10:00 AM - 2:00 PM (Oct. 21), 11:00 AM - 3:00 PM (Oct. 25)
Instructors:
Danika MacDonell
General Information
This is an interactive hands-on tutorial covering the tools involved with developing a RECAST framework for ATLAS analysis preservation and re-interpretation. The tutorial is adapted from a RECAST tutorial given as part of the first US-ATLAS Computing bootcamp organized by Samuel Meehan that ran at Lawrence Berkeley National Lab in Aug. 2019.
The first 4-hour session on Oct. 21 will cover the basic tools involved with RECASTing an ATLAS analysis, specifically code/environment preservation with gitlab-ci and docker, and yadage syntax and run commands for preserving and automating the analysis workflow. Due to the hands-on nature of this tutorial, the Oct. 21 session will only be offered on-site at the University of Victoria. However, anyone interested in the material but unable to attend the session in-person is more than welcome to check out the software-carpentry style lesson material and send any questions to the tutorial instructor (danikam1@uvic.ca), who will do her best to post the lesson material a few days in advance :-).
The second 4-hour session on Oct. 25 is more open-ended, but is broadly intended as an opportunity for the participants and instructor to discuss any lingering questions or concepts that may still be unclear from the first session, or to bring up questions/issues specific to individual analyses. This session will be offered both on-site and remotely, and anyone who may have gone through the lesson material from the first session independently is more than welcome to join in and participate in the discussion.
Participants will be encouraged to share their own expertise and help one another throughout the tutorial.
Nitty Gritty Details
Who:
The course is primarily aimed at analysts who are familiar with ATLAS software and git, and would like to learn the tools and steps involved with preserving their ATLAS analysis using the RECAST framework. No prior familiarity with docker or RECAST is required, but participants are asked to have docker installed on their laptop beforehand to save time during the tutorial (see instructions below).
Where:
3800 Finnerty Rd, Victoria, BC, Canada V8P 5C2.
Get directions with
OpenStreetMap
or
Google Maps.
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.
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.
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
(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. Many macOS users perfer iTerm2, use brew cask install iterm2 to install with Homebrew.
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
install anything.
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).
Git is part of the command-line tools for Xcode on macOS.
Run in a terminal:
xcode-select --install. This is needed for almost any
development on macOS, since it includes your compilers. If you use homebrew,
brew install git will get a slighly newer version.
Optionally install Xcode from the Mac App Store.
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. Many other editors are available in homebrew and homebrew cask.
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 the tutorial. 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 the instructor may not be able to
help with setting it up during the tutorial.
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.