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InTheLoop | 08.01.2011

August 1, 2011

Data Tracking Increases Scientific Productivity at NERSC

To effectively meet the increasing scientific demand for storage systems and services, NERSC staff must first understand how data moves within the facility. Until recently, the process of obtaining these insights was extremely tedious because the statistics came from multiple sources, including network router statistics, client and server transfer logs, storage and accounting reports—all saved as very large, independently formatted text files.

Now a dynamic database created by the NERSC Storage Systems Group continually collects statistics from all of these sources and compiles them into a single, searchable repository. The system also automatically generates daily email reports and graphs that illustrate how data moves in and out of the facility’s HPSS archival storage system, which is the largest repository of scientific data at the center. Read more.

perfSONAR MDM Expands Interoperable Monitoring to U.S.

For the first time, engineers across the GÉANT Service Area can now extend their network monitoring outside Europe to enhance end-to-end performance for users, thanks to perfSONAR MDM, the only tool for network monitoring across multiple domains. (The GÉANT network is the pan-European communications infrastructure serving Europe’s research and education community.)

The addition of eight measurement points within ESnet means that users can monitor network performance through the same, intuitive interface using consistent data formats in both Europe and the USA. The additional probe-based measurements complement the 43 European measurement points within perfSONAR MDM to provide a comprehensive end-to-end view of performance, which is particularly valuable for major global projects such as CERN’s Large Hadron Collider. Read more.

MIT Technology Review: A Network for Wild Experimentation

MIT Technology Review reports that in a few unused back alleys of the Internet, researchers are testing radical new ways of transferring information, often at speeds almost unimaginable to the home Internet user. Internet2 and ESnet are putting together experimental networks on top of dormant networking resources known as “dark fiber.” While the researchers say it will be years before the advances reach individuals and businesses, they think the work will ultimately ensure that the Internet functions smoothly in the future. For example, the experimental networks could allow researchers to update protocols, anticipate security needs, try out better hardware, and look at ways of making networks more energy-efficient. Read more.

SciDAC Tutorials Day Draws More Than 70 Participants

On July 15, the fifth SciDAC Tutorials Day was held on the campus of the University of Colorado at Denver. Held 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.

The SciDAC tutorials leverage the expertise of SciDAC researchers gathered at the main meeting by asking them to stay an extra day and present HPC, domain science, and applied math tutorials to a mostly local audience of students and researchers from nearby universities and industries. More than 70 students attended seven tutorials with twelve presenters.

Tutorials Day was organized by Andrew Uselton and David Skinner. Berkeley Lab presenters included Hank Childs, Tony Drummond, Esmond Ng, and Iwona Sakrejda.

CS Staff Present “RESTful Web Services” at OSCON ’11

Joshua Boverhof of CRD’s Advanced Computing for Science Department presented “RESTful Web Services for Scientific Computing,” co-authored with Shreyas Cholia of NERSC, at the O’Reilly Open Source Convention (OSCON ’11), which was held last week, July 25–29, in Portland, Oregon. This talk presented the NEWT API, implemented as a Python Django project, and discussed NERSC portals that are taking advantage of it.

Balakrishnan Gives Two Presentations at ICDERS Conference

CCSE postdoc Kaushik Balakrishnan gave two presentations at the 23rd International Colloquium on the Dynamics of Explosions and Reactive Systems (ICDERS), held at the University of California, Irvine, July 24–29.

The first presentation, titled “Ignition of Aluminum Particle Clouds Behind Reflected Shock Waves,” was co-authored by Balakrishnan, Allen Kuhl of LLNL, John Bell and Vince Beckner. His second presentation, similarly authored, was titled “An Empirical Model for the Ignition of Aluminum Particle Clouds Behind Blast Waves.” A third paper, authored by Kuhl, Bell, Beckner and Balakrishnan, was presented by Allen Kuhl.

These three papers discuss research focused on adaptive, numerical simulations to understand the dispersion and ignition behavior of aluminum particle clouds behind reflected shock and blast waves. Of particular interest is investigation of the ignition/combustion behavior of reactive particle clouds for a various suite of identified parameters using a novel empirical ignition model. In addition, turbulent mixing in an explosive fireball, and the dissociation of air behind blast waves, are quantified using the Implicit Large Eddy Simulation (ILES) strategy.

Correction: 25 CS Researchers Presented Results at ICIAM 2011

So many Computing Sciences researchers contributed to the 7th International Congress on Industrial and Applied Mathematics (ICIAM 2011), it’s been hard for InTheLoop to keep track of them all. Even with last week’s email corrections, we still missed Aydin Buluc’s “High-Performance Combinatorial Algorithms for the Analysis of the Electric Power Grid,” co-authored by Juan Meza. You can see the complete list of CS conference contributors here.

Safety Tip: Buckle Up on the Shuttle Bus

Seat belt use on shuttle buses is not required by the California Vehicle Code, but there are good reasons to wear them anyway. A video of a seat belt demonstration at the Volvo Safety Centre shows that a sudden stop even at the slow speed of 4.5 mph can be quite jarring.

The NHTSA study “Vehicle Performance Characteristics and Seat Belt Effectiveness in Low Speed Vehicles and Golf Cars” concluded that the potential for ejection from the seat during a cornering maneuver is significantly higher for an unbelted occupant, even for vehicles with a maximum speed of only 11 mph.

And on July 14, a UCSF shuttle bus passenger was thrown from the bus and killed when the bus collided with a big rig; three other passengers were injured. In response to this accident, the university will install seat belts on all of its buses.

Berkeley Lab’s shuttles are already equipped with seat belts—now it’s up to us to use them!

This Week’s Computing Sciences Seminars

Uncertainty Quantification Discussion Group: Low-Cost, High-Performance UQ
Monday, August 1, 10:00–11:00 am, 50F-1647 and 943-254
Dmitriy Morozov, CRD, and Katie Antypas, NERSC

The group will discuss the paper “Low Cost High Performance Uncertainty Quantification” by C. Bekas, A. Curioni, and I. Fedulova.

Display-Aware, Demand-Driven Volume Visualization of Terascale Electron Microscopy Data
Tuesday, August 2, 11:00 am–12:00 pm, 50B-4205
Markus Hadwiger, King Abdullah University of Science and Technology (KAUST)

Recent advances in high-resolution data acquisition such as electron microscopy (EM) result in volume data of extremely large size. In neuroscience, EM volumes of brain tissue have pixel resolutions of 3-5 nm and slice distances of 25-50 nm, which even for sub-millimeter tissue blocks result in hundreds of gigabytes to terabytes of raw data. The capability to interactively explore these volumes in 3D is crucial for analysis, for example to trace neural connections in the field of Connectomics. However, this poses significant challenges that require the development of novel, scalable systems for visualization and interactive analysis. This talk will give an overview of the research that we are doing in this area, with the goal of processing and visualizing data only on demand, driven by actual on-screen visibility.

Link of the Week: Science Posters Given a New Life Online

A new project dubbed Skolr promises to spread the latest science farther and faster by bringing science’s ubiquitous poster sessions online. It will work simply. At registration, presenters will be given a Web URL for poster registration. They’ll then sign up, enter their poster abstract, the title, and the names of the authors and upload the poster as a PDF. Some keyword tagging will be added to enhance searchability, and the uploaded data will complement the physical display of the posters for that meeting. Posters captured by the system will be arranged by collection, associated with particular meetings. Read more.

About Computing Sciences at Berkeley Lab

The Lawrence Berkeley National Laboratory (Berkeley Lab) Computing Sciences organization provides the computing and networking resources and expertise critical to advancing the Department of Energy's research missions: developing new energy sources, improving energy efficiency, developing new materials and increasing our understanding of ourselves, our world and our universe.

ESnet, the Energy Sciences Network, provides the high-bandwidth, reliable connections that link scientists at 40 DOE research sites to each other and to experimental facilities and supercomputing centers around the country. The National Energy Research Scientific Computing Center (NERSC) powers the discoveries of 6,000 scientists at national laboratories and universities, including those at Berkeley Lab's Computational Research Division (CRD). CRD conducts research and development in mathematical modeling and simulation, algorithm design, data storage, management and analysis, computer system architecture and high-performance software implementation. NERSC and ESnet are DOE Office of Science User Facilities.

Lawrence Berkeley National Laboratory addresses the world's most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab's scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the DOE’s Office of Science.

DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.