Users: Default Environment

Mon, 01 Jan 0001 00:00:00 +0000

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

These are the available kernels:

Python: Default Python 3 kernel, it includes commonly used data analysis and machine learning libraries. Created from the jupyter/scipy-notebook stack.
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.
RStudio: RStudio Server offers a RStudio IDE from the Notebooks interface.
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.

CVMFS

Notebooks mounts several CVMFS repositories where you can find software relevant to your community. These are accessible from the default CVMFS location /cvmfs and also linked in your home directory /home/jovyan/cvmfs. These repositories are available:

atlas-condb.cern.ch
atlas.cern.ch
auger.egi.eu
biomed.egi.eu
cms.cern.ch
dirac.egi.eu
eiscat.egi.eu
grid.cern.ch
notebooks.egi.eu

If you need access to any other repositories, please open a request in GGUS.

Installing your own kernels/environments permanently

If you want to have a completely customised environment for your Notebooks that persists across sessions, you can create your own conda environment in your home directory. Thanks to the nb_conda_kernels plugin these will show up automatically as an option to start notebooks with by following these steps:

Create a $HOME/.condarc file specifying where your environments will be created, e.g. in /home/jovyan/conda-envs/:
```
env_dirs:
 - /home/jovyan/conda-envs/
```
Create your environments as needed, make sure to install a kernel (ipykernel) for it to show automatically:
```
$ conda create -p /home/jovyan/conda-envs/myenv ipykernel scipy
```
The environment will show up in the launcher as a new option

Users: MATLAB

Mon, 01 Jan 0001 00:00:00 +0000

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

Once your server has started up (after selecting the MATLAB environment), click on the MATLAB icon
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.
- 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).
- 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. Note that the trial license is for MATLAB only and does not have any toolboxes.
More information on MATLAB licensing with this integration.
Following this, the MATLAB IDE will appear in your browser.
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. Check other examples of Live Scripts.

Limitations

Browser based MATLAB has some differences as compared to MATLAB on the desktop. For more information, see the limitations. 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.

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.

Analysing 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. Check Data Management documentation.

MATLAB support for data formats

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

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
Get in touch via GGUS for setting up access to MATLAB at the site.

Documentation – Notebooks Environments