University of Nebraska - Lincoln

Sept. 8-9, 2016

9:00 am - 5:00 pm

Instructors: Emelie Harstad, Jingchao Zhang, Adam Caprez

Helpers: Huijun Zhu, Natasha Pavlovikj, Derek Weitzel, David Swanson, William McClung

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: Nebraska Union (City Campus) - Colonial Room / 1400 R Street, Lincoln, NE 68588. Get directions with OpenStreetMap or Google Maps.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating sytem (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.

Contact: Please mail hcc-support@unl.edu for more information.

Schedule

Day 1

08:30-09:00 Set-up / Accounts
09:00-09:30 HCC Overview
09:30-10:30 Automating Tasks: Bash/Shell Programming
10:30-10:45 Coffee Break
10:45-12:00 Automating Tasks: Bash/Shell Programming (continued)
12:00-13:00 Lunch Break (sponsored by Dell)
13:00-14:30 Automating Tasks: Bash/Shell Programming (continued)
14:30-14:45 Coffee Break
14:45-17:00 Version Control with Git

Day 2

08:30-09:00 Set-up / Accounts
09:00-10:30 Introduction to HCC: resources, data handing, software modules and job submission
10:30-10:45 Coffe Break
10:45-12:00 Introduction to HCC: resources, data handing, software modules and job submission (continued)
12:00-13:00 Lunch Break (sponsored by Dell)
13:00-14:30 Parallel Programming with MPI
14:30-14:45 Coffee Break
14:45-16:00 Debugging and Profiling Tools

Etherpad: https://public.etherpad-mozilla.org/p/2016-09-08-UNL.
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.

Setup

  1. To participate in this workshop, you will need to sign up for an HCC account (if you do not already have one). Please complete the account application and DUO two-factor authentication setup before Thursday. This process requires advisor approval (via email) and a visit to the HCC offices in the Schorr Center to activate your account, so it can sometimes take a day or more to complete. Please plan accordingly. If you still do not have your account set up by Thursday, please arrive at the workshop by 8:30 a.m. to get help.

  2. Once you have your HCC account and DUO set up, please make sure that you are able to log into the HCC clusters (instructions for Windows Users and Mac/Linux Users). If you have any problems logging in, please email: hcc-support@unl.edu.

  3. *** Workshop Day 1 only! *** 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. If you are participating in the Git lessons on the first day of the workshop (Sept. 8th), you will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above). You will also need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free.

  4. *** Workshop Day 2 only!*** On Friday we will be demonstrating Allinea Performance Reports on HCC for profiling and debugging software. Please follow the setup instructions here before arriving on Friday. If you have any problems, please email us at hcc-support@unl.edu or arrive by 8:30 a.m. to receive help with the setup.

  5. *** Workshop Day 2 only!*** The Anvil lesson on Friday will require you to connect the the Anvil VPN. Please install the VPN client on your laptop in advance. Instructions here.