Research News...
ASCR Highlights Argonne Research in Reactor Simulation
Simulation Helps UT/ORNL Team Unlock the Secrets of Protein Folding
ORNL Models Next-Generation Pharmaceuticals to Fight Alzheimer's Disease
Topological Analysis Provides Deeper Insight into Hydrodynamic Instabilities
LANL Multiscale Math Team Discovers New Constraints of Rotating, Stratified Flows
INCITE Allocation Helps Achieve Coherent Control of Light in Nanoscale Devices
Upgraded Integrated Microbial Genomes Data Management System Released
Argonne Research Selected as Supercomputing 2007 Storage Challenge Finalist
Scientific Data Indexing Enhanced to Support Exascale Applications

People...
PNNL's Mohammed Khaleel Elected a Fellow of the ASME
LBNL's Julian Borrill Invited to Join NASA Team for Planning Future Mission
LBNL's Osni Marques Awarded Japanese Fellowship
Emerald Award

Facilities/Infrastructure...
Blue Gene Supercomputers Featured in Chicago Life
PNNL Recognized for Innovation in Employing IT
NERSC Adds Two More HPC Systems to Open Science Grid
NCCS Publication Wins Design Award

Outreach...
ORNL's John Drake Quoted in USA Today Article
Congressmen Learn how HPC Contributes to Competitiveness
NERSC Staff Showcases New Services and Tools at Annual User Group Meeting

Research News:
ASCR Highlights Argonne Research in Reactor Simulation
ASCR Discovery recently highlighted the reactor simulation work of Argonne National Laboratory researcher Paul Fischer in its Big Iron department (http://ascr-discovery.science.doe.gov/bigiron/fischer1.shtml).  Concerns about global climate change and fossil fuel supplies have led to greater interest in a new kind of nuclear power plant. The new-generation plants will operate at temperatures much higher than today's reactors.  And instead of water, they'll use liquid metals such as sodium, or a liquid fluoride salt to cool them.  With a grant of 1 million processor hours from DOE's INCITE program, Fischer and fellow researchers Andrew Siegel (Argonne) and Carlos Pantano (University of Illinois) are using the 2,048-processor IBM Blue Gene/L at the Argonne Leadership Computing Facility to develop computer simulations of heat transfer in coolant flowing around tightly packed nuclear fuel rods.  The computer algorithms they are designing simulate reactor core cooling.  The research will contribute to the Global Nuclear Energy Partnership (GNEP), a DOE-led international collaboration to create safe and secure nuclear power plants that minimize waste.
Contact: Paul Fischer (fischer@mcs.anl.gov)

Simulation Helps UT/ORNL Team Unlock the Secrets of Protein Folding
A team led by biophysicist Jeremy Smith of the University of Tennessee and Oak Ridge National Laboratory (ORNL) has taken a significant step toward unraveling the mystery of why proteins fold into unique, three-dimensional shapes.  Using ORNL's Cray XT4 Jaguar supercomputer as well as systems in Italy and Germany, the team revealed a driving force behind protein folding.  Its results appear in the September 18 edition of the Proceedings of the National Academy of Sciences.

ORNL Models Next-Generation Pharmaceuticals to Fight Alzheimer's Disease
Biologists and materials scientists are using the Cray XT4 Jaguar supercomputer at Oak Ridge National Laboratory (ORNL) and other systems to discover the mechanisms by which a new type of Alzheimer's drug may stop the progression of Alzheimer's plaque formation and potentially disassemble the fibrils, or fine filaments, that make up the plaques.  A team led by Ed Uberbacher of ORNL's Biosciences Division is performing first-principles calculations of Alzheimer's drugs and computing the molecular dynamics of these drugs combined with Alzheimer's fibrils to explore the mechanisms by which drug molecules attach to and reconfigure Alzheimer's peptides bound in fibrils.  "Since we can do quantum mechanical ab initio calculations on 1,000 atoms or so, we can generate this knowledge in a way that is more accurate than what pharmaceutical companies usually do," explains ORNL collaborator Phil LoCascio.  "Hopefully this method will become more widespread in industry and lead to better drug design."
(Contact Jayson Hines, hinesjb@ornl.gov)

Topological Analysis Provides Deeper Insight into Hydrodynamic Instabilities
The VACET group at Lawrence Livermore National Laboratory, led by Valerio Pascucci, has developed the first feature-based analysis of extremely high-resolution simulations of turbulent mixing.  The focus is on Rayleigh-Taylor instabilities, which are created when a heavy fluid is placed above a light fluid and tiny vertical perturbations in the interface create a characteristic structure of rising bubbles and falling spikes.  Rayleigh-Taylor instabilities have received much attention over the past half-century because of their importance in understanding many natural and man-made phenomena, ranging from the rate of formation of heavy elements in supernovae to the design of capsules for inertial confinement fusion.  However, systematic, detailed analysis has been difficult due to the extremely complicated features found in the mixing region.

Members of VACET, the Visualization and Analytics Center for Enabling Technology funded under SciDAC, at Livermore developed a novel approach to the analysis of the complex topology of the Rayleigh-Taylor mixing layer based on robust Morse theoretical techniques.  This approach systematically segments the envelope of the mixing interface into bubble structures and represents them with a new multi-resolution model allowing a multi-scale quantitative analysis of the rate of mixing based on bubble count.  This analysis enabled new insights and deeper understanding of this fundamental phenomenon by highlighting and providing precise measures for four fundamental stages in the turbulent mixing process that scientists could previously only observe qualitatively.

This work has been documented in a paper named "best application paper" at the IEEE visualization conference and later presented at the International Workshop on the Physics of Compressible Turbulent Mixing.  Follow-up work also allowed, for the first time, direct comparison of two simulations based on different physics models, grid point resolutions, and initial conditions.  Although comparison by superposition of the simulations could not yield a meaningful result, the new topological approach highlighted fundamental similarities through a multi-scale feature-based comparison.  This, in turn, validated the lower resolution large eddy simulation with respect to the higher resolution direct numerical simulation.

LANL Multiscale Math Team Discovers New Constraints of Rotating, Stratified Flows
Geophysical systems such as the ocean and atmosphere display immense variability in fluid dynamics.  Depending on factors such as latitude, depth and temperature, the fluid dynamics in a particular location in the ocean may be affected by varying degrees by two predominant influences: the rotation of the earth (as measured the Rossby number), and the local stratification of the fluid (as measured by the Froude number).  Los Alamos National Lab scientists discovered that these parameter dependencies may be explored in a systematic way by studying a quantity known as the potential enstrophy, which in turn places predictable constraints on the kinetic and potential energies of the flow.  Such constraints will be useful in benchmarking and modeling the small scales of geophysical flows over a wider range of parameters than previously possible. Consequently, the coupling between the small turbulence scales and the large climate scales may be more accurately understood.  The latter goal is of vital importance in the development of the next generation of ocean and climate models.  Recent research highlights may be found at http://math.lanl.gov/AMR/Research/Projects/oceanclimate.shtml.
(Contact: Susan Kurien, skurien@lanl.gov)

INCITE Allocation Helps Achieve Coherent Control of Light in Nanoscale Devices
Noble metal nanoparticles and arrays have been the focus of rapidly surging activity in recent years.  This interest has been fueled by applications ranging from novel sensors and medical diagnostics through nonlinear light sources and sub-diffraction waveguides to tip-enhanced molecular spectroscopy and dynamics.  Techniques for fabricating metal nanoparticle arrays are well developed, as are methods for computing their optical properties.  These properties depend on the size, shape, and arrangement of the particles.  An open question, however, is how to size, shape, and arrange the particles to yield a desired optical property or make a desired photonic device.

Upgraded Integrated Microbial Genomes Data Management System Released
A powerful set of computational tools established to ease the visualization and exploration of genomes in the public domain is now available in IMG Version 2.3 - the Integrated Microbial Genomes (IMG) data management system hosted by DOE's Joint Genome Institute (DOE JGI).  IMG, accessible to the public at http://img.jgi.doe.gov/, is a collaborative effort between DOE JGI and the Biological Data Management and Technology Center (BDMTC) in Lawrence Berkeley National Laboratory's Computational Research Division.  The new version of IMG contains a total of 2,878 genomes consisting of 729 bacterial, 46 archaeal, 40 eukaryotic, and 1,661 bacterial phage genomes, and 402 plasmids that did not come from a specific microbial genome sequencing project.  Among these genomes, 2,609 are finished and 269 are draft genomes.  IMG 2.3 contains 236 microbial genomes sequenced at DOE JGI, consisting of 157 finished and 79 draft genomes.
(Contact: David Gilbert, degilbert@lbl.gov)

Scientific Data Indexing Enhanced to Support Exascale Applications
LBNL has developed over the years an innovative indexing method particularly suitable for high-dimensional scientific datasets. The method, called FastBit, is based on partitioning each dimension range of values into bins, assigning a bitmap to each bin, and using a highly effective compression method for the bitmaps. This year the team analyzed the performance of multi-level bitmap indexes, using coarser bins in higher levels and finer bins at the lower levels. The main result showed that only two levels are necessary, and that the top level can have relatively few bins (on the order of 10-15), which adds very little overhead to index space requirements. The theoretical results were verified with experimentation showing as much as 10-fold improvement over the previous high performance of FastBit. These results are expected to benefit researchers who will need to efficiently search the very large datasets to be generated by petascale and exascale applications. LBNL scientists Arie Shoshani, Frederick Reiss, Kurt Stockinger and Kesheng Wu, with Joseph M. Hellerstein of UC Berkeley, presented their results in a paper presented at the 19th International Conference on Scientific and Statistical Database Management, which took place in Banff, Canada in July.

People:
PNNL’s Mohammed Khaleel Elected a Fellow of the ASME
PNNL's Mohammed “Moe” Khaleel has been elected a Fellow of the American Society of Mechanical Engineers. A Laboratory Fellow in PNNL's Fundamental & Computational Sciences Directorate, Khaleel was recognized for his exceptional engineering achievements and contributions to the engineering profession. Khaleel has published more than 100 technical articles and won the Federal Laboratory Consortium for Excellence in Technology Transfer of superplastic forming of aluminum and the ASME International McGrattan Literature Award. He currently manages the Computational Sciences & Mathematics Division at PNNL.

LBNL’s Julian Borrill Invited to Join NASA Team for Planning Future Mission
Julian Borrill, an astrophysicist in the Scientific Computing Group at Lawrence Berkeley National Laboratory, has been invited to join NASA's Primordial Polarization Program Definition Team (PPPDT), charged with planning the Cosmic Microwave Background Radiation (CMB) polarization mission after the upcoming Planck satellite mission.  The team includes 13 experimentalists (including the PIs of two other major CMB missions, WMAP and US Planck), one theorist, and one data analyst.  “The presence of even one data analyst is an enormous step forward, and reflects the growing recognition of the need to include data analysis in CMB mission planning and the critical role that NERSC and LBNL play in the field,” Borrill said.  Members of the PPPDT will work in collaboration with NASA Headquarters, the National Science Foundation (NSF), DOE, NASA Field Center scientists and engineers and the astronomical community to provide input during conceptual development of a CMB polarization mission.  The PPPDT will help provide the astronomy community input on questions relating to the science capabilities of a potential mission and will help disseminate information about the mission concept to the community.  See http://groups.physics.umn.edu/cosmology/PPPDT/ for more details.

LBNL’s Osni Marques Awarded Japanese Fellowship
The Japan Society for the Promotion of Science has awarded a fellowship to Osni Marques of Lawrence Berkeley National Laboratory’s Scientific Computing Group.  The fellowship allows Marques to spend 60 days at a research institution in Japan.  Marques plans to do so in February and March next year and will be based at the University of Tokyo.  The fellowship program, called “Invitation Fellowship for Research in Japan,” encourages Japanese scientists to invite their foreign colleagues and work more closely in research and academic activities.  More information about the fellowship and other programs offered by the society can be found at http://www.jsps.go.jp/english.

Emerald Award
Phani Nukala, Oak Ridge National Laboratory Senior Research Scientist and co-principal investigator of ASCR project, Low-Rank Updates in Statistical Physics Applications and Dean Williams, Lawrence Livermore National Laboratory Senior Research Scientist and principal investigator for the SciDAC project "Scaling the Earth System Grid to Petascale Data Center for Enabling Technologies," won the Senior Investigator Emerald Award, which recognizes consistent leadership in advancing basic science knowledge or discovering, developing, and implementing entirely new technologies.  The Emerald Awards, sponsored by Science Spectrum magazine, are billed as the premier awards for African Americans, Hispanics, Asian Americans and Native Americans working in the research sciences.

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Facilities/Infrastructure:
Blue Gene Supercomputers Featured in Chicago Life
IBM's Blue Gene supercomputers were featured in the Fall 2007 issue of Chicago Life, an advertising supplement to the New York Times.  The article, titled "Blue Gene Baby," notes that the Blue Gene/P will nearly triple the performance of the Blue Gene/L and could be the first supercomputer to break the petaflop barrier.  The first racks of Blue/Gene P will be shipped to Argonne National Laboratory this fall.  According to Ray Bair, Director of the Argonne Leadership Computing Facility, "One of the things we're most enthusiastic about Blue Gene [P] is the way it's designed; we're able to efficiently apply more computing power, more processors, to a problem than we can on many other machines.  It scales very well.  The communication between the processors on the IBM Blue Gene/P is about 1,000 times the speed of the internet connection to your home."
(Contact: Raymond Bair, bair@alcf.anl.gov)

PNNL Recognized for Innovation in Employing IT
InformationWeek, a leading information technology (IT) online magazine, has placed PNNL 54th out of 500 companies in a ranking that determines the country's most innovative companies employing IT in their business.  For 19 years InformationWeek has tracked the technology practices of the nation's most pioneering companies using their annual InformationWeek 500 report.  This report examines business and technology best practices and uses the findings to benchmark companies IT strategies.  Key report areas include increasing efficiency and productivity, the customer and IT risk management, globalization, IT spending and technologies deployed.

NERSC Adds Two More HPC Systems to Open Science Grid
DOE's National Energy Research Scientific Computing Center (NERSC) has deployed new services that make the Open Science Grid (OSG) more widely available to its researchers, who can use the grid to manage their work at multiple computing sites.  NERSC's IBM p575 POWER5 system named Bassi and the Opteron cluster named Jacquard are the latest additions to a list of systems joining the OSG, whose distributed computing network is made up of 53 sites at universities, national labs and computing centers in the North and South America, Europe and Asia.  Another NERSC system, the SGI Altix 350 named DaVinci, joined the OSG in April this year.  The OSG marshals the software, computing, storage and other expertise of many of its 119 member sites which, in addition to the sites that provide computing resources, include research institutions that use the OSG and software developers responsible for building the OSG infrastructure.  Instead of dealing with different authentication processes and software at each site, the scientists can go through the OSG to manage their computing jobs and file data at various computing sites.
(Contact: Ucilia Wang, uwang@lbl.gov)

NCCS Publication Wins Design Award
A publication from the National Center for Computational Sciences (NCCS) recently won Oak Ridge National Laboratory (ORNL) an American Graphic Design Award.  The promotional magazine, entitled "15 Years of Leadership Computing," chronicled the history of supercomputing at ORNL from its inception in 1992 to the NCCS's current status as one of the top high-performance computing centers in the world.  Over the years the NCCS has assisted researchers in their efforts to tackle some of science's most pressing questions in areas as diverse as automotive materials and supernova explosions.  The award was sponsored by Adobe Systems, Inc.
(Contact Jayson Hines, hinesjb@ornl.gov)

Outreach:
ORNL's John Drake Quoted in USA Today Article
John Drake, a researcher and group leader for Computational Earth Sciences at Oak Ridge National Laboratory, was quoted in the USA Today article Climate Model Predicts Hot Decade.  In the article Drake points out that, “In the climate-modeling world, a short prediction is considerably harder than a long one.  That’s because natural variability in weather has a stronger effect in the short term than when averaged out over 100 years.  But the ability to produce accurate, 10-year predictions will be important for world leaders charged with making climate-related decisions.”
Click here to read the entire USA Today article.
Click here to read the Science article referred to in USA Today.

Congressmen Learn how HPC Contributes to Competitiveness
On August 30, Senator Lamar Alexander and U.S. Representative Zach Wamp visited Oak Ridge National Laboratory to see first-hand how the National Center for Computational Sciences (NCCS) is advancing the recent landmark legislation entitled "America COMPETES."  The legislation, aimed at boosting America's competitiveness, promotes scientific innovation through increased federal funding for research and development and various educational initiatives.  Sean Ahern, the visualization lead of the Scientific Computing Group at the NCCS, explained how the NCCS's supercomputers make it possible to study the breakdown of grasses and cellulose, which could be used for the production of alternative fuel sources.  Ahern also discussed the work of ORNL's Ed Uberbacher, whose recent simulations shed light on drug interactions with Alzheimer's disease and reveal the disease's fundamental structure.  Finally, Ahern detailed the NCCS partnership with General Motors, which seeks to make automobiles more efficient by recycling exhaust heat and converting it to electricity.
(Contact Jayson Hines, hinesjb@ornl.gov)

NERSC Staff Showcases New Services and Tools at Annual User Group Meeting
Dozens of NERSC users convened at the supercomputer center in mid-September for a four-day meeting and training, where they learned about new services, software and the Cray XT4 supercomputer that is scheduled for production deployment before the end of the year.  The annual NERSC Users’ Group meeting provided an opportunity for researchers to meet with the NERSC staff and get a close-up look at NERSC resources that would support their scientific pursuits.  “It was good to meet other users and learn about services that will enable us to carry out our projects smoothly,” said Stephane Ethier, vice chair of the NERSC Users Group Executive Committee and a researcher from the Princeton Plasma Physics Laboratory.  “The users also received critical training on the new NERSC-5 system, the 19,320-core Cray XT4 computer Franklin, which will allow them to make efficient use of this exciting new platform.” The event began with presentations and scientific talks by NERSC staff and users, followed by training on using Franklin, including compiling, debugging, profiling, and optimizing jobs for the best performance.