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This is a short guide to describe how to use jupyter nootebook on Izar through ssh port forwarding.

Installing IPython and Jupyter

The key to successfully installing the tools is using python virtual environments.

  1. Load the compiler you want to use and python using modules

    $ module load gcc
    $ module load python
    $ module load intel
    $ module load python
  2. Create a virtual environment

    In the following, we use GCC but the same procedure applies to Intel compiler. In your home folder, create a virtual environment:

    $ virtualenv -p python3 --system-site-packages opt/venv-gcc
    
    Running virtualenv with interpreter /ssoft/spack/arvine/v1/opt/spack/linux-rhel7-skylake_avx512/gcc-8.4.0/python-3.7.7-drpdlwdbo3lmtkcbckq227ypnzno4ek3/bin/python3
    Already using interpreter /ssoft/spack/arvine/v1/opt/spack/linux-rhel7-skylake_avx512/gcc-8.4.0/python-3.7.7-drpdlwdbo3lmtkcbckq227ypnzno4ek3/bin/python3
    Using base prefix '/ssoft/spack/arvine/v1/opt/spack/linux-rhel7-skylake_avx512/gcc-8.4.0/python-3.7.7-drpdlwdbo3lmtkcbckq227ypnzno4ek3'
    New python executable in /home/user/opt/venv-gcc/bin/python3
    Also creating executable in /home/user/opt/venv-gcc/bin/python
    Installing setuptools, pip, wheel...
    done.
    
  3. Activate virtual environment

    $ source opt/venv-gcc/bin/activate
    
    (venv-gcc) [user@izar ~]$
  4. Install Jupyter and ipyparallel

    (venv-gcc) [user@izar ~]$ pip install jupyter ipyparallel
    Collecting jupyter
    ..
    ..
  5. Set a passwordless access to Izar by using ssh key and have the following in your ~/.ssh/config file on your personal computer. It is assumed that you are inside the EPFL network.

    Host izar
    Hostname izar.epfl.ch
    User [username]
    
  6. Run jupyter notebook and ipcluster on Izar.
    The script below is a template that allows you to start ipcluster on a compute node of Izar. You can copy it in a file called launch_jupyter.sh for example. It has to be placed in your home (or you have to modify it accordingly). All the modules that jupyter may need have to be loaded here otherwise it won't be able to use them. As an example, here, we show the setup necessary to use TensorFlow to provide an example that match real scenario as much as possible. Please use the modules you need for your case.

    launch_jupyter.sh
    #!/bin/bash -l
    #SBATCH --job-name=ipcluster
    #SBATCH --nodes=1
    #SBATCH --exclusive
    #SBATCH --time=01:00:00
    #SBATCH --output jupyter-log-%J.out
    
    module load gcc/8.4.0-cuda   cuda/10.2.89   cudnn/7.6.5.32-10.2-linux-x64   mvapich2/2.3.4-cuda py-tensorflow
    
    source opt/venv-gcc/bin/activate
    profile=job_${SLURM_JOB_ID}
    echo "creating profile: ${profile}"
    ipython profile create ${profile}
    
    echo "Launching controller"
    ipcontroller --ip="*" --profile=${profile} &
    sleep 10
    
    echo "Launching engines"
    srun ipengine --profile=${profile} --location=$(hostname) 2> /dev/null 1>&2 &
    
    ipnport=$(shuf -i8000-9999 -n1)
    
    XDG_RUNTIME_DIR=""
    echo "${hostname}:${ipnport}" > jupyter-notebook-port-and-host
    jupyter-notebook --no-browser --port=${ipnport} --ip=$(hostname -i)

    Launch your job as usual:

    sbatch launch_jupyter.sh

    Once the job is running analyze the output jupyter-log-[SLURM_ID].out. Then, look for a line like the following:

        Or copy and paste one of these URLs:
            http://10.91.27.63:8504/?token=4b17ae5cfa505b5470dc84bb5240ab43ae714aa9480a163c
    
    

    It has the form:

    http://<IP ADDRESS>:<PORT NUMBER>/?token=<TOKEN>
  7. On your local machine do the following with the information provided by the above step

    ssh -L <PORT NUMBER>:<IP ADDRESS>:<PORT NUMBER> izar -f -N

    For our example, this gives:

    ssh -L 8504:10.91.27.63:8504 izar -f -N
  8. Now you should be able to access to Izar compute node through the web browser by pasting the following address

    http://localhost:<PORT NUMBER>/?token=<TOKEN>

    For our example, this gives:

    http://localhost:8504/?token=4b17ae5cfa505b5470dc84bb5240ab43ae714aa9480a163c
  9. Create a jupyter nootebook and add the following

    import ipyparallel as ipp
    c = ipp.Client(profile='job_[SLURM_JOB_ID]')
    view = c[:]

    Replace [SLURM_JOB_ID] with the job number you obtain by running the command: squeue -u $USER



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