Lawrence Berkeley National Laboratory

Aug 19-23, 2019

9:00 AM - 6:00 PM

Instructors: Dan Guest, Matthew Feickert, Giordon Stark, Danika MacDonnel, Henry Schreiner, Karol Krizka, Kelly Rowland, Kunal Marwaha

Helpers: Shih Chieh Hsu, Zachary Marshall, Nils Krumnack, Samuel Meehan, Adam Parker

General Information

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.

Before attending the workshop, please work through the pre-workshop exercises
Link to pre-workshop material.


This event is supported by National Science Foundation grants OAC-1829707 and OAC-1829729 (FIRST-HEP), Cooperative Agreement OAC-1836650 (IRIS-HEP) and The Carpentries. Participant support has been provided by the US-ATLAS Operations program through the LBNL Analysis Support Center.

Nitty Gritty Details

Who: 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 pre-workshop material.

Where: 1 Cyclotron Rd, Berkeley, CA 94720, USA. Get directions with OpenStreetMap or Google Maps.

When: Aug 19-23, 2019. 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). 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:

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 samuel.meehan@cern.ch for more information.

Indico: In addition to this workshop page, more information and scheduling can be found on the indico event page - https://indico.cern.ch/event/816946/.

EGroup: Subscribe and communicate using the email list usatlas-computing-bootcamp-2019@cern.ch egroup - Subscribe Here.

Mattermost: Group discussion can also occur dynamically using the Mattermost application - Mattermost Invite Link.


Surveys

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

Pre-workshop Survey

Post-workshop Survey


Schedule

Pre-workshop Activities

Pre-workshop Material Pre-workshop Activities
Software Carpentry Survey Link to SWC Pre-Survey
USATLAS Survey Link to USATLAS Pre-Survey

Monday

09:00 Introduction to Git
12:00 Lunch
13:00 ATLAS-GitLab
12:00 Welcome Reception @ Jupiter Pizza

Tuesday

ATLAS-CMake</td>
09:00 Building Code with CMake
12:00 Lunch
13:00

Wednesday

09:00 Testing in Python and CI/CD
12:00 Lunch
13:00 ATLAS-CI/CD

Thursday

ATLAS/GitLab</td>
09:00 Distribution/Enviornments with Docker
12:00 Lunch
13:00
17:00 Coding after your PhD - Panel Discussion
19:00 Bootcamp Dinner @ Great China

Friday

Module 1 The "Real" Analysis Payload - EventLoop
Module 2 Debugging the Proper Way - GDB

Post-workshop Activities

Software Carpentry Survey Link to SWC Post-Survey
USATLAS Survey Link to USATLAS Post-Survey

Syllabus

Version Control with Git

  • Creating a repository
  • Making a merge request
  • Organizing a project with submodules
  • Usage of CERN GitLab

CMake

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

Continuous Integration

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

Docker

  • Packaging a project in an image
  • Analysis preservation
  • RECAST and 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. Select "Use the nano editor by default" and click on "Next".
    3. 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.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Select "Use Windows' default console window" and click on "Next".
    7. Click on "Install".
    8. 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 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.

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).

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).

  1. Open https://www.anaconda.com/download/#linux with your web browser.
  2. 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.)
  3. Open a terminal window.
  4. Type
    bash Anaconda3-
    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:
    cd Downloads
    Then, try again.
  5. 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).
  6. 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.

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

Download Docker for Windows instructions.

Docker Desktop for Windows is the Community Edition (CE) of Docker for Microsoft Windows. To download Docker Desktop for Windows, head to Docker Hub.

Please read the relevant information on these pages, it should take no more than 5 minutes.


Download Docker for MacOS instructions.

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:

  • CentOS
  • Ubuntu

  • 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.