Slurm Jupyter Kernel

Manage (create, list, modify and delete) and starting jupyter slurm kernels using sbatch.

slurmkernel is able to connect to a kernel started on a compute node using SSH port forwarding. You can specify a SSH proxy jump, if you have to jump over two hosts (e.g. a loadbalancer)

Features & Use-Cases

• Start Remote Jupyter kernel using sbatch (Slurm)
  • Access to your local filesystem with remote code execution
• Manage existing Slurm Jupyter kernel
• Use the template module to use pre-defined script templates for remote installation and local kernel creation
• Custom environment variables supported (e.g. JULIA_NUM_THREADS)

Table of Contents

• Slurm Jupyter Kernel
  • Features & Use-Cases
  • Table of Contents
  • Installation
    • Install using pip
  • Requirements for usage
  • Create a new kernel
    • Template module (Script templates)
      • Example
    • IPython Example
      • Remote Host
      • Localhost
    • Set kernel-specific environment
  • Using the kernel with Quarto
    • Example
  • Get help

Installation

slurm_jupyter_kernel must be installed locally where the Jupyter notebooks will run.

Install using pip

python3 -m pip install slurm_jupyter_kernel

Requirements for usage

• SSH-Key based authentication

You need a running SSH agent with the loaded key file to access the loginnode without a password.

Create a new kernel

We assume to install the Jupyter kernel tools into your $HOME directory on your cluster.

Template module (Script templates)

With $ slurmkernel template {list, use, add, edit} you can use pre-defined script templates to initialize your remote environment (IJulia, IPython, ...), add new script templates or edit existing templates.

If you want to create your own script templates, see here: Create Script Templates

Example

$ slurmkernel template use --proxyjump lb.hpc.pc2.de --loginnode login001 --user hpcuser1 --template ipython

You will be interactively asked for the required information if you do not pass any arguments when calling slurmkernel template use

IPython Example

Remote Host

1. load required software (if necessary)
2. Create a Python virtual environment
3. Install the IPython package (ipython, ipykernel)
4. Create a wrapper script and mark it as executable

remotehost ~$ module load lang Python
remotehost ~$ python3 -m venv remotekernel/
remotehost ~$ source remotekernel/bin/activate
(remotekernel) remotehost ~$ python3 -m pip install ipython ipykernel; deactivate
remotehost ~$ echo -e '#!/bin/bash\nmodule load lang Python\n\nsource remotekernel/bin/activate\n"$@"' > remotekernel/ipy_wrapper.sh && chmod +x remotekernel/ipy_wrapper.sh

Localhost

5. Kernel Remote Slurm kernel with command slurmkernel

notebook ~$ slurmkernel create --displayname "Python 3.8.2" \
--slurm-parameter="account=slurmaccount,time=00:30:00,partition=normal" \
--kernel-cmd="\$HOME/remotekernel/ipy_wrapper.sh ipython kernel -f {connection_file}" \
--proxyjump="lb.n1.pc2.uni-paderborn.de" \
--loginnode="login-0001" \
--language="python"

Set kernel-specific environment

If you want to set kernel specific environment variables (e.g. JULIA_NUM_THREADS for the number of threads) just extend the jupyter kernelspec file with env.

Parameter for slurmkernel:

--environment="JULIA_NUM_THREADS=4"

More information here: https://jupyter-client.readthedocs.io/en/stable/kernels.html

Using the kernel with Quarto

What is Quarto?

https://quarto.org/

• Install kernel as shown above
  • Make sure that you pass the --language flag as well.
    • e.g. python or julia

Example

Get help

$ slurmkernel --help

usage: Tool to manage (create, list, modify and delete) and starting jupyter slurm kernels using srun [-h] [--version] {create,list,edit,delete,template} ...

positional arguments:
  {create,list,edit,delete,template}
    create              create a new slurm kernel
    list                list available slurm kernel
    edit                edit an existing slurm kernel
    delete              delete an existing slurm kernel
    template            manage script templates (list, use, add, edit)

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit