11:00 am - 6:00 pm EDT (UTC-5) 10:00 am - 5:00 pm CDT (UTC-6) 8:00 am - 3:00 pm PDT (UTC-8) 17:00 - 24:00 CET (UTC+2)
Instructors:
Joseph Haley, Cecilia Duran, Matthew Feickert, Giordon Stark, Elizabeth Wickes, Karol Krizka, Amber Roepe, Henry Schreiner, Elodie Resseguie
Helpers:
Danika MacDonell, Robin Newhouse, Mark Neubauer, Zach Marshall, Nils Krumnack
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 https://indico.cern.ch/e/bootcamp2021.
If you need a password or other information to access the training,
the instructor will pass it on to you before the workshop.
Requirements:
Participants must have access to a computer with a
Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.
All work will be carried out on the UChicago Analysis Facilty. Before the start of the workshop, you must create an account on the UChicago Analysis Facilty (instructions below) and be able to ssh into the UChicago system.
Visit our ATLAS Discourse Forum at CERN (do not confuse with discord 👾) and go to US Tier3 User Support for support and friendly discussion .
Let's play!! :
Let's hang out chatting and playing some minigames at Gather Town
( `ｰ`)/ ~*⌒..●
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
to-be-announced
for more information.
Code of Conduct
Everyone who participates in activities related to the Bootcamp is required to conform to the Code of Conduct.
To participate in this
US ATLAS
workshop,
you will need access to software as described below.
You will also need an account on the new UChicago Tier 3 Center, as well as an up-to-date web browser.
The UChicago analysis facility has an account authorization protocol, so
use your institutional or CERN identity when signing up so that it is easier
to verify people's identity and keep track of information.
If you haven't used Zoom before, go to the
official website
to download and install the Zoom client for your computer.
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, RStudio, your web browser, etc..)
and the window for the Zoom video conference client open.
In order to see both at once,
we recommend using one of the following set up options:
Two monitors: If you have two monitors,
plan to have the tool you are learning up on one monitor and
the video conferencing software on the other.
Two devices: If you don't have two monitors,
do you have another device (tablet, smartphone) with a medium to large
sized screen? If so, try using the smaller device as your video
conference connection and your larger device (laptop or desktop)
to follow along with the tool you will be learning about.
Divide your screen: If you only have one device
and one screen, practice having two windows
(the video conference program and one of the tools you will be using
at the workshop) open together.
How can you best fit both on your screen?
Will it work better for you to toggle between them
using a keyboard shortcut?
Try it out in advance to decide what will work best for you.
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.
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.
From the dropdown menu select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
On the page that says "Adjusting the name of the initial branch in new repositories", ensure that
"Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
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.)
Ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
Ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
Ensure that "Use Windows' default console window" is selected and click on "Next".
Ensure that "Default (fast-forward or merge) is selected and click "Next"
Ensure that "Git Credential Manager Core" is selected and click on "Next".
Ensure that "Enable file system caching" is selected and click on "Next".
Click on "Install".
Click on "Finish" or "Next".
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.
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
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.
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 the default that instructors use in the workshop.
It is installed along with Git.
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.
Video Tutorial
nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.
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).
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)
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.
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.)
Open a terminal window and navigate to the directory where
the executable is downloaded (e.g., `cd ~/Downloads`).
Type
bash Anaconda3-
and then press
Tab to autocomplete the full file name. The name of
file you just downloaded should appear.
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).
Close the terminal window.
Docker
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.
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.
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.
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.
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.