Journey to the Compute

Two day hands-on workshop for Docker, Singularity, and leveraging HPC and cloud resources.

Journey to the Compute, Episode 1: Containers to deal with dependencies

Containers and why they're useful

Where can you get containers

1. Pre-built containers

• Docker Hub
• Biocontainers

2. Building your own containers
3. Limitations

• Docker for Windows
• No Singularity
  • Can convert Docker containers into Singularity containers on Windows
  • Docker2Singularity

Journey to the Compute, Episode 2: XSEDE Bound and Down, Dockered Up and Truckin'

Bingo list of resources

• HPC
  1. National a. CyVerse Discovery Environment b. XSEDEComet (GPU!)
  2. Local a. University of Arizona HPC (UA affiliates only)
• Cloud services
  1. Academic a. CyVerse Atmosphere b. Jetstream
  2. Industry a. Amazon Web Services b. Google Cloud Services

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Peer-reviewed Publications

Kurtzer GM, Sochat V, Bauer MW (2017) Singularity: Scientific containers for mobility of compute. PLOS ONE 12(5): e0177459. https://doi.org/10.1371/journal.pone.0177459 Upendra Kumar Devisetty, Kathleen Kennedy, Paul Sarando, Nirav Merchant, Eric Lyons. Bringing your tools to CyVerse Discovery Environment using Docker. DOI: http://dx.doi.org/10.12688/f1000research.8935.3

Tools and Cyberinfrastructure Documentation

Bringing Analysis Apps to the CyVerse Discovery Environment Docker2Singularity support moving Docker containers into Singularity containers in Windows and Mac.

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Useful Links

• Clouds, Clusters, and Containers workshop
• Docker with CyVerse webinar and demo

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Acknowledgements

This work was adapted from previous work done by Upendra Devisetty (@upendrak), Tyson Swetnam (@tyson-swetnam), and John Fonner (@johnfonner).

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Workshop Events

• Meetup Day 1 June 2017 Attendees: 35

• Meetup Day 2 July 2017 Attendees: 31