ASCR Monthly Computing News Report - July 2010

In this issue:


Fifth Annual SciDAC Conference Draws 350 Computational Scientists
DOE’s Scientific Discovery through Advanced Computing (SciDAC) program held its fifth annual conference July 11-15 in Chattanooga, Tennessee. Oak Ridge National Laboratory (ORNL) organized this year’s event, which was chaired by Deputy Laboratory Director for Science and Technology Thomas Zacharia. More than 350 scientists from various regions and disciplines came together for technical talks about recent findings, collaboration on new technologies, and networking within the computational science community.
Steven Koonin, DOE Under Secretary for Science and the event’s keynote speaker, summarized the importance of collaboration between the SciDAC attendees during his talk. “[Collaboration] brings together these elements I was talking about — laboratory experiments, real-world operating experience, and simulation capabilities or modeling capabilities — to try and make something bigger than each of those bases and have a real impact on the energy program,” he said. Koonin also addressed impending challenges presented by the drive to exascale capabilities — roughly one thousand times the speed of today’s fastest supercomputers — by 2018.
The last night of the conference was centered on a Visualization Night competition, where teams submitted simulations that accompany the billions of calculations on supercomputers.
10 Visualization Projects Awarded OASCRS at SciDAC’10 Conference
At the 2010 SciDAC Conference held July 11-15 in Chattanooga, Tenn., the annual Vis Night event was held, with 32 scientific visualizations submitted. About 160 conference attendees participated in the event and voted for their favorite visualizations. The top 10 entries were presented with OASCAR Awards (named for the DOE Office of Advanced Scientific Computing Research).
Researchers in Argonne National Laboratory’s Computing, Environment, and Life Sciences directorate, in collaboration with scientists at the University of Alabama, the University of Massachusetts, and the Flash Center at the University of Chicago, topped the voting. Here is a list of the Top 10 visualizations.
FIRST: Verification Study of Buoyancy-Driven Turbulent Nuclear Combustion for Three Different Physical Situations
By Ray Bair (ANL), Anshu Dubey (Flash Center, University of Chicago), Robert Fisher (University of Massachusetts-Dartmouth), Jonathan Gallagher (Flash Center, UofC), Randy Hudson (ANL and Flash Center, UofC), Don Lamb and Dongwook Lee (Flash Center, UofC), John Norris and Mike Papka (ANL and Flash Center, UofC), Katherine Riley (ANL), and Dean Townsley (University of Alabama)
SECOND: Binary Galaxy Cluster Merger, Simulated using the Flash Code, Mass Ratio 1:1, with an Offset Impact, Four Different Views
By John Zuhone (Harvard-Smithsonian Center for Astrophysics), Don Lamb (Flash Center, University of Chicago)




TIED FOR THIRD: Visualization of Convective Flow with Integral Surfaces

By Christoph Garth, Hari Krishnan, Kenneth I. Joy (all of Institute for Data Analysis and Visualization, University of California, Davis)




TIED FOR THIRD: Evolution of a Galaxy Cluster in Adaptive Mesh Refinement Cosmological Simulations
By Samuel W. Skillman (DOE Computational Graduate Fellow, Center for Astrophysics and Space Astronomy, University of Colorado at Boulder), Brian W. O'Shea (Department of Physics and Astronomy, Michigan State University), Matthew J. Turk (Center for Astrophysics and Space Sciences, University of California, San Diego)



FOURTH: Clean Energy for the Future with the ITER Reactor
By Jamison Daniel, David Pugmire, Michael Matheson and Sean Ahern (all of Oak Ridge National Laboratory)



TIED FOR FIFTH: Type Ia Supernova: Turbulent Combustion on the Grandest Scale
By Hank Childs (Lawrence Berkeley National Laboratory [LBNL]), Haitao Ma and Stan Woosley (University of California, Santa Cruz), John Bell, Ann Almgren and Andy Nonaka (LBNL).
TIED FOR FIFTH: Particle Dynamics in a Fluidized Bed Reactor

By Kenny Gruchalla and, Perrine Pepiot (National Renewable Energy Laboratory), Olivier Desjardins (University of Colorado at Boulder)



TIED FOR SIXTH: Hybrid Particle Finite Element Simulation of Impact, Perforation, and Fragmentation

By Randall Hand and Miguel Valenciano (DOD High Performance Computing Modernization Program Data Analysis and Assessment Center), Eric Fahrenthold and Kwon Joong Son (University of Texas, Austin)


TIED FOR SIXTH: Hurricane Season

By Prabhat, Michael Wehner and E. Wes Bethel (all of Lawrence Berkeley National Laboratory)



SEVENTH: Electromagnetic Wake in an Energy Recovery Linac Vacuum Chamber with Moving Simulation Window

By Greg Schussman, Rich Lee, Liling Xiao and Cho-Kuen Ng (all of SLAC National Accelerator Laboratory), Ken Moreland (Sandia National Laboratories)

Fourth Annual Tutorials Program at SciDAC Conference Proves Popular
For the fourth consecutive year, the SciDAC Outreach Center organized a day of tutorials in conjunction with the annual SciDAC Conference. This year, 78 students attended three full-day tracks and four half-day tracks led by 15 presenters. The July 16 SciDAC Tutorials Day was held at the University of Tennessee at Chattanooga (UTC). Held each year on the day following the main SciDAC meeting, Tutorials Day provides open and free tutorials on a wide range of subjects in scientific computing. The focus is on bringing the benefits of DOE’s investments in SciDAC to new researchers in academia and industry.
In addition to the material presented, the day also provides important networking opportunities. For example, SciDAC Outreach Center Head David Skinner noted that he had a hallway discussion with a group of undergraduate students attending tutorials who didn’t know that DOE “did computing too. Helping them connect the dots between their science interests and what ASCR has to offer hopefully provides a catalyst for greater things,” Skinner said.
More information is on the SciDAC Tutorials website


ORNL Researchers Use Supercomputers to Simulate Pedot
Researchers Bobby Sumpter and Vincent Meunier at Oak Ridge National Laboratory (ORNL) used computational simulations to help demonstrate and understand epitaxial growth in polymers, foreshadowing a plastic chip process that could combine the high speed of silicon with the low cost of plastic. These findings are published as “Step-by-step growth of epitaxially aligned polythiophene by surface-confined reaction” (Lipton-Duffin et al.) in the Proceedings of the National Academy of Sciences. The research team included scientists from Université du Québec and McGill University in Canada.
The conductive polymer called Pedot (polythiophene) is already widely used in LEDs, displays and solar cells, but not in a crystalline form. The Oak Ridge researchers said demonstrating epitaxial growth of Pedot could lead to improved, inexpensive organic semiconductors with much better energy efficiency and performance. Sumpter and Meunier from ORNL’s Center for Nanophase Materials Sciences with appointments in the Computer Science and Mathematics Division collaborated in the project by analyzing the results through a “virtual microscope.” Based on density functional theory calculations and simulations performed on ORNL supercomputers, the “virtual microscopy” revealed the highly organized structure of the polymer arrays. By examining the polymer formation with the conventional means of scanning tunneling microscopy combined with the virtual microscopy, the team was able to clearly illustrate the construction and bonding of Pedot arrays.
Contact: Jayson Hines, Jayson Hines, hinesjb@ornl.gov
NERSC, LLNL to Serve as Primary Computing Resources for LHC’s ALICE Data
For about one month a year, the nuclei of lead atoms traveling near the speed of light will collide in the Large Hadron Collider’s (LHC) ALICE experiment, generating a fireball about 100,000 times hotter than the core of our Sun. At these temperatures protons and neutrons dissolve into a “particle soup” of quarks and gluons, known as the quark-gluon plasma — a state of matter that first occurred at the birth of the Universe almost 14 billion years ago, a few millionths of a second after the Big Bang. By watching this “soup” cool, physicists hope to better understand the nature of matter, which makes up everything from galaxies to humans.
For the month that these lead ions collide, the ALICE experiment will collect over 10 terabytes of data per day, equivalent to the amount of information that could be stored on 20,000 DVDs. About 10 percent of this data will travel from the LHC in Switzerland to the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory (Berkeley Lab) and to Lawrence Livermore National Laboratory (LLNL) in Northern California via DOE’s Energy Sciences Network (ESnet). These facilities will provide the primary computing and storage resources for the ALICE collaboration in North and South America.
Exploring Particle-in-Cell/Hybrid Simulations of Fast Ignition
Fusion energy, a potential long-term energy solution that is both safe and environmentally friendly, is being explored through a number of approaches, many of which include extensive computational modeling. The “fast ignition” approach currently pursued at DOE’s National Ignition Facility in California is an alternative to conventional inertial confinement fusion. The fast ignition scheme separates the compression and heating phases from ignition, much like an internal combustion engine. In the gasoline engine, the fuel is compressed by the piston, and then ignited by the spark plug. In fast ignition, the driving lasers are the pistons, compressing the fuel to high density; then a second laser’s high-intensity pulse serves as the “spark.”
Researchers from the University of California, Los Angeles have implemented a newly invented particle-in-cell (PIC)/magnetohydrodynamics hybrid method that is 300 to 30,000 times faster than full PIC. The group is running three hybrid simulations of fast ignition targets, plus some full PIC/transport runs on Intrepid, the Blue Gene/P supercomputer at the Argonne Leadership Computing Facility.



Figure 1: Fast ignition schematic.

Contact: John Tonge, tonge@physics.ucla.edu
Hubble Telescope Verifying Computational Identification of Supernovae Candidates
An innovative sky survey called the Palomar Transient Factory (PTF), using resources at NERSC, has been tracking relatively rare and fleeting cosmic events, like supernovae and gamma ray bursts, since June 2009. When an extremely likely supernova candidate is found, the team can request that the Hubble Space Telescope use its powerful cameras to follow up. In July, the PTF sent its 16th such potential supernova to the orbiting telescope. The work is part of the program “Verifying the Utility of Type Ia Supernovae as Cosmological Probes: Evolution and Dispersion in Ultraviolet” led by Richard Ellis at Caltech.
Every night the PTF camera at Palomar Observatory in Southern California automatically snaps pictures of the sky, then sends those images to NERSC via DOE’s Energy Sciences Network (ESnet) and the National Science Foundation’s High Performance Wireless Research and Education Network (HPWREN). To enable the fast turnaround needed to verify supernovae before they become too dim, researchers at Caltech worked with NERSC to develop the Real-time Transient Detection pipeline, an automated system that analyzes the terabytes of data every night, and have secured time on some of the world’s most powerful ground-based telescopes to conduct immediate followup observations as events are identified. Once an interesting event is discovered, NERSC machines send its coordinates to Palomar’s 60-inch telescope and others for followup observations within minutes. Peter Nugent, a staff scientist in Berkeley Lab’s Computational Research Division (CRD) and the NERSC Analytics Group, is also the Real-time Transient Detection Lead for the PTF project.
Contact: Peter Nugent, PENugent@lbl.gov
Berkeley Lab Staff Contribute to SIAM Annual Meeting
The Society for Industrial and Applied Mathematics (SIAM) held its annual meeting July 12–16 in Pittsburgh, PA. As usual, members of LBNL’s Computational Research Division were well represented among the speakers:

  • David Bailey and Juan Meza co-authored “A Machine Learning Approach to Intrusion Detection for High Performance Computing” and co-organized (with Ali Pinar of Sandia National Laboratories) a session on “Mathematics of Complex Distributed Interconnected Systems.”
  • Phil Colella co-authored “Local Mesh Refinement for Plasma Physics” with Bei Wang and Greg Miller of UC Davis.
  • Inez Fung of the Earth Sciences Division gave an invited talk on “Mathematical Challenges in Climate Change Science.”
  • Bakytzhan Kallemov, David Trebotich, and Greg Miller co-authored “A Multi-Scale Model for Polymer-Laden Flows Coupling Stochastic Particle Dynamics with Continuum Fluid Mechanics.”
  • Xiaoye Sherry Li gave an invited talk on “Factorization-Based Sparse Solvers and Preconditioners.” She also organized a session on “Architecture-Aware Algorithms.”
  • Kamesh Madduri presented “Hybrid Parallel Programming for Massive Graph Analysis.”
  • Brian Van Straalen presented “An Embarrassingly Parallel Benchmark to Study Architecture Heterogeneity.”
At the SIAM Conference on the Life Sciences, held in conjunction with the general meeting, Kirsten Fagnan of NERSC presented “Computational Modeling of Extracorporeal Shock Wave Therapy.”
Contact: Linda Vu, LVu@lbl.gov


PNNL’s Lin to Serve on Editorial Board for International Uncertainty Publication
Guang Lin, a computational mathematics researcher in the Fundamental & Computational Sciences Directorate at Pacific Northwest National Laboratory (PNNL), has been invited to serve on the editorial board for the prestigious International Journal for Uncertainty Quantification. The publication features information in the areas of analysis, modeling, design, and control of complex systems in the presence of uncertainty across all areas of physical and biological sciences. Lin will lead the team that reviews submissions and makes recommendations on which manuscripts to accept for publication. The 11-member editorial board includes representatives from other national laboratories, as well as universities and industry. Lin is the principal investigator on an ASCR-funded project that focuses on extracting and reducing data from massive volumes of information to quantify and reduce the uncertainty in climate models.
Contact: Guang Lin, guang.lin@pnl.gov
NERSC’s John Shalf Talks Parallel Programming Languages with ISGTW
Ever wonder what parallel programming is and how it can advance science? John Shalf, the team lead of the Advanced Technologies Group at NERSC, discussed the scientific need for parallel programming and its future in a Q&A conducted by International Science Grid This Week ISGTW) newsletter. Among many topics covered, Shalf explains the difference between parallel programming languages and programming languages, as well as emerging trends in computing. According to ISTGW Editor Miriam Boon, the article was the newsletter’s most-read posting ever.
Sandia’s Pavel Bochev Gives Invited Lecture, Participates in Industrial Math Panel
Pavel Bochev of Sandia National Laboratories was invited to speak about novel uses of optimization and control ideas for the solution of transport problems at a conference on “Non-standard numerical methods for PDEs” (partial differential equations). The conference was organized by the Institute for Applied Mathematics and Technologies (IMATI) at Pavia, Italy, and the National Research Council of Italy. The conference was attended by leading researchers from the EU and the U.S.
Bochev also participated in a panel on Understanding the Evolution of Applied Mathematics in Industry which took place at the 2010 annual SIAM meeting in Pittsburgh. Discussion at the panel focused on recent trends in applied mathematics and their potential long-term impacts on the discipline.


ESnet Seeking Proposals for Experiments using ANI Testbed
Want try out some new ideas in network research? ESnet is now accepting proposals to run experiments on its reconfigurable testbed. ESnet’s ARRA-funded Advanced Networking Initiative testbed is a high-performance environment where researchers will have the opportunity to prototype, test and validate cutting-edge networking concepts. The testbed will support research including multi-layer multi-domain hybrid networks, network protocols, component testing for future capabilities, protection and recovery, automatic classification of large bulk data flows, high-throughput middleware and applications, and other innovative ideas in a realistic network environment, but with no risk of breaking anything.
To submit a proposal, first review the instructions. Proposals are due October 1, 2010. Decisions will be made January 10, 2011, when the Phase 1 version of the testbed is up and running. The phase 1 version is a set of 10 Gbps connected layer 1, 2, and 3 equipment that will be deployed on a dark fiber ring ESnet acquired in Long Island (LIMAN: Long Island Metropolitan Area Network). This will mainly be of interest to researchers doing experiments at layers 1-3, or middleware/application research at 10 Gbps.
ESnet Launches New ReadyTalk Service for Audio/Web Conferencing
ESnet, DOE’s Energy Sciences Network, has switched its audio/web conferencing infrastructure from Cisco MeetingPlace to a different commercial service provider – ReadyTalk Inc. ReadyTalk audio/web conferencing features:
  • Free, no reservations required, audio/web conferencing
  • 24-hour customer care toll-free number
  • Toll-free domestic and international access (over 100 countries) to audio conferencing
  • Each account can accommodate to 96 ports
Current users funded by the DOE Office of Science will receive an email containing new account information from ReadyTalk. User registration for new audio/web conferencing service started July 30, 2010. The Cisco MeetingPlace audio bridge will continue to operate until 5 p.m. Friday, Sept. 30, 2010 (PDT), but no new MeetingPlace registrations will be accepted after July 30. These changes only apply to audio conferencing services, not video. ESnet will upgrade the video conferencing infrastructure in the fall/winter 2010.
Questions? Contact: trouble@es.net


Berkeley Lab Hosts Weeklong Workshop on Cloud Computing
The forecast for many aspects of computing definitely calls for clouds, but cutting through the hype and getting a clear picture on the possibilities and limitations of cloud computing requires intensive hands-on sessions. To this end, Berkeley Lab’s Computational Research Division (CRD) hosted a weeklong workshop on cloud computing July 19-23. The Center for Information Technology Research in the Interest of Society (CITRIS) at UC Berkeley helped host the workshop. Participating organizations helping Berkeley Lab provide content included UC Berkeley, UC Davis, Yahoo!, Amazon, Eucalyptus Systems, the University of Virginia, and Microsoft. NERSC contributed both workshop content and computing resources. Participation was limited to 45, and the limit was quickly met. Among the topics covered during the workshop were an overview of cloud computing, software and systems training, data management and analysis, and experiences in using research and commercial cloud services.
Contact: Deb Agarwal,DAAgarwal@lbl.gov
UT/ORNL Conference Pairs Bioscience with Computation
To learn to apply supercomputing to biology and medicine, college seniors, graduate students, and postdoctoral fellows from around the country gathered in Knoxville, Tennessee to take part in a conference sponsored by the University of Tennessee (UT) and Oak Ridge National Laboratory (ORNL). The Summer School in Biophysics at UT/ORNL: Computational and Experimental Challenges took place July 7–10. While introducing students to careers in biophysics, which explores the applications of physics to biological problems, speakers also highlighted the importance of ORNL’s computational capabilities in addressing biological challenges. Many had used OLCF’s Jaguar, the world’s most powerful supercomputer, for their research. Dean Myles of ORNL’s Center for Structural Molecular Biology, for example, used Jaguar when developing models of macromolecular complexes.
Each day keynote speakers from different disciplines spoke. Lucy Malinina, a structural biologist at the Center for Cooperative Research in Biosciences in Spain, focused on biomedicines. Andrew McCulloch, a bioengineer at the University of California, San Diego, spoke about multiscale modeling and systems biology as they relate to the heart. Zaida Luthey-Schulten, a chemist at the University of Illinois at Urbana-Champain, shared simulations and visualizations of interactions between RNA and protein complexes. Maxim Frank-Kamenetskii, a biomedical engineer at Boston University, explained targeting duplex DNA. And Ruben Abagyan, a pharmaceutical scientist at UC San Diego, discussed challenges in chemogenomics and drug discovery.
ICiS Workshop on Computational Methods and Terabase Metagenomics
Computational biologist Folker Meyer of Argonne’s Mathematics and Computer Science Division, together with Rick Stevens (director of Computing, Environment, and Life Sciences at Argonne) and Jack Gilbert (Plymouth Marine Laboratory) organized a one-week workshop titled “Computational Methods and Terabase Metagenomics.” The workshop, held in Snowbird, Utah, July 17-24, was the first of those to be sponsored by the Institute for Computing in Science (ICiS), Argonne National Laboratory’s new community-driven institute. The aim of ICiS is to bring the computational science community together to work on challenging problems and to develop future leaders in the use of computation to advance science.
At the July metagenomics workshop, bioinformatics and microbial ecology communities focused on the development of a trillion-base-pair metagenome that captures the genomic information from the vast majority of species in an ecosystem and from which scientists will be able to determine major variations in genes and genomes. Meyer led a breakout session on the computational requirements for such a terabase and co-led another session on defining the key questions and devising a strategy for implementing the metagenomics terabase.
Contact: Gail Pieper, pieper@mcs.anl.gov
LBNL Introduces High School Students to Careers in Computing, Networking
Berkeley Lab Computing Sciences hosted 15 local high school students at a Workshop on Careers in Computing and Networking as part of an outreach program to introduce various career options in scientific computing and networking. The sessions were held at both the main Lab and the Oakland Scientific Facility (where the NERSC supercomputing center is housed) from July 26-29 and included presentations, hands-on activities and tours of various research facilities. The program was developed with input from computer science teachers at Berkeley High, Albany High, Kennedy High (in Richmond) and Oakland Tech, and teachers referred students they thought would most benefit from such a program. Staff from NERSC, CRD, ESnet and the IT Division presented on topics ranging from disassembling and reassembling desktop computers, cyber security war stories, algorithms for combustion and astrophysics, the role of applied math, networking, science portals and Green Flash. Tours included the NERSC machine room, the Nation Center for Electron Microscopy and a combustion laboratory.
“I really liked listening to these professionals in a really friendly environment that I otherwise wouldn’t have ever experienced,” commented one Albany High student. “Amazing!”
Contact: Jon Bashor, jbashor@lbl.gov
Berkeley Lab’s Peter Nugent Sparks Students’ Interest in Supernovae
Peter Nugent, leader of Berkeley Lab’s Computational Cosmology Center, gave a talk on “Supernovae, Supercomputing and the Fate of the Universe” for the 2010 Physics In and Through Cosmology Workshop held July 19-30 at UC Berkeley. The fourth annual workshop for high school students and teachers was sponsored by the Berkeley Center for Cosmological Physics, led by 2006 Nobel Prize winner George Smoot. Nugent also signed up several students to serve as computational astronomers in the Supernova Zoo project.
Contact: Peter Nugent, PENugent@lbl.gov
Berkeley Lab’s Juan Meza Gives Two Talks at Rice University
Juan Meza, the head of Berkeley Lab’s High Performance Computing Research Department, returned to his alma mater, Rice University, to give two talks as part of the Rice Alliance for Graduate Education and the Professoriate (Rice-Houston AGEP) Program. On July 23, Meza spoke first on “Computing and the Carbon Cycle: The Search for Clean Energy,” then followed up with some solid advice on “Navigating the Job Interview.”
Contact: Juan Meza, JCMeza@lbl.gov