US-ATLAS Computing Bootcamp 2020

Online (link)

Aug 24-28, 2020

10:00 am - 5:00 pm (UTC-5)
8:00 am - 3:00 pm (UTC-7)
5:00 pm - 12:00 am (UTC+2)

Instructors: Matthew Feickert, Giordon Stark, Elizabeth Wickes, Karol Krizka, Justin Chiu, Luke Polson, Amber Roepe, Henry Schreiner, Danika MacDonell, Bingxuan Liu, Alex Schuy, Robin Newhouse

Helpers: Mark Neubauer, Zach Marshall, Nils Krumnack, Adam Parker

General Information

This bootcamp is organized as a part of the US-ATLAS support center to help you be more productive researchers. It is run with the additional help of The Carpentries (Elizabeth Wickes) and IRIS-HEP/Princeton (Henry Schreiner). Both of these organizations aim to help researchers get their work done in less time and with less pain by teaching them basic research computing skills.

This is a hands-on bootcamp that will cover basic concepts and tools, including version control, building code with CMake, testing your code with continuous integration, and packaging/distributing your code with containers. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Before attending the bootcamp, it is necessary to work through the pre-bootcamp exercises

Who: The course is primarily aimed at Ph.D. students and new postdocs within the ATLAS experimental collaboration. However, the morning sessions of each day may be relevant to other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: online at If you need a password or other information to access the training, the instructor will pass it on to you before the workshop.

When: Aug 24-28, 2020. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below). If you currently have a Windows machine, it is recommended to either have Windows Subsystem for Linux (WSL 2) installed or to dual boot Ubuntu. There are some known issues with working with Windows and it will be easier if you avoid it.

Accessibility: We are dedicated to providing a positive and accessible learning environment for all. Captions will be provided for the full bootcamp by White Coat Captioning. Please notify the instructors in advance of the bootcamp if you require any accommodations or if there is anything we can do to make this bootcamp more accessible to you.

Contact: Please email for more information.

Code of Conduct

Everyone who participates in activities related to the Bootcamp is required to conform to the Code of Conduct.



09:40 (UTC-5) Welcome
10:00 (UTC-5) Introduction to Git, Getting started with GitHub
13:00 (UTC-5) Lunch Break
14:00 (UTC-5) ATLAS-GitLab


10:00 (UTC-5) Building Code with CMake
13:00 (UTC-5) Lunch Break
14:00 (UTC-5) ATLAS-CMake


010:00 (UTC-5) Containerization with Docker
13:00 (UTC-5) Lunch Break
14:00 (UTC-5) GitLab Pipelines


010:00 (UTC-5) RECAST and Analysis Preservation
13:00 (UTC-5) Lunch Break
14:00 (UTC-5) RECAST and Analysis Preservation


Module 1 Introduction to Machine Learning
Module 2 Sustainable Software Development


Version Control with Git

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

Building Software with CMake

  • Building a basic program
  • Usage of libraries
  • ATLAS CMake wrappers

Continuous Integration

  • Writing automated tests for code
  • Running automated tests with CI


  • Packaging a project in an image
  • Analysis preservation


To participate in a ATLAS 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.

Install Discord for videoconferencing

If you haven't used Discord before, go to the official website to download and install the Discord client for your computer. You will recieve the invite link to the Discord server for the bootcamp in an email.

Set up your workspace

Like other Carpentries workshops, you will be learning by "coding along" with the Instructors. To do this, you will need to have both the window for the tool you will be learning about (a terminal, your web browser, etc..) and the window for the Discord video stream open. In order to see both at once, we recommend using one of the following set up options:

This blog post includes detailed information on how to set up your screen to follow along during the workshop.

The Bash Shell

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

  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 "Default (fast-forward or merge) is selected and click "Next"
    8. Ensure that "Enable file system caching" and "Enable Git Credential Manager" are selected and click on "Next".
    9. Click on "Install".
    10. Click on "Finish" or "Next".
  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.

Video Tutorial

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 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

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

Video Tutorial

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 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 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 You will need a supported web browser.

You will need an account at 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.

For macOS, 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.

Video Tutorial

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 it is installed along with Git. We would recommend installing another editor described below, like VS Code, in addition.

Others editors that you can use are VS Code, Atom, 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 should be pre-installed. We would recommend installing another editor described below, like VS Code, in addition. See the Git installation video tutorial for an example on how to open nano.

Others editors that you can use are VS Code, Atom, BBEdit or Sublime Text.

Video Tutorial

nano is a basic editor and should be pre-installed. We would recommend installing another editor described below, like VS Code, in addition.

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


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).

  1. Open 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.

Video Tutorial

  1. Open with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open 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 (or Return depending on your keyboard). 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 (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.


Docker is a powerful tool that allows you to perform a virtualization of your environment but completely in software. It allows you to bundle up the installation of tools for use by others in a uniform way and we will be using it throughout this bootcamp. Installing docker is absolutely necessary and there are directions to do this in each operating system. For those of you that are using a Windows operating system, if you already have docker running and are comfortable using it, that is fine. However, if you do not, then be aware that its usage on Windows can be challenging and none of the tutors know how to use such a setup. Therefore, we highly reccomend that you reconsider your decision to use the Windows operating system as a high energy physicist.

  1. It is highly recommended that you DO NOT use Windows. Few individuals use this OS within the HEP community as most tools are designed for Unix-based systems. If you do have a Windows machine, consider making your computer a dual-boot machine - Link to Directions.
  2. Download Docker for Windows instructions.
  3. Docker Desktop for Windows is the Community Edition (CE) of Docker for Microsoft Windows. To download Docker Desktop for Windows, head to Docker Hub.
  4. Please read the relevant information on these pages, it should take no more than 5 minutes.
  1. Download Docker for MacOS instructions.
  2. Docker is a full development platform for creating containerized apps, and Docker Desktop for Mac is the best way to get started with Docker on a Mac. To download Docker Desktop for MacOS, head to Docker Hub.
  3. Please read the relevant information on these pages, it should take no more than 5 minutes.
  4. Another common way to install packages on Mac OSX is via the homebrew package manager. In the case of docker, you can easily install docker by setting up homebrew and executing brew cask install docker.
  1. Downloading and installing Docker for Linux may be slightly more difficult but please contact the organisers or tutors as soon as possible so they can help with any problems.
  2. Here are the instructions for two popular Linux distributions:
  3. CentOS
  4. Ubuntu
  5. Instructions for other Linux distributions can be found on the Docker docs pages.
  6. Be sure to read the Docker documentation on post-installation steps for Linux and managing Docker as a non-root user. This will allow you to edit files when you have started up the Docker container from your image.