This document covers the frequently asked questions for the EOSC EU Node Interactive Notebooks Service. In case you seek enlightenment on a specific term used in the context of interactive notebooks, you may also try consulting our Glossary.

How do I install library X?

You can install new software easily on the notebooks using mambaa (a fast drop-in alternative to conda) or pip. The %mambaa and %pip magics can be used in a cell of your notebooks to do so, e.g. installing rdkit:

%mamba install rdkit

Once installed you can import the library as usual.

Warning

Any modifications to the libraries/software of your notebooks will be lost when your notebook server is stopped (automatically after 1 hour of inactivity)!

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/
.condarc
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
  • Then the environment will show up in the launcher as a new option

Can I request library X to be installed permanently?

Yes, contact us through the EOSC EU Node Help Desk.

How do I invite someone to co-edit my notebook?

This is referred to as Real-Time Collaboration (RTC Mode) and the procedure is documented in a separate User-initiated sharing and Real-time collaboration.

What happens when I close the browser?

Your server will shut down after an hour of inactivity. That is, if you come back within an hour of disconnecting, you will find your environment as you left it. Once that hour elapses, your home storage is synchronized into the File Sync’n’share service, where you can find your data. Coming back to the interactive notebooks service, the contents of your home directory will be restored from File Sync’n’share, so that you will find your environment almost in the state you left it.

Why does my kernel keep restarting?

During your work the kernel may unexpectedly restart with a message box saying: Kernel Restarting, the kernel for <notebook name> appears to have died. It will restart automatically:

This happens most often because your program runs out of memory. You can close other open files, optimize your notebook for memory use, or request/use a larger server with more memory. Your current memory consumption and quota are shown in the status bar at the bottom of your interactive environment.

Why have my files disappeared?

First a word of assurance: With most probability your files have not disappeared!

Some relevant components of the service ecosystem may experience failures, or undergo maintenance. It is possible that the Interactive Notebooks environment fails to mount (connect) to the File Sync’n’share Service, and your files stored in there are not visible in your file listing.

You can still use the Interactive Notebooks service, but your storage is volatile. Be sure do download your work if you need to keep it.

You may go directly to the File Sync’n’share interface if you need to check your files are there, or access them.

You may try restarting your Interactive Notebooks server using the Hub Control Panel – it will retry mounting your File Sync’n’share storage.

How do I publish my notebooks for others to see?

There are multiple repository services for open science, that accommodate notebooks. A summary of the most prominent ones is available in Publishing Notebooks.

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