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CCL Workshop 2012

"Scalable Software for Scientific Computing"

Monday, June 11-12th, 2012 at the University of Notre Dame

The 2012 CCL workshop will be held June 11-12th on the campus of the University of Notre Dame. The theme of this year's workshop is Scalable Software for Scientific Computing. This workshop is an opportunity to learn more about scalable software from the CCL and other related projects, see how others are applying it to advance their research, and to provide some input into the direction of our research and software development. The workshop will be of interest to researchers, faculty, and students involved in either the scientific objectives or the software tools of scalable science.

The first day of the workshop will feature a lineup of experts in scalable scientific computing, particularly those with applications in the fields of bioinformatics, molecular dynamics, and high energy physics. These speakers will discuss their scientific objectives, present their current techniques for scalable computing, and reflect on the current software-related barriers to new discovery. The second day will consist of presentations from the CCL team on new developments in our software, followed by informal breakout sessions where you can meet with members of the CCL team to exchange ideas, get help with technical problems, and plan out future software developments.


Monday, June 11th, 200 McKenna Hall Conference Center

8:30 - Welcome and Introduction

  • Welcome and Introduction
    Douglas Thain, University of Notre Dame
  • 8:45 - Workflows in Bioinformatics and Genomics

  • Use cases and challenges of distributed workflows at JCVI
    Andrey Tovchigrechko, J. Craig Venter Institute
  • Why I finally BLASTed five hundred million sequences (and the many ways it failed)
    Scott Emrich, University of Notre Dame
  • Assemble ALL the things: Tackling soil metagenomics
    C. Titus Brown, Michigan State University
  • Is there an app for that?
    Nirav Merchant, University of Arizona
  • 10:15 - Coffee Break

    10:30 - Massively Parallel Molecular Dynamics Applications

  • Development and Application of an Automatic Force Field Optimization Method
    Lee-Ping Wang, Stanford University
  • Massively Parallel Ensemble Methods Using Work Queue
    Badi Abdul-Wahid, University Notre Dame
  • Large-Scale Reactive Molecular Dynamics: Methods, Applications, and Challenges
    Ananth Grama, Purdue University
  • GPU-Accelerated Analysis of Petascale Molecular Dynamics Simulations with VMD
    John Stone, University of Illinois - Urbana/Champagne.
  • 12:00 - Lunch

    A buffet lunch of soup, sandwiches, and dessert will be served at the Morris Inn, just across the street. After lunch, we suggest you take a leisurely 15-minute stroll up the quad to see the golden dome, and then return to McKenna Hall.

    1:30 - Data Management in High Energy Physics

  • Chirp in the ATLAS Computing Environment
    Rodney Walker, CERN
  • Data Management Challenges in CMS
    Michael Hildreth, University of Notre Dame
  • Any Data, Any Time, Anywhere: Increasing data accessibility for HEP
    Brian Bockelman, University of Nebraska
  • CernVM-FS in Parrot
    Daniel Bradley, University of Wisconsin
  • 3:00 - Coffee Break

    3:15 - Floods and Earthquakes!

  • Storm surge predictions on Azure and HathiTrust Research Center: two datapoints in the large-scale space
    Beth Plale, Indiana University
  • Managing and preserving data for the NEES distributed earthquake engineering community
    Thomas Hacker, Purdue University
  • 4:00 - Open Discussion

  • How can the CCL most effectively support your research activity?
  • What software features and capabilities are most essential?
  • How can we improve our software development process?
  • How should NSF software projects interact with each other?
  • 5:00 - Adjourn

    Dinner Monday night is on your own. We suggest meeting about 7pm at Eddy Street Commons for a variety of casual dining options.

    Tuesday, June 12th, 200 McKenna Hall

    8:30 - New Developments From the CCL Team

  • Release Management and New Capabilities in Chirp
    Patrick Donnelly, University of Notre Dame
  • What's New in Work Queue
    Michael Albrecht, University of Notre Dame
  • Elastic Applications in the Cloud
    Dinesh Rajan, University of Notre Dame
  • A Compiler Toolchain for Workflows
    Peter Bui, University of Notre Dame
  • 10:15 - Coffee Break

    10:30 - Small Group Breakout Sessions

  • Workflows and Bioinformatics - 200 McKenna Hall
  • Work Queue and Molecular Dynamics - 108 DeBartolo Hall
  • Data Access and High Energy Physics - 113 DeBartolo Hall
  • 12:00 - Adjourn


    Registration is now closed.


    Notre Dame is a 15 minute taxi ride from the South Bend Airport (SBN). The South Shore Line also offers rail service from downtown Chicago to the South Bend Airport. By car, Notre Dame is just off exit 77 on Interstate 80/90, about 1.5 hours from Chicago.

    Rooms have been reserved at the Inn at St Mary's, please reserve with the group code 120610NDAC. The hotel offers regular shuttle service to/from the Notre Dame campus, just call 574-232-4000 to arrange a pickup. Another option is the Ivy Court Inn, which is a 10-15 minute walk from the meeting location.

    Both Monday and Tuesday mornings will begin in room 200 of the McKenna Hall Conference Center. Tuesday breakout sessions will be in various offices in Fitzpatrick Hall.

    The following map shows the hotel and the meeting location:

    View CCL Workshop Map in a larger map