Date: Monday, July 23rd
Time: 8:30 AM to 5 PM
Location: Rivers
For this session at PEARC18, we are piloting a mechanism to help research computing practitioners share and develop solutions with others in the field who share their challenges or interests by providing a hackathon opportunity where interested users can work directly with projects before, during, and after the conference.
Rather than simply working through tutorials, this hackathon will focus on participants bringing their real-world problems and applications and engaging with project developers, hackathon organizers, and each other to create solutions and share these with the community.
The theme of this initial hackathon is reproducible and portable computing. We are featuring several projects around this theme that participants can choose to engage with starting now, at the face-to-face hackathon at PEARC18, and after the conference.
Participants are invited to engage with any of the projects listed below.
Send email to pearc18hackathon@gmail.com to let us know you are planning to join the hackathon and indicate which project(s) you would like to work on.
You may certainly propose to work on aspects of more than one project. The ideas for each project are our suggestions, but we welcome suggestions from participants. Feel free to send any questions to pearc18hackathon@gmail.com.
To help participants gain initial familiarity with a particular project, we provide links to tutorial materials with each project. However, as mentioned, we strongly encourage participants to bring their real-world applications and challenges and use the hackathon as an opportunity to implement something that will benefit them. When possible, we encourage everyone to share their solutions with the community so all can benefit!
Do you have an application you'd like to put into a Docker container to run with Singularity on your own HPC system, an XSEDE system, or another resource? Bring your application to the hackathon and let us help you containerize it!
Check out these container tutorial materials to get you started!
- Get your own real-world workflow (containerized if you wish!) running in the portable workflow manager, Makeflow.
- Harness all available resources (desktops, clusters, clouds, grids) with the Work Queue lightweight distributed execution system.
- Get your workflow included in the official list of Makeflow example workflows!
Check out these Makeflow tutorial materials to get you started!
Bioconda is a channel of the conda package manager specializing in bioinformatics software. Each bioconda package automatically has a Docker BioContainer created for it that is uploaded to Quay.io. There are a number of ways to engage with Bioconda and BioContainers at the hackathon:
- Add or update a bioinformatics package that you need to Bioconda and BioContainers
- Integrate BioContainers with HPC environments
- Improve tools and documentation for working with BioContainers
- A laptop with a wifi connection
- Familiarity with Linux command line
- An XSEDE portal account
- The following software installed on your laptop
- SSH client
- Docker
| Time | Activity |
|---|---|
| 8:30 – 9:00 AM | Introduction to the Hackthon |
| 9:00 – 10:00 AM | Project Overview by Project leads – Form Teams |
| 10:00 – 10:30 AM | Morning Break |
| 10:30 – 12:00 PM | Hack away! |
| 12:00 – 1:30 PM | Lunch |
| 1:30 – 3:00 PM | Hack away! |
| 3:00 – 3:30 PM | Afternoon Break |
| 3:30 – 4:30 PM | Wrap-up hackathon projects and document |
| 4:30 – 5:00PM | Final progress presentations by teams |
Philip Blood, Alex Ropelewski, Marcela Madrid: PSC
Carrie Ganote, Bhavya Nalagampallipapudesh, Sheri Sanders, Tom Doak: Indiana University
Nate Kremer-Herman: University of Notre Dame