Content about TeraGrid

Video of the Week - Earthquake simulation wins SciDAC award

The many visualizations that come out of high performance computing centers can be fantastically beautiful. This simulation of a 7.8 magnitude earthquake in Southern California is no exception.
That's probably why it was recognized recently at the SciDAC (Scientific Discovery through Advanced Computing) Vis Night awards as one of the top ten scientific visualizations of 2009.
The simulation, which has been affectionately dubbed 'The Big One,' used resources via the San Diego Supercomputer Center, the Texas Advanced Computing Center, the Southern California Earthquake Center, and Teragrid.
This video of The Big One was recently posted on the WIRED Science Blog, along with the other nine award winners. Check out the rest, which are just as fantastic, at www.wired.com/wiredscience.
—Miriam Boon, iSGTW

Feature - Computing enables identification of microbe DNA in soil

Jonathan Eisen collects samples gathered by the Alvin submarine during a recent trip to the ocean floor.
Image courtesy of J. Eisen, UCD.

The traditional method for studying a microbe is to cultivate it in the lab and examine its biology in detail. However, lab cultivation is possible for only a small fraction of microbe species. Scientists have thus turned to metagenomics – the computation-reliant study of DNA extracted from environmental samples rather than from cultivated organisms.In metagenomics, scientists grind up samples containing many different organisms and extract all the DNA they can, not knowing which pieces of DNA came from which organisms. A one-gram soil sample can contain up to several million species of microbes all mixed together. The scientists sequence small, random fragments of the DNA to identify species and determine how they function, explained Jonathan Eisen, University of California,

Feature - Grid-enabled virus hunting

3D replica of senecavirus, a pathogen discovered several years ago by researchers in Pennsylvania. UC San Francisco researcher Eric Delwart and his colleague Chunlin Wang of Stanford University use the RENCI-developed TeraGrid Science Gateway and the Open Science Grid to access grid computing resources in their search for new viruses.
Image courtesy of the Institute for Animal Health, UK

Researchers use distributed computing to make sequence analysis faster and easier.DNA sequencing and sequence analysis happens daily in many biological sciences laboratories, but analyzing large sets of genetic data increasingly requires computing resources beyond the capabilities of most labs. The search for the best hardware and software led Eric Delwart, a professor of laboratory medicine at the University of California, San Francisco, and a senior investigator at the Blood Systems Research Institute, and Chunlin Wang, a research associate at the Stanford Univ

Feature - Poker, parallelism and payoff

Image courtesy of PSC

You won’t find them at the Vegas casinos and what they do is hard to call gambling, but it’s fair to say that Tuomas Sandholm and grad student Andrew Gilpin of Carnegie Mellon’s School of Computer Science are professional poker players. Last July in Chicago — at the AAAI (Association for the Advancement of Artificial Intelligence) Computer Poker Competition, involving 19 programs from six countries — they walked away with no pile of cash but, nevertheless, were the biggest winners. Their field, game theory, in which Sandholm’s work is internationally recognized, describes conflict in which the payoff is affected by actions and counter-actions of intelligent opponents. Head-to-head poker between two players is a prominent example of what’s called two-person zero-sum games: One player wins what the other loses.
In recent years, poker has emerged as an AI challenge much as chess was for

Announcement - TeraGrid announces new GIG director Matt Heinzel. Image courtesy of TeraGrid  Chicago native Matt Heinzel, former deputy director for TeraGrid's Grid Infrastructure Group (GIG), became the new GIG director on April 2. In this role, he occupies an office at Argonne National Laboratory, not far from the University of Chicago, where TeraGrid coordinates the GIG. “Matt has been serving as the lead administrative officer of the TeraGrid GIG. Appointing him to the position of GIG director was an easy decision for me and a well-deserved promotion for Matt," said Ian Foster, TeraGrid GIG principal investigator. “His dedicated leadership has helped to shape TeraGrid as we know it. I look forward to working with him in this new role.”  Heinzel brings with him many years of technology-related administrative experience. Prior to leading the TeraGrid GIG, he held various senior information technology management positions, including Technical Services Director, Senior Manager of Business Syste

Announcement - Student participation in TeraGrid 2009 Image courtesy of TeraGrid  High school, undergraduate and graduate students are invited to participate in TeraGrid 2009 as volunteers, by submitting posters, and by competing in a programming contest.Venue: Arlington, Virginia Dates: TeraGrid '09: 22-25 June 2009Register as volunteer: by 15 May 2009Submit poster: by 15 April 2009Register a team for programming contest: by 15 April 2009 Contacts:Volunteers:  Jenett TillotsonPosters:  Scott Lathrop or Edee Norman WizieckiProgramming contest: Charlie Peck This email address is being protected from spam bots, you need Javascript enabled to view it This email address is being protected from spam bots, you need Javascript enabled to view iThe 2009 TeraGrid conference to be held June 22-25 in Arlington, Virginia, will showcase the capabilities, achievements, and impact of this national network of high-performance computing resources. Students from high school through graduate programs

Feature - Nancy Wilkins-Diehr: “Follow what you enjoy” Nancy Wilkins-Diehr, head of the TeraGrid Science Gateways, shown passing the final “gateway” at the Boston Marathon. “I'm probably best known at the Supercomputer Center for my running at lunchtime,” she says. She also enjoys cooking, entertaining, playing flute and spending time with her husband and 12-year-old son Julius. Image courtesy of Boston Athletic Assn. ISGTW interviewed Nancy Wilkins-Diehr, head of the TeraGrid Science Gateways project. She shared her thoughts on her work, how she got where she is, and how young people can keep their career options open. iSGTW: Please tell us what you do in TeraGrid.NW-D: I lead the Science Gateways program in the TeraGrid.  The gateway program connects high end supercomputers with Web portals designed by scientists for scientists.  We're able to extend the capabilities of scientists, often without them even knowing they are using the TeraGrid.iSGTW: What has been your career path

Video of the week - Remarks from a grid school graduate Video courtesy of John Urish. Samer Al-Kiswany, a graduate student at the University of British Colombia, attended the Florida International Grid School in January 2008.In November, while attending SC08, he spoke with Open Science Grid about what he learned at the school and how it has helped him move forward with his research.Al-Kiswany describes his motivation for attending the school, enumerates the most valuable things he learned there, and discusses his current work and achievements in his field of grid storage.The 2008 school was organized jointly by Open Science Grid, TeraGrid, the SC07 Education Program together with CHEPREO, CIARA at Florida International University, and the Computation Institute of The University of Chicago.

Announcement - Deadline to apply for time on TeraGrid: 15 Jan Image courtesy of TeraGrid   Last chance—hurry! Scientists, engineers, and other U.S. researchers have until January 15, 2009 (12:00 midnight local times) to apply for allocations of high-performance computer time and storage resources that are available through the TeraGrid for the allocation period of: April 1, 2009, through March 31, 2010 A simpler application process is now in effect.  Awards of any size can now be submitted to any of the four quarterly allocations review meetings via POPS, the system for TeraGrid allocation requests. Start-up and education staff allocation requests are handled separately.  More information  

Feature - Security through collaboration, part I: Today’s cyber security climate Once, most attacks on computer systems were committed by individuals, motivated by ego gratification, greed or revenge. But as computing resources increase in size and complexity, cyberattacks are increasingly the work of criminal organizations and hostile governments, motivated by large-scale illicit financial profit, sabotage, and espionage.Image courtesy of NCSA. Randal Butler, Co-Director of the CyberSecurity Directorate at the National Center for Supercomputing Applications, University of Illinois , contributed this article, the first of a two-part series.The grid offers many advantages for computing, as we all know. But it offers one singular disadvantage: a grid is only as strong as its least secure site. The cyber attacks we see today typically span multiple systems, sites and even countries, as attackers use increasingly sophisticated methods both to gain access and to obfuscate their location. FBI sources tell us that today’s att

Feature - Office of Cyberinfrastructure at NSF: the first two years Daniel Atkins is a professor in the School of Information and the College of Engineering at the University of Michigan and Associate Vice President for Research Cyberinfrastructure.Image courtesy of Daniel Atkins. Cyberinfrastructure (CI) has become a vital tool for scientific research and discovery.  A system of distributed computing, storage, software and management using the network as its backplane, and for which the complexity is largely hidden from the user, CI has the potential for revolutionizing the way science and engineering research is conducted, says Daniel Atkins, former and initial director of the National Science Foundation’s  Office of Cyberinfrastructure.With an initial annual budget of $185 million, the office coordinates and supports the development of CI resources, tools, and services. In its conception, the office focused almost exclusively on high performance computing. Over the course of Atkins’ tenure, its vision bro

Feature - GEON A model showing a three-dimensional view of a typical landscape, without Lidar. Image courtesy of Chaitan Baru A mysterious world of complex geological processes lies hidden beneath the earth’s crust and produces the amazing topographic features on the surface. To better understand these hidden processes, scientists must probe the earth’s surface for clues of what goes on underneath.To do this, geoscientists use lasers to scan earth’s surface and capture elevation points over large areas with high accuracy. These Light Detection and Ranging (LiDAR) scans allow geoscientists to map key topographic regions more precisely than ever before. The current collection of LiDAR data sets contains more than 7 billion data points, amounting to close to 5 terabytes of data.The problem is that to store, process and analyze these large data sets requires extensive computing resources that many scientists do not have. To solve this problem, the Geosciences Network (GEON) project, based at the San Diego Supercomp