Duke University
The Edge Workshop Room, Bostock Library, 411 Chapel Dr, Durham, NC 27708Oct 27-29, 2015
9:00 am - 4:30 pm
General Information
The Open Science Grid (OSG) is a national scale distributed infrastructure for scientific computing. The OSG Connect service provides easy access to the resources that OSG provides. The OSG also offers training and tutorials for the scientists and researchers. As part of our training service we are offering an extended Software Carpentry workshop which augments instruction on basic Linux tools and programming with tutorials on using distributed high throughput computing workflows on the OSG. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.
Software Carpentry's mission is to help scientists and engineers become more productive by teaching them basic lab skills for computing like program design, version control, data management, and task automation.
Duke Research Computing offers services that are useful to research computing “as it is practiced” across Duke and often in collaboration with researchers at other institutions. Duke Research Computing offers wide-ranging education and training opportunities to the Duke community and seeks in its activities to bring researchers together who apply computational and quantitative methods to every field represented in the University’s faculty.
This workshop is being run by the OSG, in collaboration with Software Carpentry and Duke Research Computing.
Instructors: David Champion, Bala Desinghu, Rob Gardner, Emelie Harstad, Mats Rynge, Suchandra Thapa
Helpers: Tom Milledge, Lincoln Bryant
Who: The course is aimed at graduate students, post-doctoral researchers and other researchers.
Where: The Edge Workshop Room, Bostock Library, 411 Chapel Dr, Durham, NC 27708. Get directions with Google Maps.
Requirements: Participants must bring a laptop with `SSH` installed (see setup for more details).
Contact: For more information, please email: clv4@duke.edu, balamurugan@uchicago.edu
Registration
Event is free but registration required. Space is limited for the event. To register, please visit here .
Schedule
Introduction to Unix, Oct-27th, 9.00 AM - 12.00 PM
Location: The Edge Workshop Room, Bostock Library
Instructor: Emelie
| 09:00 - 10.30 | Introduction to the Unix shell - (Slides) Emelie |
| 10.30 - 10.45 | Coffee break |
| 10:45 - 12.00 | Introduction to the Unix shell (continued) - Emelie |
| 1:30 - 3.00 | Version control with Git - Bala |
| 3.00 - 3.15 | Coffee break |
| 3:15 - 4.30 | Version control with Git (continued) - Bala |
Python Programming - I, Oct-28th, 9.00 AM - 12.00 PM
Location: The Edge Workshop Room, Bostock Library
Instructor: David
| 09:00 - 10.30 | Building programs with Python (Part 1) - David |
| 10.30 - 10.45 | Coffee break |
| 10:45 - 12.00 | Building programs with Python (Part 1, continued) - David |
Python Programming - II, Oct-28th, 1.30 PM - 4.30 PM
Location: The Edge Workshop Room, Bostock Library
Instructor: Suchandra
| 1:30 - 3.00 | Building programs with Python(Part 2) - Suchandra |
| 3.00 - 3.15 | Coffee break |
| 3:15 - 4.30 | Building programs with Python(Part 2, continued) - Suchandra |
What is High Throughput Computing and how can it speed up my research? Oct-28th, 6.00 PM - 8.00.PM (Special Event)
Speaker: Dr. Robert Gardner
Location: Gross Hall, 2nd floor - Connection Space
| 6:00 - 8.00 | Talk, Pizza and Informal Discussion |
Basics of High Throughput Computing
Oct-29th, 9.00 AM - 12.00 PM
Location: The Edge Workshop Room, Bostock Library
Instructors: Emelie, Mats and David
| 09:00 - 9.30 | Introduction to OSG - (Slides) Emelie |
| 09:30 - 10.30 | Job Scheduling with HTCondor - Mats |
| 10.30 - 10.45 | Coffee break |
| 10:45 - 11.30 | Trouble Shooting Failed Jobs - Mats |
| 11.30 - 12.00 | Connecting the Campus to Grid Resources - David |
Large Scale High Throughput Computing
Oct-29th, 1.30 PM - 4.30 PM
Location: The Edge Workshop Room, Bostock Library
Instructors: Suchandra, Bala and Mats
| 1:30 - 2.30 | Handling Data - Suchandra |
| 2:30 - 3.00 | Scaling Up Computing Resources (R and MATLAB runtime examples) - Bala |
| 3.00 - 3.15 | Coffee break |
| 3:15 - 4.00 | Handling Job Dependencies - DAGMan - Bala |
| 4:00 - 4.30 | Large Scale Computation with Pegasus - Mats |
Setup Instructions
Instructions to set up the required software on Linux, Windows, and Mac laptops, and OSG sign up information.
We will do all the exercises on
login.duke.ci-connect.net. If you
do not have an account on Duke CI Connect, please sign up. If
you have an account on Duke CI Connect but forgot the password, click here. You also
need SSH installed on your laptop. For details, see the
setup guide
Lessons
Course material for the workshop.
Survey
Post Workshop Survey (unix, git and python)
Post Workshop Survey (high throughput computing)