How to install jupyter kernel for Matlab#

In this tutorial, I will describe i) the steps to create a kernel for Matlab and ii) get the matlab_kernel working in Jupyterhub on Levante.

Prerequisites#

  • conda environment with python 3.9

  • matlab_kernel package

  • matlab python engine (from the matlab module)

  • python bindings

Note

For some reasons, there will be no centralized kernel for Levante in jupyterhub.

Matlab release#

Check this table first when you create the conda environment.

To check the available Matlab modules on Levante:

module list matlab

which (currently) returns:

  • matlab/R2021b-gcc-11.2.0

Instructions#

Please follow these steps to install and enable the matlab_kernel in Jupyterhub.

1. Conda env#

Create a conda environment to install matlab_kernel package.

module load python3
conda create -n matlab python=3.9
source activate matlab

2. Matlab Kernel#

In the conda env:

python -m pip install matlab_kernel
python -m matlab_kernel install --user

A kernel specification kernel.json is now available under .local/share/jupyter/kernels/matlab.

You need to edit that file and change the path to python, it should point to the python from the conda environment.

{"argv": ["/home/../../.conda/envs/matlab/bin/python", "-m",

3. Python engine and bindings#

I will be using Matlab R2021b

(matlab) [k@l40106 ~]$ cd /sw/spack-levante/matlab-R2021b-klsayl/extern/engines/python/
(matlab) [k@l40106 python]$ python setup.py build -b $HOME
running build
running build_py
(matlab) [k@l40106 python]$

This will create a directory lib/matlab in your home directory.

4. Move/copy the directory to the conda env#

Now, you move/copy the lib/matlab into path/to/your/conda_env/lib/python3.9/site-packages/matlab

(matlab) [k@l40106 python]$ cd
(matlab) [k@l40106 ~]$ mv lib/matlab/ .conda/envs/matlab/lib/python3.9/site-packages/matlab

Note

You can delete the lib/matlab from your HOME directory if everything work!

Testing#

../../_images/matlab.png

  • start jupyterhub session

  • create a new notebook with matlab kernel

  • disp('hello from MATLAB')

hello from MATLAB

Or try this notebook.

Troubleshooting#

  • Matlab engine not found

ImportError:
Matlab engine not installed:
See https://www.mathworks.com/help/matlab/matlab-engine-for-python.htm

This means you missed step 2.

  • SetuptoolsDeprecationWarning: Invalid version: ‘R2021b’

Downgrade setuptools to version 58.2.0

python -m pip install setuptools==58.2.0

References#

[1] Calysto/matlab_kernel

[2] https://am111.readthedocs.io/en/latest/jmatlab_install.html

[3] http://www.jmlilly.net/jupyter-matlab

How to re-enable the deprecated python kernels?   DKRZ CMIP Data Pool