Notebooks Environments

Available Environments in EGI Notebooks

Jupyter is an extensible environment that supports different programming languages. For the EGI service we have enabled two different environments:

  • the default environment including commonly used languages like Python, R, and Julia.
  • the MATLAB environment, for running MATLAB.

After logging into the service, you will be shown a form for selecting the environment, pick the desired one and click start

environmet selection

Default environment

The default environment includes a set of kernels that are automatically built from the EGI-Federation/egi-notebooks-images GitHub repository. These are the ones available:

  • Python: Default Python 3 kernel, it includes commonly used data analysis and machine learning libraries. Created from the jupyter/scipy-notebook stack.

  • DIRAC / Python 2: A python 2 kernel that includes a DIRAC installation for interacting with the EGI Workload Manager service.

  • Julia: The Julia programming language with the libraries described in jupyter/datascience-notebook.

  • R: The R programming language with several packages from the R ecosystem as provided by jupyter/r-notebook and some extra libraries.

  • Octave: The Octave programming language installed on its own conda environment (named octave).

If you want to add a new kernel, just let us know and we will discuss the best way to support your request.

MATLAB environment

EGI offers MATLAB on the cloud using the MATLAB Integration for Jupyter and shares data and code with other EGI users. MATLAB is also available directly on compute services offered by the members of the EGI Federation.

MATLAB on the EGI infrastructure can be used by scientists and engineers for Open Science by enabling them to share their data and code using computational notebooks.

Before getting started

MATLAB Licenses

To use the MATLAB Integration on the EGI Notebooks service, a supported MATLAB license is required. You can also use the toolboxes linked to your MATLAB license.

If you are unsure of your MATLAB license type, contact your System Administrator or MathWorks support.

Tutorials

If you are not familiar or have limited experience with MATLAB, MATLAB Onramp provides a free, self-paced tutorial. Additional Onramps are available for other topics using MATLAB.

Getting started

  1. Once your server has started up (after selecting the MATLAB environment), click on the MATLAB icon

    matlab-icon

  2. A dialog for handling MATLAB licensing will appear.

    • Individual and Campus Wide MATLAB Licenses

      If you have access to a MATLAB Individual License or a MATLAB Campus Wide License, use the Online License Manager tab to log in using your MathWorks account (does not need to match the email used on the EGI Identity Provider) and click on next.

      matlab-online-license

    • Concurrent/Network Licenses

      If you have Network Licenses, enter the port@hostname of your License Server on the Network License Manager tab of the login screen. Before doing so, please check with your system administrator about allowing the EGI access to your on-prem Network License Manager (License Server).

      matlab-network-license

    • Free trial MATLAB Licenses If you do not have a MATLAB license and would like to try it out, you can download a free MATLAB trial license here. Note that the trial license is for MATLAB only and does not have any toolboxes.

    More information on MATLAB licensing with this integration can be found here.

  3. Following this, the MATLAB IDE will appear in your browser.

    matlab-ide

  4. To facilitate sharing your research output, you can use MATLAB Live Scripts combining rich text, equations, images, code and inline output all in one document. Live Scripts can be accessed from the Live Editor tab. Here is an example of a tutorial Live Script from the EGI webinar showing steps required to analyze some public COVID-19 data with MATLAB. Some other examples of Live Scripts can be found here.

Limitations

Browser based MATLAB has some differences as compared to MATLAB on the desktop. For more information, see the limitations here. Additionally, Simulink is not supported on the EGI at this time.

Restarting, stopping or signing out of the MATLAB session

At any time, clicking on this symbol will bring up a dialog to stop, restart or sign out of the current MATLAB session.

matlab-session

matlab-status

Open Science using MATLAB on EGI Notebooks

You can access publicly available datasets via the EGI DataHub and analyze them in-the-cloud directly using MATLAB, without the need for time consuming downloads. Your MATLAB code can also be shared with your community in a variety of interoperable and open formats.

Analyzing public datasets using MATLAB on EGI

This short video and this webinar explains how to access EGI Data Services from MATLAB in detail. Data from different data providers can be accessed from the DataHub. More information on Data Management from Notebooks and persistent storage can be found here.

MATLAB support for data formats

MATLAB supports several scientific and standard data formats including web data and those from specialized hardware.

Sharing data and code

You can share your data and analyses by sharing your EGI provided persistent storage space with others. Users belonging to a specific community can request community Notebooks.

Interoperability with Python and other languages

You can collaborate with users of other languages by calling these languages (eg. Python) from MATLAB for conducting specific analyses. You can also save data in formats compatible with other languages.

Here are some other ways in which MATLAB enables Open Science

Using MATLAB on other EGI services

In addition to MATLAB on EGI Notebooks, you can also use your MATLAB license to access MATLAB on any of the Institutions participating in the EGI Federation. To run your compute-intensive MATLAB code faster or to run code in parallel, you will need MATLAB Parallel Server and MATLAB Parallel Computing Toolbox on your MATLAB license. If you have access to a Campus Wide License , you can now scale up to use all available workers on the HPC cluster of your choice.

To access MATLAB on any site of the EGI Federation, follow these steps.

  • Check if you have access to MATLAB Parallel Server and Parallel Computing Toolbox

  • Ask the system administrator of the site about MATLAB as part of EGI

  • Contact Shubo Chakrabarti at MathWorks or Enol Fernandez at EGI for setting up access to MATLAB at the site.

Last modified July 2, 2021 by Enol Fernández : Add MATLAB docs (#239)