ATLAS+CMS Analysis Preservation Bootcamp

CERN

Feb 17-19, 2020

9:00 - 17:30

Instructors: Stefan Wunsch, Savannah Thais, Giordon Stark, Samuel Meehan, Danika MacDonell, Clemens Lange, Lukas Heinrich

Helpers: Leonora Vesterbacka, Emma Torro Pastor, Brendan Regnery, Mason Proffitt, Thea Aaarestad

General Information

The Run-2 data set is awesome! And both the ATLAS and CMS collaborations are working to make the most of it by creating innovative analyses to learn from the data set. However, these analyses should not disappear when the people who wrote the code move on. Luckily, throughout the course of Run 2, a number of tools have permeated HEP computing culture that can be used to help ensure that analyses are preserved in a robust way, thereby facilitating the reproduction of our own results. This joint bootcamp with members from the ATLAS and CMS collaborations aims to introduce analyzers who are already proficient in basic analysis tools and concepts (e.g. C++, Python, event selection, limit setting) to the next level of robust analysis. This includes CI/CD, Dockerization, REANA/Yadage workflows, and more tools that are used throughout all corners of industry.

Who: If you have ever spent hours banging your head against code that someone gave you as a starting point, either because it doesn’t compile or segfaults immediately upon running or simply spits out empty histograms - this bootcamp is for you. If you know someone who thinks that Docker is so great and won’t stop advocating for it - this workshop is for you. If you are going to be doing science at the LHC in Run 3 - this workshop is for you. And if you are thinking of moving to a career outside of academia - this workshop is for you. This bootcamp will be particularly useful for those who are in the midst of an analysis at the moment, as it will give you knowhow about tools that you can put to practice immediately. However, this is not a pre-requisite for attending, but rather it will be of greatest utility for such individuals.

Where: Meyrin, Switzerland. Get directions with OpenStreetMap or Google Maps.

When: Feb 17-19, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system that they have administrative privileges on. They need access to LXPLUS and should have a grid certificat valid for either the CMS or ATLAS VO. A few specific software packages installed (listed below) will be useful.

Accessibility: We are committed to making this workshop accessible to everybody.

Materials will be provided in advance of the workshop and large-print handouts are available if needed by notifying the organizers in advance. If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email awesome-workshop@cern.ch for more information.


Code of Conduct

Everyone who participates in CERN activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Please also refer to the schedule posted on Indico.

Monday

Before Pre-workshop survey
09:00 Version control with Git
10:30 GitLab CERN
12:00 Lunch break
13:00 Continuous Integration
14:00 Catch-up Time
15:00 ATLAS/CMS GitLab sessions
17:30 Re-Ana Discussion with Theorists and Reception
18:30 END

Tuesday

09:00 Intro to Docker
12:00 Lunch break
13:00 Catch-up Time
14:00 ATLAS/CMS Docker sessions
19:00 Dinner
21:00 END

Wednesday

09:00 CERN REANA
12:00 Lunch break
13:00 Catch-up Time
14:00 ATLAS/CMS sessions
17:00 Wrap-up
17:15 Post-workshop Survey
17:30 END

Syllabus

Git(Lab) Essentials

  • Creating a Repository
  • Recording Changes to Files: add, commit, ...
  • Viewing Changes: status, diff, ...
  • Ignoring Files
  • Working on the Web: clone, pull, push, ...
  • Resolving Conflicts
  • GitLab specifics
  • Where to Host Work, and Why
  • Reference...

Continuous Integration

  • What does continuous integration mean?
  • Writing tests
  • Integrating with GitLab
  • Writing YAML files
  • Reference...

Docker

  • Writing a Dockerfile
  • Building your own containers
  • Using your containers
  • Using container with GitLab
  • Reference...

REANA


Setup

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select "Use the nano editor by default" and click on "Next".
    3. Ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    4. Ensure that "Use the native Windows Secure Channel library" is selected and click on "Next".
    5. Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    6. Ensure that "Use Windows' default console window" is selected and click on "Next".
    7. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    8. Click on "Install".
    9. Click on "Finish".
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

The default shell in some versions of macOS is Bash, and Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in a terminal and press the enter/return key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Git should be installed on your computer as part of your Bash install (described above).

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on macOS and Linux is usually set to Vim, which is not famous for being intuitive. If you accidentally find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are BBEdit or Sublime Text.

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.

Python

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

We will teach Python using the Jupyter Notebook, a programming environment that runs in a web browser (Jupyter Notebook will be installed by Anaconda). For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Video Tutorial
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.
  1. Open https://www.anaconda.com/distribution/#download-section with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter. You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter to approve the default location for the files. Type yes and press Enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.