Dan Guest, Matthew Feickert, Giordon Stark, Danika MacDonnel, Henry Schreiner, Karol Krizka, Kelly Rowland, Kunal Marwaha
Shih Chieh Hsu, Zachary Marshall, Nils Krumnack, Samuel Meehan, Adam Parker
This workshop is organized as a part of the US-ATLAS support center to help you be more
researchers. It is being organized in conjunction with the FIRST-HEP initiative, which allows us to profit from their expertise,
as well as that of the Software Carpentry, the organization which provides this flashy page and two of your
amazing instructors (Read More Here). 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 workshop 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.
The course is primarily aimed at graduate students 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. However, if you will be participating in the afternoon sessions, you should have completed the
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). It is highly recommended that you DO NOT choose to use Windows. If you currently have a windows machine, please make it dual boot with Linux -
follow these instructions.
Code of Conduct: Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.
Accessibility: We are committed to making this workshop
accessible to everybody.
The workshop organizers have checked that:
The room is wheelchair / scooter accessible.
Accessible restrooms are available.
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.
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.
Select "Use the nano editor by default" and click on "Next".
Keep "Use Git from the Windows Command Prompt" selected and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.
Click on "Next".
Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
Select "Use Windows' default console window" and click on "Next".
Click on "Install".
Click on "Finish".
If your "HOME" environment variable is not set (or you don't know what this is):
Open command prompt (Open Start Menu then type cmd and press [Enter])
Type the following line into the command prompt window exactly as shown:
setx HOME "%USERPROFILE%"
Press [Enter], you should see SUCCESS: Specified value was saved.
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 all versions of macOS is Bash, so no
need to install anything. You access Bash from the Terminal
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.
The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
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
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
for keeping your email address private provided at GitHub.
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
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"
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.
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.
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
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).
Download the Python 3 installer 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.)
Open a terminal window.
and then press
Tab. The name of the file you just downloaded should
appear. If it does not, navigate to the folder where you
downloaded the file, for example with:
Then, try again.
Press Return. 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).
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.
If you already have docker running and are comfortable using it, that is fine. However, if it is new to you, it is highly recommended that you DO NOT use Windows during this bootcamp as the use of docker can pose unique challenges due to permissions on most Windows versions. 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
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.
Please read the relevant information on these pages, it should take no more than 5 minutes.
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.
Here are the instructions for two popular Linux distributions:
Instructions for other Linux distributions can be found on the Docker docs pages.
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.