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IMPACT January 2013

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What's New in XSEDE

J A N U A R Y 2 0 1 3

"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.

From modeling by Finol and colleagues, the interior of an abdominal aortic aneurysm, showing wall thickness and indicating wall stress (increasing from blue to red).

Patient-specific computational modeling

Researchers at The University of Texas San Antonio (UTSA) are using XSEDE consulting and computing resources to better asses risk of abdominal aortic aneurysm (AAA) rupture. Ender Finol, director of the Vascular Biomechanics and Biofluids Laboratory at UTSA, and colleagues used a series of medical images of individual cases to develop protocols for computational modeling of patient-specific AAA features.

XSEDE consultants at Pittsburg Supercomputing Center (PSC) provided advice on options and coding in developing a method to initialize the computational models — to set boundary conditions — based on individual profiles. This method takes into account aortic wall thickness, slice by slice, aiding in predicting wall-stress distribution for each patient. Results from computations on XSEDE-allocated Pople (now decommissioned) and Blacklight at PSC show wall stresses are more sensitive to changes in AAA shape; therefore, suggesting that rupture risk may be characterized in relation to AAA morphology. The goal of this kind of individualized modeling is to asses individual risk in order to help guide decisions about surgical intervention in the future.

Stampede at TACC now online

Performing at nearly 10 petaflops, Stampede at the Texas Advanced Computing Center (TACC) is now operational and available to the national open science community as an XSEDE-allocated resource. The scale of Stampede delivers opportunities in computational science and technology research, from highly parallel algorithms to high-throughput computing, from scalable visualization to next generation programming languages. Any researcher at a U.S. institution can submit a proposal to request an allocation of cycles on the system, with 90% of the system dedicated to XSEDE. Lonestar 4, which went online in Feb. 2011, will remain an XSEDE-allocated resource with Ranger retiring on Feb. 4 after five years of stellar performance and contributions to scientific and engineering research.

Read more about TACC's Stampede

XSEDE deploys Globus Online for data transfer

Globus Online is the first service to pass the XSEDE Operations Acceptance Test. The approval for production deployment makes it an official software service on XSEDE. Globus Online is a file transfer and synchronization service that is specifically geared to the big data needs of the research community, with Web, command line and REST interfaces. This software-as-a-service makes it much simpler for researchers to transfer and synchronize large volumes of data between systems.

Using their XSEDE User Portal credentials, researchers can access Globus Online's simple web interface to move data between any two XSEDE resources. This milestone builds on the long-standing relationship between XSEDE and Globus Online. XSEDE researchers have used their robust file transfer services since the project's inception in July 2011—and it is now a recommended and supported service for all XSEDE users.

ten thousand words of ipsum lorem text as generated by lipsum.

Ten Thousand Words = Lipsum. (2012). 10,000 Words of Generated Ipsum Lorem Text Retrieved January 6, 2012, from http://www.lipsum.com/ . 5 inches squared 30 MB evan meaney + amy szczepanski digital image / usa / 2012

Award-winning unconventional visualizations

An art project created using XSEDE resources has won the jury prize for the Distributed Microtopias exhibition at the 15th Annual Finger Lakes Environmental Film Festival (FLEFF). Performed by the Remote Data Analysis and Visualization Center (RDAV) and University of Tennessee (UT), Knoxville, artist Evan Meaney, the collaborative work entitled "Null_Sets" is a collection of artwork that visualizes the size and structure of data.

The artwork was created using an open-source script developed at RDAV, an XSEDE-sponsored resource, allowing for whole bodies of text to be exported as digital images. This included anything from classic literature to HTML to genomic data. Amy Szczepanski, Research Assistant Professor of Electrical Engineering and Computer Science UT and coordinator of education, outreach, and training for RDAV, says the techniques developed in this project laid the groundwork for a larger project that will likely use the Nautilus supercomputer at the National Institute for Computational Sciences (NICS) in the future.

Using open grid computing to understand brain function

The Brain Trauma Research Center (BTRC) at the University of Pittsburgh is using XSEDE to realize the full potential of brain mapping with the hopes to improve outcomes following brain injury. Brain function is mediated by electrical current within populations of neurons, and Magnetoencephalography (MEG) samples the fluctuating magnetic fields produced by these currents with an array of sensors positioned outside a patient's head. To optimize MEG recordings, BTRC's functional brain mapping method uses a "referee consensus" metric which multiplies the information provided by more than 1,000. Each instance runs independently of all others and is short lived (about four hours), requiring about 500,000 CPU hours to handle a 20 minute data set from each volunteer. This makes the application ideally suited for grid computing, and without XSEDE and the Open Science Grid (OSG), BTRC's effort would have stalled.

XSEDE in a nutshell

Following are events, deadlines and opportunities related to XSEDE.

Submissions for the XSEDE13 conference are due March 8. XSEDE13, July 22-25 in San Diego

XSEDE offering a FREE online parallel computing course

XSEDE and European Grid Infrastructure seek submissions describing collaborative research

Registration open for Tapia Celebration of Diversity Conference