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IMPACT November 2012

N O V E M B E R 2 0 1 2

"What's New in XSEDE" is a monthly e-newsletter providing information on scientific discoveries made possible by the Extreme Science and Engineering Discovery Environment, as well as the people, places, and programs involved. XSEDE is a five-year high-performance computing project supported by the National Science Foundation.

Nuclear Excision Repair of a PAH-derived lesion. Still images extracted from animation courtesy of Yuqin Cai. (Follow link below to see animation.)

How some carcinogens evade removal

A New York University (NYU) research team is using simulations created on XSEDE-allocated resources to understand how some carcinogens evade removal by stabilizing the very DNA they attack. Suse Broyde, a biology professor at NYU, and her team turned to Longhorn, Lonestar and Ranger at the Texas Advanced Computing Center (TACC) to create the simulations. They revealed the lesions caused by the most potent carcinogens were the most resistant to repair. The five-ringed structure of these carcinogens provided ample stacking opportunities, which stabilized the DNA much better than the four- and three-ringed structures of the others that were examined. Knowing which lesions are repair-resistant could play an important role in preventative medicine.

Sherlock unlocks secrets of Big Data at PSC

The Pittsburgh Supercomputing Center (PSC) has a new new data appliance system called Sherlock. It features massive multi-threading, shared memory, and hardware optimizations for exceptionally efficient execution of graph algorithms. Sherlock is an experimental system funded through the National Science Foundation's Strategic Technologies for Cyberinfrastructure (STCI) program, allowing the research community to gain experience with its architecture while tackling exciting research challenges. Sherlock prototype projects include learning about social networks involving online and telephone interactions, cluster finding in astrophysics, and genome sequence assembly.

Read more about PSC's Sherlock

High-tech experiments and simulations put enzymes in motion at NICS

A team of three professors at the University of Tennessee, Knoxville (UTK), is using Kraken at the National Institute for Computational Sciences (NICS) to combine high-tech experiments with high-performance computing to probe the function of critical enzymes. The team applied the experimental technologies of neutron scattering at Oak Ridge National Laboratory and nuclear magnetic resonance spectroscopy at UTK in concert with molecular dynamics supercomputer simulations involving Kraken to gain an in-depth understanding of motions in the enzyme cytochrome P450. Understanding the various internal motions these enzymes undergo to bind different drugs will aid in the design of medicines in the future.

The University of Texas team on the SC12 exhibit floor after learning they won the overall competition. Standing (left to right): John Lockman (TACC), Reid Douglas McKenzie, Anant Rathi, Andrew Wiley, Michael Teng, Steve Sofhauser (Dell), John Cazes (TACC). Kneeling (left to right): Julian Michael, Craig Yeh. Not pictured: Carlos Rosales.

XSEDE-allocated resources aid student victory at SC12

University of Texas at Austin students used a combination of XSEDE-allocated resources that include Longhorn and Lonestar to lead their team to victory during the seventh annual Student Cluster Competition (SCC) at the Supercomputing Conference (SC12) in Salt Lake City. The SCC challenges teams of six undergraduates each in a 72-hour, real-time battle. Mentored by John Lockman, John Cazes, Carlos Rosales-Fernandez of XSEDE and TACC, the team designed, built, optimized and ran the fastest and most efficient cluster computing system, as well as demonstrated the greatest sustained performance across a series of applications and scientific workloads.

NCSA shares in award for excellence in government/industry collaboration

The National Center for Supercomputing Applications (NCSA) and their Private Sector Program (PSP) along with the National Digital Engineering and Manufacturing Consortium (NDEMC) received the 2012 HPCwire Editors' Choice Award for Best HPC Collaboration between Government and Industry. PSP is a founding partner in NDEMC, a public-private partnership to support and enhance the use of modeling and simulation among America's small and medium manufacturers and shares in the HPCwire award. NCSA's PSP assists with digital modeling, simulation, computing, and data challenges enabling companies to reduce production costs, accelerate time to market, and compete effectively in the global marketplace.

Visitors to the booth pinned their location on XSEDE's maps.

XSEDE greets global visitors at SC12

More than 25 XSEDE-related presentations were included in the technical program at the Supercomputing Conference (SC12), and XSEDE partners staffed 14 booths on the exhibit floor. An estimated 1,000 SC12 attendees visited the XSEDE booth throughout the conference and learned more about the project, its progress, its partners and successes during the last year as well pinning their location on XSEDE's world maps.

XSEDE in a nutshell

Following are events, deadlines and opportunities related to XSEDE.

XSEDE issues Call For Participation in annual conference, XSEDE13, July 22-25 in San Diego

Registration now open for Tapia Celebration of Diversity Conference