Southeast Missouri State University

March 16, 2020

9:00 am - 4:30 pm

Instructors: Carrie Brown

Helpers: Marcus Bond

General Information

These lessons were created using Software Carpentry materials and in the SWC style. 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".

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: Magill Hall of Science - Room 226, 900 Parker Dr, Cape Girardeau, MO 63701. Get directions with OpenStreetMap or Google Maps.

Parking: Attendees with a valid parking permit can park in the lot on the corner of Henderson St. and New Madrid St. Guest parking passes available upon request. Please contact workshop organizers for details

When: March 16, 2020. 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).

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 or for more information.


Day 1

08:30 Check in and Setup
09:00 Automating Tasks with the Unix Shell
10:30 Morning break
11:00 Automating Tasks with the Unix Shell (Continued)
12:00 Lunch break
13:00 Introduction to HPC
14:30 Afternoon break
15:00 Introduction to HPC (Continued)
16:00 Wrap-up
16:30 END


The Unix Shell

  • Files and Directories
  • History and Tab Completion
  • Pipes and Redirection
  • Looping Over Files
  • Creating and Running Shell Scripts
  • Finding Things
  • Reference...

Using HPC Resources

  • Why Use a Cluster?
  • Working on a remote HPC system
  • Scheduling jobs
  • Accessing software
  • Transferring files
  • Best practices for HPC usage


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.

There are several pieces of software you will wish to install before the workshop. Though installation help will be provided at the workshop, we recommend that these tools are installed (or at least downloaded) beforehand.


All students should have an SSH client installed. SSH is a tool that allows us to connect to and use a remote computer as our own. Please follow the directions below to install an SSH client for your system.


Install MobaXterm from

macOS or Linux

Mac and Linux come with SSH clients preinstalled. You do not need to install anything additional.