FAQ

Basics

Known issues and limitations

Basics


How can I use the Notebook interface?

There is plenty of documentation about Jupyter notebooks online. A gallery of notebooks from which you can start is available on this site.

 


How can I copy data from / to the Cloud?

The mechanism envisaged to carry out such operations is synchronisation via CERNBox. You can always use tools such as wget or scp from the terminal window.

You can find a set of examples here that you can clone in your CERNBox so that they become available to SWAN as well!

 

 


How can I share my work with someone?

All sharing functionalities are entirely delegated to CERNBox. You can share subdirectories of your synchronised space via the CERNBox web interface. See these instructions for more details.

 

 


How can I browse my directories?

There are three ways in which you can browse your files:

  • You can use your own machine simply synchronising CERNBox on your local disk.
  • You can use the CERNBox web interface. You will be able to visualise several file types among which notebooks and ROOT files.
  • You can use the Jupyter web interface. Some file types will be browsablebesides notebooks, mainly textual formats.

 

 


What software packages are at my disposal?

The software is distributed in collections, the LCG releases. An LCG Release is a set of several (~200) software packages consistently built together. These collections of software products are located on CVMFS. The elements of a particular LCG release can be inspected here. ATLAS and LHCb rely for their production software stacks on LCG releases.

 

 


How can I install software that is not provided by the LCG releases?

LCG releases on CVMFS incorporate new packages quite frequently, so if you think there is a missing package that can be potentially useful for a significant number of users, please let the SWAN team know (swan-talk at cern.ch)

On the other hand, you can install packages on your CERNBox and, if necessary, configure your environment to pick them up in SWAN (see Can I customise the environment of my container?). A typical case is the installation of Python packages, which only requires to run pip from a SWAN terminal:

  • pip install --user package_name

As a result of running this command, the package will be installed on your CERNBox and it will be picked by any notebook you open after that. Since the package is on your CERNBox, it will be also available in any new session you start in SWAN.

 

 


Can I customise the environment of my container?

Yes you can. SWAN adopts a "single image approach": a lightweight container image is deployed while CVMFS is exploited to provide all the software.

Before creating your container you are prompted a form which allows you to select:

The environment script is a bash shell script that you can write to define your environment variables.
You can use it to make available to the notebooks packages that you need for your work and are located in your CERNBox (or on EOS). In order to better locate your script on EOS, you can use the CERNBOX_HOME enironment variable: this is automatically resolved to your home directory in EOS.

 

 


I need a normal shell. How can I use one?

You can access a shell on your container in the browser. Just click on the New drop-down menu (upper right corner)

and select Terminal.

 

 


How can I obtain a Kerberos ticket?

You can obtain a Kerberos ticket with the kinit command within a terminal. Alternatively you can achieve that within a notebook. For example, in Python:

import getpass
import os
os.system("echo %s | kinit" %getpass.getpass() ) 

This will open an text box where you will be able to input your password. No risk to save it in the notebook by mistake!

 

 


Can I resume my container after logging out?

Yes, by default you are proposed to go back to your container. Just hit the green My Server button upon login. Please keep in mind that a mechanism is in place to terminate containers which have been inactive for a while.

 


How can I terminate my container?

Go to Control Panel (button on the upper right corner)

 

and then hit the Shutdown my Notebooks button.

 


How can I use notebook extensions?

SWAN provides a set of common notebook extensions, whose description can be found at:

https://github.com/ipython-contrib/jupyter_contrib_nbextensions

In addition, ipywidgets can also be used:

https://github.com/ipython/ipywidgets

 

Most notebook extensions enrich the notebook interface with new JavaScript features and, therefore, they need to be activated before opening a notebook. In order to activate an extension, you can open a SWAN Terminal (see I need a normal shell. How can I use one?) and execute the following command:

  • jupyter nbextension enable extension_name

For example, in the case of ipywidgets you could do:

 

Any notebook you open after activating an extension will show that particular extension. Note that you could also do the activation inside a notebook cell (Python or C++), like in the following example for the spellchecker extension; in this case, you will need to refresh your notebook page after the activation to see the extension.

 

If you want a subset of extensions to be activated every time you open a new session in SWAN, you can include the activation commands in your customization script (see Can I customise the environment of my container?).

 


Where can I find the SWAN logo?

Here you can find the SWAN logos.

 

Known issues and limitations

 


Which browsers have issues with Jupyter?

Up to now two browsers have been identified to be suffering from some issues in rendering correctly Jupyter, in particular in dealing with websockets: Internet Explorer and Chrome.

In case you have troubles you can move to Safari or Firefox.


I cannot open my notebook: what can I do?

If you encounter this error make sure that, from a SWAN terminal, you remove this temporary directory in your CERNBox: ~/.local/share/jupyter. The latest deployment of SWAN implements an optimisation which makes it redundant.


Next morning my session seems dead, why?

Your session is terminated automatically after 6 hours of inactivity. Your notebook is autosaved. Close your window and log in to SWAN again.

 

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