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InTheLoop | 05.14.2012

May 14, 2012

Floating Robots Track Water Flow with Smart Phones

To understand how water flows through the Sacramento-San Joaquin Delta, 100 mobile sensors were placed into the Sacramento River on May 9 to make critical measurements every few seconds. Once collected, this data was transmitted to NERSC for assimilation and analysis. Two-thirds of the water in California passes through the Sacramento-San Joaquin Delta, providing drinking water for 22 million Californians and supporting agriculture valued at tens of billions of dollars. Understanding how the water flows through the Delta on its way to pumping stations and San Francisco Bay is imperative to balance conflicting demands on this critical resource. Read more.


New Accelerator Will Study Steps on the Path to Fusion Power

The Neutralized Drift Compression Experiment, NDCX-II, has recently marked successful completion. Designed with the aid of computer simulations executed at NERSC, the accelerator was created to study warm dense matter, an important research field in itself and particularly relevant to nuclear fusion. NDCX-II will test a variety of technologies in preparation for a new generation of power plants on Earth that will mimic the engines of the stars. Read more.


Energy Secretary Chu on How HPC Will Change Our Energy Future

Forbes Magazine sat down for an exclusive interview with U.S. Energy Secretary Steven Chu, who shared his thoughts on the current state of supercomputing. The Nobel Prize-winning scientist is betting that these super machines will play a key role in designing new products and solving longstanding energy challenges: from better engines to advanced nuclear reactors. He’s backing his bet with significant resources, offering some of the Department’s world-leading supercomputers for use by industry leaders. Read more.


Designers Dig Out Drawing Board in Quest for Exascale Computing

ASCR Discovery reports that the architects of tomorrow’s exascale computers are designing systems that borrow from and contribute to an unlikely source: the consumer electronics industry. The result will be systems exquisitely designed to meet the needs of scientists studying complex systems such as jet engine efficiency, large-scale weather patterns, and earthquake models. Associate Lab Director Kathy Yelick and CRD Advanced Technologies Group Lead John Shalf are among the experts interviewed. Read more.


Hank Childs Wins 2012 DOE Early Career Award

Hank Childs of the Computational Research Division’s Visualization Group has been honored with a 2012 DOE Early Career Award. This is the third year of the Early Career Research Program managed by the U.S. Department of Energy’s Office of Science, and Childs is one of four researchers from the Lawrence Berkeley National Laboratory (Berkeley Lab) who were honored. In total, there were 68 award recipients from 47 institutions. Read more.


Berkeley Lab-Mentored High School Girls Win National Contest to Develop Science Ed App

After taking top honors among their peers from Albany and Berkeley High Schools, a team of five girls from Albany High beat out 10 other teams from high schools around the country to win the 2012 Technovation Challenge. The challenge is a 10-week program in which teams of girls develop science education apps for smartphones. The team was mentored by Sufia Haque of Berkeley Lab’s Engineering Division and Taghrid Samak of the Computational Research Division. In all, 24 women at the Lab served as mentors to girls participating in the program. Read more.


ESnet to Share Expertise at Europe’s Premier Networking Conference

ESnet staff members Eric Pouyoul, Jon Dugan, and Bill Johnston are among the speakers scheduled to present at the 2012 TERENA Networking Conference to be held May 21–24 in Reykjavík, Iceland. The conference, sponsored by the Trans-European Research and Education Networking Association, is the largest and most prestigious European research networking conference. Read more.


CRD Staff to Participate in Inria@Silicon Valley Workshop in Paris

The second workshop Berkeley-Inria-Stanford 2012 (BIS’12) is being hosted by Inria in Paris on May 21–22, 2012. It is co-organized by UC Berkeley, Inria, and Stanford University, in partnership with CITRIS and the French Ministry of Foreign Affairs. BIS’12 is part of the joint research program Inria@SiliconValley. The objectives of this workshop are twofold: first, to present the current state of scientific collaborations, and second to work on proposals for future ambitious joint projects.

Deb Agarwal is giving an invited talk on “Driving Data Management for Science Using the 20 Questions Approach” and will participate in a panel discussion on “Big Data: Scientific and Societal Challenges.” Other Computational Research Division participants include Esmond Ng, who is collaborating on “Fast and Scalable Hierarchical Algorithms for Computational Linear Algebra”; and Jim Demmel, who is collaborating on “Communication Optimal Algorithms for Linear Algebra.”


Berkeley Lab Staff Contribute to SIAM Conference on Imaging Science

The 2012 SIAM Conference on Imaging Science is being held on May 20–22 in Philadelphia, PA. New devices capable of imaging objects and structures from nanoscale to the astronomical scale are continuously being developed and improved, and as result, the reach of science and medicine has been extended in exciting and unexpected ways. The impact of this technology has been to generate new challenges associated with the problems of formation, acquisition, compression, transmission, and analysis of images. Several Berkeley Lab researchers are giving presentations at the conference:

  • Filipe Maia, NERSC: “Real-Time Ptychographic X-Ray Image Reconstruction.”
  • Stefano Marchesini, Advanced Light Source: co-organized session on Algorithms for Diffractive Imaging; presentation title unavailable.
  • Ralf Grosse-Kunstleve (co-author with Nicholas Sauter), Physical Biosciences Division: “Computational Challenges for Biological Structure Determination Using X-Ray Diffraction.”
  • Chao Yang, Computational Research Division: “Algorithms for Single Molecule Diffractive Imaging”; co-organized session on Algorithms for Diffractive Imaging.

Celebrating the Establishment of the Simons Institute for the Theory of Computing

A recent $60 million award to UC Berkeley from the Simons Foundation will establish the campus as a worldwide center for theoretical computer science. The grant funds the creation of a new institute where leading computer theorists and researchers from around the globe will converge to explore the mathematical foundations of computer science and extend them to address challenges in fields as diverse as mathematics, health care, climate modeling, astrophysics, genetics, economics, and business.

A panel discussion featuring distinguished faculty from computer science, math and statistics as well as representatives from industry will celebrate the establishment of the Institute on Monday, May 21. The founder of the Simons Foundation, Jim Simons, who earned his Ph.D. in Mathematics from UC Berkeley in 1961, will give the opening remarks. Berkeley Lab Deputy Director Horst Simon will participate in the panel discussion. The event will begin at 9:30 a.m. in Sutardja Dai Hall. Go here for program details and to register.


This Week’s Computing Sciences Seminars

Heat-Assisted Magnetic Recording Head-Disk Interface: Mechanics, Modeling and Simulation
Tuesday, May 15, 10:00–11:00 am, 50A-5132
Joanna Bechtel, UC Berkeley

In order to compete with solid-state drives, hard drives must continue to improve storage capacity and reliability while keeping costs low. A new technology known as heat-assisted magnetic recording (HAMR) is the leading candidate to achieve large increases in the storage capacity of hard disk drives. During HAMR data writing, a laser delivered by a near-field optical system locally heats the magnetic disk to several hundreds of degrees within a few nanoseconds. The models and simulation codes used to predict head-disk interface reliability must be re-evaluated to include new thermal issues. This presentation addresses two components of the head-disk interface: the air bearing that supports the recording head flying over the spinning disk at minimum clearances of less than 5 nm and the 1–2 nm thick layer of protective polymer lubricant coating the disk.

The air bearing code solves the pressure generation in the air bearing, which is governed by the lubrication equation. Rarefaction effects are taken into account by including coefficients derived from kinetic theory. While traditional hard disk drives are approximately isothermal, the heat delivered to the disk during the write cycle in HAMR dissipates so that local air properties and a more general non-isothermal lubrication equation have been implemented. The flow and evaporation of the polymer lubricant is predicted with a simulation tool that incorporates temperature and thickness dependencies of evaporation, viscosity, and disjoining pressure into a continuum lubrication model.

DREAM Seminar: Eliminating Concurrency Bugs with Control Engineering
Tuesday, May 15, 4:00–5:00 am, 540 Cory Hall, UC Berkeley
Stéphane Lafortune, University of Michigan

We present a control engineering approach to the elimination of certain classes of concurrency bugs in concurrent software. Based on a model of the source code extracted at compile time and represented in the form of a Petri net, control techniques from the field of discrete event systems are employed to analyze the behavior of the concurrent program. The property of deadlock-freedom of the program is mapped to that of liveness of its Petri net model, called a Gadara net. A new methodology for Iterative COntrol of Gadara nets (labeled ICOG), is developed for synthesizing control logic that is liveness-enforcing and maximally-permissive. ICOG relies upon the technique of Supervision Based on Place Invariants developed for Petri nets subject to linear inequality constraints. The synthesized control logic, in the form of monitor places, is then implemented by program instrumentation. At run-time, the control logic will provably enforce deadlock-freedom of the program without altering its control flow. The results presented pertain to the case of circular-wait deadlocks in multithreaded programs employing mutual exclusion locks for shared data. However, the methodology can be applied to tackle other classes of concurrency bugs. This is collaborative work with the members of the Gadara team: http://gadara.eecs.umich.edu

Direct Numerical Simulations of Temporally Developing Turbulent Reacting Jets
Thursday, May 17, 10:30–11:30 am, 50A-5132
Shashank, Stanford University

Liquid fueled engines are ubiquitous in the transportation sector since they minimize the weight and volume of the propulsion system. The combustion that occurs in these engines is an inherently multi-physics process, involving fuel evaporation, reaction kinetics, and high levels of turbulence. These physics are often difficult to characterize experimentally, due to the extreme environments associated with device operation. A desire for high fidelity data that explains the complex interaction between different physical mechanisms motivates the use of direct numerical simulation (DNS) as an investigation tool. In this study, a reacting DNS is used to investigate the issue of regime identification, which is a particularly challenging and important problem in combustion modeling.

Three-dimensional DNS of temporally developing jets of liquid and gaseous n-heptane have been performed to study auto-ignition in conditions that are representative of a diesel engine environment. In the case of liquid fueled simulations the continuous phase is described using an Eulerian representation whereas Lagrangian particle tracking is used to model the dispersed phase. The chemical kinetics are described using a reduced n-heptane chemical mechanism that involves 42 species and 304 reactions.

The DNS data is used to assess and evaluate different components of large eddy simulation (LES) combustion models. Attention is focused on flamelet-based models, which invoke the so-called presumed probability density function (PDF) formalism. Flamelet combustion models typically assume that burning occurs in either a fully premixed or in a fully non-premixed regime. However, previous work has shown that the premixed and non-premixed regimes interact and often lead to partially premixed combustion. In the current study, the temporal jet DNS data is used to perform an a-priori analysis of an extension of the partially premixed model that accounts for auto-ignition effects. The results of this analysis demonstrate the importance of unsteady effects, and of accounting for the interaction between different modes of combustion.


Link of the Week: Thomas Sterling: “I Think We Will Never Reach Zettaflops”

As supercomputing makes its way through the petascale era, the future of the technology has never seemed so uncertain. In an HPCwire interview, HPC veteran Thomas Sterling, Professor of Informatics and Computing at Indiana University, takes us through some of the most critical developments in high performance computing, explaining why the transition to exascale is going to be very different than the ones in the past and how the United States is losing its leadership in HPC innovation. 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.