Applying Best Practices in Practice: SciOps with the Agave Platform

Date: Monday, November 12, 2018 Time: 8:30am - 5:00pm Location: Kay Bailey Hutchison Convention Center, Dallas, TX Registration: Registration

Abstract

Science Gateways provide web-based methods of accessing collection of applications, data services, and tools that enable domain scientists who are not familiar with computers to make use of computational science. Agave provides a collection of these data services and tools in a form that can easily wrap around existing, traditional applications and HPC systems and transform them into a usable gateway.

In addition, over the last four years, the popularity of container technologies such as Docker, Singularity, and Shifter resulted in their adoption within traditional HPC data centers. While not yet the dominant workload within many of the major centers, the portability of containerized applications has led to an explosion in the availability of bespoke and custom built codes alike.

This containerized approach to computational science has enabled contributions by hundreds of new developers by bringing scalable, heterogeneous HPC to the web. It has empowered existing command line users by allowing them to commoditize their existing codes and pipelines as reproducible building blocks, and it has lowered the barrier to HPC for thousands more end users by giving them flexibility in how they interact with science and computation. This tutorial introduces these concepts to a new audience.

Schedule

Time	Presenter	Topic
40 min	Presenter	Introductions and [Overview](https://docs.google.com/presentation/d/1cKXnmUFuGULlSMWsixtitLywcuD9pY7pWaqwdG2FjnI)
10 min	Presenter	Jupyter, Sanbox, and Logging In
20 min	Presenter	Good Enough Practices for Scientific Computing
30 min	Presenter	Code, Build, and Test
20 min	Presenter	Practicing Good Enough Data, Collaboration, and Organization Practices
30 min	Presenter	Hands on with Agave
40 min	Presenter	Docker and Singularity
20 min	Presenter	Practicing Good Enough Software and Change Management Practices
40 min	Presenter	Automation and Benchmarking
20 min	Presenter	Practicing Good Enough Automation & Replication Practices
40 min	Presenter	Packaging, Publishing, and Portability
20 min	Presenter	Practicing Good Enough Publication and Preservation Practices
20 min	Presenter	Practicing Best Practices at Home
10 min	Presenter	Conclusion/Wrap-Up

Presenters

Steven Brandt
Louisiana State University

Biography

Steven Brandt obtained his Ph.D. from the University of Illinois at Champaign-Urbana for his research in numerical simulations of rotating black holes. He currently serves as an adjunct faulty member in the Department of Computer Science & Engineering and is involved in research into making parallel programming more effective. He works with the STEllAR team led by Dr. Hartmut Kaiser, and helps lead the Cactus Frameworks effort. He is PI on grants relating to Cactus Frameworks development and cyberinfrastructure for the Coastal Hazards Collaboratory.

Kathy Traxler
Louisiana State University

Biography

Kathy Traxler is an Education, Outreach and Training coordinator for CCT. She now works with professors, who secured grants needing EOT programs, to develop and implement these programs. Kathy received her B.S. in Computer Science from Southeastern LA University in 1988. She then went to University of Southern MS and received a M.S. in Computer Science in 1991. She taught and was undergraduate advisor in LSU's Computer Science department from June of 1993 through May of 2003. when she moved to CCT to work with students and develop EOT activities.

John Fonner
Texas Advanced Computing Center

Biography

John Fonner earned a Ph.D. in Biomedical Engineering at the University of Texas at Austin, where he used a blend of experimental and computational techniques to study binding interactions between peptides and conducting polymers for implant applications in the nervous system. He joined the Life Sciences Computing group at TACC in 2011 and has served on a number of projects that help life sciences researchers leverage advanced computing resources, both through training and through the development of better tools and cyberinfrastructure.

Rion Dooley
Texas Advanced Computing Center

Biography

Rion Dooley is principal investigator on the Agave Project a Science-as-a-Service API platform allowing researchers worldwide to manage data, run code, collaborate freely, and integrate their science anywhere. His previous projects span areas of identity management, distributed web security, full-stack application development, data management, cloud services, and high performance computing. He earned his Ph.D. in computer science from Louisiana State University. Rion actively puts his wife and two daughters at the top of his list of accomplishments. He hopes his work can someday edge out dancing teddy bears and smear-proof lipstick on their lists of favorite inventions.

Acknowledgement

This material is based upon work supported by the National Science Foundation Plant Cyberinfrastructure Program (DBI-0735191), the National Science Foundation Plant Genome Research Program (IOS-1237931 and IOS-1237931), the National Science Foundation Division of Biological Infrastructure (DBI-1262414), the National Science Foundation Division of Advanced CyberInfrastructure (1127210), the National Science Foundation Computing and Communication Foundations (1539567), and the National Institute of Allergy and Infectious Diseases (1R01A1097403).

Special thanks

Special thanks go out to Shuai Yuan for his help on the Jupyter GUI notebook.