August 16-17 2018
Instructors: Stephen Andrews, Cameron Bates, Andrew Fraser, Christopher Malone
Helpers: Austin McCartney
This set of workshops is designed to teach good software development
practice to students, post-docs and staff from Los
Alamos National Laboratory. Some funding for these lessons has been
provided by the Advanced Simulation and Computing project.
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".
To sign up for this course, visit the IC wiki sign up page. This site is accessible from the internal network. Enter your Z-number and then 'add' the Software Carpentry course. Registration is on a first-come-first-served basis and is limited to 40 participants.
Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
When: August 16-17 2018. 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). They are also required to abide by Software Carpentry's Code of Conduct.
Accessibility: We are committed to making this workshop accessible to everybody. The workshop organizers have checked that:
Contact: Please email firstname.lastname@example.org for more information.
Please be sure to complete these surveys before and after the workshop.
|09:00||Automating tasks with the Unix shell|
|13:00||Building programs with Python|
|09:00||Automation with make|
|13:00||Version control with Git|
We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Enable-WindowsOptionalFeature -Online -FeatureName Microsoft-Windows-Subsystem-Linux
Installing, this may take a few moments...
Installing, this may take a few minutes... Installation successful! Please create a default UNIX user account. The username does not need to match your Windows username. For more information visit: https://aka.ms/wslusers Enter new UNIX username:
Enter new UNIX password:
Enter new UNIX password: Retype new UNIX password:
Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully
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 supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).
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 can be installed on your computer following Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
as Git is a command line program.
For older versions of OS X (10.5-10.8) use the
most recent available installer labeled "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, try
typing the escape key, followed by
:q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.
nano is a basic editor that can be used for all the modules in this workshop, it is included in the Ubuntu distribution
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.
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. 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).
sudo apt-get install python3-numpy python3-matplotlib jupyter-notebook
This should return to the Bash terminal.
import numpy matplotlib exit()
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 DownloadsThen, try again.
yesand press enter to approve the license. Press enter to approve the default location for the files. Type
yesand press enter to prepend Anaconda to your
PATH(this makes the Anaconda distribution the default Python).
GNU make is a tool for automating your workflow
$ which maketo test
$ which maketo test