d_y = cuda.to_device(y)
d_out = cuda.to_device(out)

# run kernel
threads_per_block = 128
blocks_per_grid = 32
add_kernel[blocks_per_grid, threads_per_block](d_x, d_y, d_out)
cuda.synchronize()

# output result 
print(d_out.copy_to_host()) # Should be [1...4096]

External links

  • DockerHub
  • For information about runtime options supported by the startup script in the Jupyter image, see Common Features in the Jupyter Docker Stacks documentation
  • The Rocker Project ("Docker Containers for the R Environment")