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Brock University

March 25-26, 2017

9:00 am - 4:00 pm

Instructors: James Desjardins

Helpers: Andrew Lofts

General Information

Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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".

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.

Where: 500 Glenridge Avenue, St.Catharines, Ontario. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a few specific software packages installed (listed below). They are also required to abide by Software Carpentry's Code of Conduct.

Contact: Please mail jdesjard@sharcnet.ca for more information.


Schedule

March 25th, 2017

Arrival Pre-workshop Survey
09:00 Orientation and Basics of Unix shell
10:30 Coffee
10:45 Automating tasks with the Unix shell
12:00 Lunch break
13:00 Version control with Git
14:30 Coffee
14:45 Version control with Git
15:45 Wrap-up

March 26th, 2017

09:00 Introduction to Octave/Matlab basics
10:30 Coffee
09:00 Handling data and writing functions in Octave/Matlab
12:00 Lunch break
13:00 Introduction to SHARCNet basics
14:30 Coffee
14:45 Using Octave on SHARCNet systems
15:45 Wrap-up
Dismissal Post-workshop Survey

Etherpad: http://pad.software-carpentry.org/2017-03-25-brocku.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.


Syllabus

The Unix Shell, Day 1 AM

  • Files and directories
  • History and tab completion
  • Pipes and redirection
  • Looping over files
  • Creating and running shell scripts
  • Finding things
  • Reference...

Data handling with Octave/Matlab, Day 2 AM

  • Analyzing Patient Data
  • Writing MATLAB Scripts
  • Repeating With Loops
  • Making Choices
  • Creating Functions
  • Defensive Programming
  • Reference...

GIT Version Control, Day 1 PM

  • Creating a repository
  • Recording changes to files: add, commit, ...
  • Viewing changes: status, diff, ...
  • Ignoring files
  • Working on the web: clone, pull, push, ...
  • Resolving conflicts
  • Open licenses
  • Where to host work, and why
  • Reference...

Working with Octave at SHARCNet, Day 2 PM

  • Logging into SHARCNet
  • File management at SHARCNet
  • using login node, development node, and compute nodes
  • loading the Octave software module
  • Using Octave in the development node
  • Introduction to the SHARCNet scheduler
  • Submitting Octave jobs to the scheduler
  • Monitoring jobs at SHARCNet

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.

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Click on "Next".
    4. Click on "Next".
    5. Click on "Next".
    6. Select "Use Git from the Windows Command Prompt" 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.
    7. Click on "Next". Keep "Checkout Windows-style, commit Unix-style line endings" selected.
    8. Select "Use Windows' default console window" and click on "Next".
    9. Click on "Next".
    10. Click on "Finish".

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). You may want to keep Terminal in your dock for this workshop.

Linux

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 (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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.

Linux

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 yum 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 Mac OS X 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.

Windows

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

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.

Mac OS X

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 Text Wrangler or Sublime Text.

Linux

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.

Octave/Matlab

For the Octave/Matlab session using either Octave or Matlab will work. If you already have a Matlab license and it is installed on your computer you do not need to install Octave. If you wish to purchase a Matlab license or install a trial version visit MathWorks (note that a trial installation may take up to a week to set up). Octave is an open source scientific computing language that is highly compatible with Matlab. The instructor of this session will be using Octave 4.0.0 in the demonstrations. For Octave installation instructions visit the Octave Download page.

SHARCNet

SHARCNet is a High Performance Computing (HPC) consortium that offers free resources to Canadian researchers and their international collaborators. The HPC resources come in the form of compute and storage hardware, documentation and training, as well as expert support. In order to take part in the hands on SHARCNet session, attendees are required to have a SHARCNet account prior to arriving at the session. In order to get a SHARCNet account follow these getting a SHARCNet account instructions (note that a SHARCNet account may take up to a week to set up).