Notebooks for the IPMU Course : Practical Statistics for Particle Physics Analyses

This is the git repository containing the notebooks for the IPMU statistics course given by L. Moneta and L. Lyons. The agenda of the event is at

http://indico.ipmu.jp/indico/event/119/

The hands-on session of the course consists of Jupyter notebooks which can be run on the CERN SWAN service ( https://swan./cern.ch )

Getting the repository

First thing to do before running the tutorial notebooks is to clone the git repository. The course should be run on SWAN, where dedicated accounts will be provided. n a nutshell, "SWAN (Service for Web based ANalysis) is a platform to perform interactive data analysis in the cloud". It gives you access to the LCG software stacks and to your CERNBOX files.

• If you have a CERN account already you can use it for the course. You need to have an active CERNBOX to use Swan. If you have never used CERNBOX before, you need to just login in (https://cernbox.cern.ch/).

• If you don't have a CERN account, a temporary accounts is made available for the course. CERNBOX shoukd be activated in these account. In case it is not you will get an error connecting to SWAN. In this case please login first at https://cernbox.cern.ch/.

Please fill also the form for the temporary account registration, https://goo.gl/forms/ZhoVzBjiQVEiTjsn2

If you have a local ROOT installation with Python enabled and you have installed also the python Jupyter and Metakernel packages you can run the notebooks locally on your computer, by typing root --notebook In this case you can go directly to the 5th item.

Alternatively you can download a Virtual machine (CernVM) which contains all the needed software to run the notebook locally

Instructions for SWAN:

1. Connect to SWAN ( https://swan./cern.ch )
2. Select Go to my Notebooks
3. Customize SWAN by using the default 88 software stack version or the Development Bleeding Edge. The development version is reccomended if you intend to run some notebooks in Python.
4. Select Start My Session
5. Create a Terminal window, by using the New command in the top right corner
6. Clone the git repository by typing git clone https://github.com/lmoneta/stat-course-ipmu.git
7. Go back to the previous browser window (SWAN Home) and select the stat-course-ipmu directory. The notebook will be now visible
8. Select the desired notebook

Swan and Jupyter notebooks quick start

If you never used jupyter notebooks, you can find some quickstart information at the following links What is a jupyter notebook?, Notebook Basics, Running Code.

For more information on SWAN, see the swan website: https://swan.web.cern.ch

• If you think think the Jupyter notebook is stuck, open a terminal on swan and execute top: if the cpu is not being used (0%) by any of your processes, you may have to restart the Jupyter kernel.

• There is a known issue when executing import ROOT in a Python notebook, which may get stuck. However this problem should not be present anymore with the latest development version of SWAN.

IMPORTANT:

• Please only have one notebook at the time on swan (you have to select the "running" tab and shutdown the notebook when done)
• Please avoid Chrome, it has known problems restarting kernels.
• Try to avoid performing expensive computations: swan is meant for fast prototyping.
  • Each swan container has 2 GB of ram assigned, and only one core assigned

Instructions for using the Virtual Machine Image

Alternatively you can run ROOT and also the notebook using a Virtual Machine which contains all the required software.

• You need to have VirtualBox installed on your computer. If you don't have it download it from https://www.virtualbox.org/wiki/Downloads

• Download the CernVM image from https://cernbox.cern.ch/index.php/s/oKBM14VDqGFT7Wl

• Open the image in VirtualBox and Start the machine

• Login with the given User name and given password

• Open a terminal window

• configure the environment by sourcing this script:

  . . /cvmfs/sft.cern.ch/lcg/views/LCG_88/x86_64-centos7-gcc62-opt/setup.sh

• clone the git repository with the notebooks as described before

git clone https://github.com/lmoneta/stat-course-ipmu.git

• Run the notebook by typing in the terminal

  root --notebook

Instructions for updating the Notebook repository

These are the instructions in case you need to update the repository to get the last version of the notebooks.

• Open first a Terminal window.

• Check first if you have changed some files (Notebooks) in your repository by typing:

git status

• git status will show if you have modified some files (notebooks) locally. In this case, if you don't want to loose your changes just do:

git stash

• Update then your local repository by doing:

git pull --rebase

• Reapply now your changes.

git stash apply

In case of conflicts you might need to fix them by merging manually the changes or copying your modified files in a new directory and clone again the repository, using git clone https://github.com/lmoneta/stat-course-ipmu.git