ASCR Monthly Computing News Report - July 2008

The monthly survey of computing news of interest to ASCR is compiled by Jon Bashor (JBashor@lbl.gov) with news provided by ASCR Program Managers and Argonne, Fermi, Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, Pacific Northwest and Sandia National labs. Contact information and links to additional information, where available, are included with each article.

In this issue...


R&D100 Award for LBNL's SciDAC-Supported Search Technology
An indexing technology developed by researchers at Lawrence Berkeley National Laboratory which allows users to search massive datasets up to 40 times faster has been recognized with a 2008 R&D 100 award. The award, presented by R&D Magazine, "provides a mark of excellence known to industry, government, and academia as proof that the product is one of the most innovative ideas of the year." The awards will be presented at a special ceremony in Chicago in October.
FastBit was developed by Kesheng "John" Wu, Arie Shoshani, Ekow Otoo, and Kurt Stockinger of the Scientific Data Management Group in Berkeley Lab's Computational Research Division. The project was supported by the Department of Energy's Scientific Discovery through Advanced Computing (SciDAC) program, which develops software for accelerating computational science. For more information about FastBit, select the link below
UCI Researchers, OLCF Staff Conduct Breakthrough Fusion Simulation
A team of researchers from the University of California-Irvine (UCI), in conjunction with staff at Oak Ridge National Laboratory's Leadership Computing Facility (ORLCF), completed what it says is the largest run in fusion simulation history. The team, led by Yong Xiao and Zhihong Lin of UCI, used 93 percent of the ORLCF's flagship supercomputer Jaguar, a Cray XT4, with the fusion code GTC (Gyrokinetic Toroidal Code), the key production code of two fusion SciDAC projects (GPS-TTBP and GSEP). The simulation primarily studied electron transport in ITER (because in ITER the fusion process will primarily heat electrons, electron transport will be more important compared to existing fusion devices). ITER is the international fusion reactor project being built in France.
To successfully produce a fusion reaction, an extremely hot ionized gas known as a plasma must be confined magnetically for a sufficient period of time. Previous research has shown that heat transport for both the ions and the electrons in the plasma is far greater than theory predicts (the electron heat transport can be two orders of magnitude greater). This larger-than-expected heat transport could lead to confinement failure within one second, quickly rendering energy production impossible if reactor designs are not modified to accommodate it. The researchers discovered, among other things, that for a device the size of ITER, the containment vessel will demonstrate GyroBohm scaling, meaning that the heat transport level is inversely proportional to the device size. In other words, the simulation supports the ITER design: a larger device will lead to more efficient confinement. "The success of fusion research depends on good confinement of the burning plasma," said Xiao. "This simulation size is the one closest to ITER in terms of practical parameters and proper electron physics."
Contact: Jayson Hines, hinesjb@ornl.gov
EMSL and NERSC Computers Contribute to Search for Green Alternative to Gas
One hurdle to producing hydrogen as an affordable, green alternative to gasoline is the exorbitant price of platinum, gold, and other precious metals used to drive the catalytic reactions. Scientists from Pacific Northwest National Laboratory's Institute for Interfacial Catalysis and Southern Illinois University completed a theoretical study on how an inexpensive ceria catalyst can decompose a simple alcohol into hydrogen. To conduct this research, the team used the supercomputer and VASP software in the DOE's Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility at PNNL, and the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory. Citation: Mei D, NA Deskins, M Dupuis, and Q Ge. 2008. "Density Functional Theory Study of Methanol Decomposition on the CeO2 (110) Surface." Journal of Physical Chemistry C 112(11):4257-4266.
Researchers Seek lingua franca so Fusion Codes Can Converse In Coupled Model
Physicist Don Batchelor of Oak Ridge National Laboratory is trying to solve a Babel-esque problem by creating a common language and a computational framework that will allow diverse software codes to communicate with each other in simulations of plasma - the hot, ionized gas that fuels nuclear fusion reactors. Right now only some codes can share data. Different data formats and data names confound communication between many codes. Also challenging is getting codes to couple, or provide information to other codes at specific times to solve equations about the evolving state of plasma.. Coupling is a tough task because a factor described by one code depends on another factor described by some other code. “We’ve developed basically a lingua franca whereby different physics codes can talk to each other,” Batchelor says.
He and a team of more than two dozen researchers at 10 institutions used resources at the Oak Ridge Leadership Computing Facility to make progress toward developing an integrated plasma simulator. The work was made possible with an allocation of 1.7 million processor hours on the facility’s Cray Jaguar XT4 supercomputer through the INCITE program. Controlling plasma is the key to producing energy from future commercial reactors, and improved simulation capability is needed to support ITER, Batchelor says.
Contact: Jayson Hines, hinesjb@ornl.gov
ALCF Blue Gene/P Helps Identify Electrical Mechanisms for Cardiac Arrhythmias
In work funded by the National Institutes of Health, Gene Network Sciences researchers are using INCITE allocations on the Argonne Leadership Computing Facility's Blue Gene/P to rapidly test hypotheses for the initiation and maintenance of cardiac rhythm disorders. These large-scale computer simulations represent a promising tool to help identify the underlying electrical mechanisms for dangerous arrhythmias and determine the effects of interventions, such as drugs, that may prevent or exacerbate these arrhythmias.  Certain activation sequences have proven to be particularly effective at inducing arrhythmias in canine experimental models. The researchers plan to study these sequences in large-scale simulations of the canine heart to identify the mechanism by which wave break and the induction of an arrhythmia might occur.
Contact: Jeff Fox, jeff@gnsbiotech.com
OLCF System Models Hummingbird Flight
Hummingbirds, despite their small size, may be the key to big advances in aerial surveillance technology. "The mechanisms these animals employ to sustain flight do not seem to follow traditional aerodynamic theory and practice," said Andrew Johnson of Digital Rocket Science, who recently used the Phoenix supercomputer at Oak Ridge National Laboratory's (ORNL's) Leadership Computing Facility (ORLCF) to model and better understand the hummingbird's flight. One potential application of this research is the more efficient design of micro air vehicles, tiny machines that could mimic hummingbirds to provide military and police units with improved surveillance, reconnaissance, and related activities.
Johnson is comparing his hummingbird flight simulations with experimental data gathered from collaborators at Oregon State University (Doug Warrick) and the University of Portland (Bret Tobalske). "The results achieved from simulation are more comprehensive," said Johnson, adding that researchers can "plug in different wing types, frequencies, maneuvers, etc."  He used approximately 10,000 hours on the NCCS's Cray X1E Phoenix supercomputer to do just that. The end product: a series of movies that show air pressure on the top and bottom of the hummingbird wing, computed lift-and-drag curves, and animations of cross-section velocity vectors at various locations.
Contact: Jayson Hines, hinesjb@ornl.gov
PNNL to Lead Three-Year Project on Fault Tolerance Research
Current and future extreme-scale computers are composed of millions of components that make hardware faults likely while running applications. ASCR, under the FASTOS-2 program, has funded the SFT-2 Scalable Fault Tolerance for Petascale Computers research to address these faults. The three-year project, led by Pacific Northwest National Laboratory in collaboration with Ohio State University and Oak Ridge National Laboratory, will develop fault tolerant technologies for global address space programming models using virtualization and fault resilient runtime for malleable applications. This will complement other efforts that focus on MPI applications. This project follows on a previous SFT-1 project that also focused on fault tolerance.
Contact: Jarek Nieplocha, jarek.nieplocha@pnl.gov
International Panel Discussion Looks at What it Means to Be Green
At the 2008 International Supercomputing Conference in Dresden, Germany, LBNL Associate Laboratory Director Horst Simon chaired a panel discussion on the topic "Is HPC Going Green?" John Shalf of NERSC was one of the panelists, along with others from the U.S., Japan and Germany. You can read HPCwire Editor Michael Feldman's summary of the discussion at the following link:


LBNL's Juan Meza Recognized for Inspiring Under-Represented Students
Juan C. Meza, Department Head and Senior Scientist for the High Performance Computing Research Department in the Computational Research Division at Lawrence Berkeley National Laboratory, has been named recipient the Blackwell-Tapia Prize, following the recent announcement of Meza receiving the SACNAS Distinguished Scientist Award. The Blackwell-Tapia Prize is awarded every second year in honor of the legacy of David H. Blackwell and Richard A. Tapia, two distinguished mathematical scientists who have been inspirations to more than a generation of African American, Latino/Latina, and Native American students and professionals in the mathematical sciences. The SACNAS (Society for Advancement of Chicanos and Native Americans in Science) Distinguished Awards recognize scientific achievement, teaching, and mentorship of underrepresented minority students.
Contact: Juan Meza, JCMeza@lbl.gov
Moe Khaleel Named Mechanical Engineer of the Year by ASME Section
Moe Khaleel, director of PNNL's Computational Sciences and Mathematics Division and a PNNL Fellow, received the "ASME Setting the Standard 2008 Mechanical Engineer of the Year award" from the Columbia Basin Section of ASME (American Society of Mechanical Engineers) International. Khaleel was recognized for his leadership and contributions to computational engineering, specifically in increasing thermal efficiency of data centers, and fuel cell technologies. Khaleel's current research interests are tuned to world energy systems and the future role for fuel cell systems. He is the national coordinator for a program dealing with the modeling and simulation of Solid Oxide Fuel Cell as part of the Solid Energy Conversion Alliance.
As director of PNNL's Computational Sciences and Mathematics Division, Khaleel leads the effort to provide scientific and technological solutions through the integration of high performance computing, data intensive computing, computational sciences, mathematics, scalable data management, and bioinformatics to advance the laboratory's mission areas.
ORNL's Hoffman Presents Papers at Environmental Modeling, Software Meeting
In July, Forrest Hoffman (ORNL Computer Science and Mathematics Division) presented two papers at the International Congress on Environmental Modeling and Software (iEMSs 2008) biennial meeting in Barcelona, Spain. One paper described the application of multivariate spatio-temporal cluster analysis to environmental problems, including ecoregionalization, sampling network analysis and design, and model/data comparison, including a variety of new algorithm improvements that have dramatically reduced the computational run time of the analysis tool and allow even larger data sets to be included in analyses.
The second paper presented the Carbon-Land Model Intercomparison Project (C-LAMP) to the international modeling community. This paper focused on the modeling protocol and metrics for evaluating terrestrial biogeochemistry models. Both of the papers are available in the Proceedings of the iEMSs Fourth Biennial Meeting: International Congress on Environmental Modelling and Software (iEMSs 2008), ISBN 978-84-7653-074-0. Hoffman's research is funded primarily by the Office of Biological and Environmental Research (OBER), Climate and Environmental Sciences Division.
Contact: Jayson Hines, hinesjb@ornl.gov
PNNL's Katrina Waters Appointed to Editorial Board of Toxicology Journal
Dr. Katrina Waters, a senior research scientist at the Pacific Northwest National Laboratory, has been appointed to the editorial board of Toxicology and Applied Pharmacology for a three-year term beginning July 1, 2008. The toxicology journal publishes original scientific research pertaining to action of chemicals, drugs, or natural products to animals or humans. Waters is currently involved in the Systems Toxicology of Nanomaterials focus area of the Environmental Biomarkers Initiative and the PNNL Center for Novel Biomarkers of Response. Her research includes biosignature discovery from integrated microarray and proteomic data describing lung inflammation from nanoparticle exposure and environmental exposures, including disease susceptibility factors. Waters joined PNNL in 2004. Prior to that, she was a senior research biochemist in Molecular & Investigative Toxicology at Merck Research Labs in West Point, PA.
Contact: Katrina Waters, katrina.waters@pnl.gov
TOP500's Erich Strohmaier to Lead LBNL's Future Technologies Group Lead
Erich Strohmaier, one of the co-founders and editors of the twice-yearly TOP500 list of the world's most powerful supercomputers, has been named the new Group Lead for the Future Technologies Group in LBNL's Computational Research Division. In addition to his work with the TOP500 list - Strohmaier has compiled all 31 lists to date - he has also published numerous influential articles in the areas of performance modeling, evaluation, and optimization. Strohmaier is a co-PI in the Performance Evaluation Research Institute funded under DOE's SciDAC program and he is also working on performance characterization and benchmarking projects for other federal agencies. His current work on APEX-Map, which seeks to characterize application performance, has been used to help identify performance problems on several of DOE's supercomputers.
Contact: Erich Strohmaier, EStrohmaier@lbl.gov


Leading Edge Analytics, Visualization Coming to ALCF's Blue Gene/P Intrepid
The IBM Blue Gene/P Intrepid at the Argonne Leadership Computing Facility will soon have the data analytics and visualization capability to complement its distinction as the fastest computer in the world for open science and the third fastest overall computer in the world. Argonne awarded GraphStream, Inc., Belmont, CA, a contract that will help to make data analytics and visualization at this scale possible through the world's largest installation of NVIDIA Quadro Plex S4 external graphics processing units (GPU). This new supercomputer installation, nicknamed Eureka, will allow researchers to explore and visualize the data they produce with Intrepid. The powerful installation will offer 104 dual quad core servers with 208 Quadro FX5600 GPUs in the S4s. Argonne made the announcement at SciDAC 2008 in Seattle, Wash.
"During a massive computation on Intrepid, torrents of data can be unleashed onto the multi-petabyte parallel file system," ALCF acting director Pete Beckman said. "For example, in just a little over a minute, Intrepid can produce the equivalent of 1,000 DVDs of file data. Eureka will be used to peer ever deeper into scientist's data, from simulations of the electrical signals of the human heart to exploding supernova. Aided by Eureka, scientists will plow through the tidal wave of data produced by Intrepid faster than ever before, searching for new insights."
Contact: Pete Beckman, beckman@alcf.anl.gov
Center to Focus on Multithreaded Architectures for National Security Applications
Pacific Northwest National Laboratory, in conjunction with Cray, Inc., Sandia National Laboratories, and the Georgia Institute of Technology, has been awarded $4 million from the intelligence community to establish the Center for Adaptive Supercomputing Software, focused on Multithreaded Architectures (CASS-MT), to conduct research in emerging application areas of interest to national security on advanced architectures such as the Cray XMT. The center will be the first of its kind due to its focus on non-traditional parallel applications in national security that have been very difficult to map effectively to mainstream clusters. The virtual center also will develop and enhance the underlying systems software and programming abstractions to enable the efficient use of multithreaded systems for innovative applications. Many of these applications, such as graph-based analyses, have highly irregular memory access and parallelism patterns and can thus benefit from the underlying support for latency tolerance and fine-grained parallelism offered by multithreaded systems. Multithreaded architectures are processing platforms that can be used to run parallel applications that require access to terabytes of data arranged in a random and unpredictable manner.
The center will initially host a 16-processor Cray XMT multithreaded system. This system will be expanded to a 64-processor system starting in October/November 2008.
Contact: Daniel Chavarria, daniel.chavarria@pnl.gov
Fermilab to Install Cluster for Analyzing Experimental Data
The Fermilab Computing Division has just completed the purchase of 750 capacity compute nodes configured with dual quad core 2.66 GHz processors. Installation in the Grid Computing Center is expected in early fall. The nodes will be used to analyze data from the CDF, Dzero and CMS experiments.
Contact: David J. Ritchie, ritchie@fnal.gov


SciDAC 2008 Conference Presents Exciting New Results
The fourth annual Scientific Discovery through Advanced Computing (SciDAC) Conference was held June 13-18, 2008, in Seattle, Washington. The conference was organized by Rick Stevens, Associate Laboratory Director of Computing, Environment, and Life Sciences at Argonne National Laboratory. Over 350 participants attended this year's talks, poster sessions, and tutorials, which ranged from astrophysics, biology, chemistry, fusion sciences, and nuclear physics applications to advances in applied mathematics and computer science as enabling technologies. While the principal focus was on SciDAC accomplishments, the conference also included presentations by DOE INCITE recipients who discussed their work on DOE's leadership-class computing facilities. Another feature new to the SciDAC conference series was an electronic theater and video poster session, with more than 50 scientific visualizations presented on high-resolution large-format displays. In addition, reflecting the increasing international interest in petascale computing, this year's conference included several presentations from European groups. For links to conference talks and posters, go to the following link:
Summer Computing Workshops Being Held at Argonne
Two computing workshops will be held at Argonne National Laboratory in July and August. At the Leap to Petascale Workshop on July 29-31 at the Argonne Leadership Computing Facility (ALCF), attendees will learn about the petascale resources available. IBM and ALCF performance engineers will help them scale and tune their applications on 40 racks of Blue Gene/P. Sponsors include the ALCF, Blue Gene Consortium, and Argonne National Laboratory.
Contact Chel Lancaster, lancastr@alcf.anl.gov
The Blue Gene Consortium Open Source Workshop on August 12-13 at Argonne will provide consortium members with an understanding of the BG/P open source community organization and business model, cover ongoing and potential research activities, describe IBM's involvement, and brainstorm on future activities. Sponsors include the BG Consortium, Argonne Mathematics and Computer Science Division, ALCF, and IBM.
Contact: Ed Jedlicka, jedlicka@mcs.anl.gov
ESCC, Internet2 Joint Techs Workshop Highlights Latest in Advanced Networking
The ESnet Site Coordinating Committee (ESCC) and Internet2 Joint Techs Workshop held their summer session July 20 - 24, in Lincoln, Nebraska. Hosted by the University of Nebraska - Lincoln, the conference brings together thought leaders in the research and education community to explore and discuss important technology issues and the latest advancements in next-generation networking. Presentations had have four main focus areas including: The Coming Crisis in Routing and Networking, Campus Networking, Wide Area Networking Issues, and Security. In addition, MPLS, Dynamic Circuit Networking and Network Performance Workshops were held July 19 and 20 preceding the main Joint Techs sessions.
Since 1998 the Joint Techs Workshop has drawn together advanced networking engineers and featured tutorials, presentations, Birds-of-a-Feather meetings, in-depth technical sessions and demonstrations of state-of-the-art high-performance networking technologies. For more information, visit their web site at this link: