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InTheLoop | 10.04.2011

October 4, 2011

Oct. 6 Meeting on Computational Partnerships with HEP, BER, BES, and NP

A Lab-wide informational meeting on funding opportunities under DOE’s Scientific Discovery through Advanced Computing (SciDAC) Program will be held from 11:30 a.m. to 1:00 p.m. Thursday, Oct. 6, in the Building 50 Auditorium. All staff interested in learning more about the solicitations for proposals for partnerships involving FES, HEP, BER, BES, and NP are invited to attend the meeting, which will be led by Esmond Ng of the Computational Research Division. The solicitations can be found here.

Former Lab Computer Security Expert Gene Schultz Dies

Eugene Schultz, a former member of the Lab’s Computer Protection Program and internationally known computer security expert, died unexpectedly yesterday after suffering a stroke while traveling. Schultz, who joined Berkeley Lab in 2001, worked for more than six years at Lawrence Livermore National Laboratory, where he founded DOE’s Computer Incident Advisory Capability (CIAC).

A memorial service is tentatively planned for Saturday, Oct. 8, in Livermore. For more information, visit http://www.caringbridge.org/visit/geneschultz, where you will be asked to create an account.

At the time of his retirement in 2005, Schultz had authored or co-authored five books on computer security and taught hundreds of hours of security awareness courses. He estimated that he had taught a total of 1,500 people from Berkeley Lab, LLNL, SLAC and DOE in his training courses taught here at the Lab.

In 2002, Schultz was inducted into the Information Systems Security Association Hall of Fame. He also served as editor-in-chief of Information Security Bulletin, a London-based information security journal. In 1998 he received the Information Systems Security Association’s Professional Achievement Award. He also published more than 80 articles. In 2002, Elsevier Science named him as editor-in-chief of its leading computer security journal, “Computers and Security.”

Jim Mellander, a member of the NERSC Networking and Security Group, was a close friend of Schultz. Schultz and Mellander, along with Carl Endorf of Illinois, co-authored a book entitled “Intrusion Detection and Prevention,” which was published just before Christmas 2003 by McGraw Hill/Osborne. Scott Campbell of NERSC served as technical expert for the book.

“He mentored and encouraged me, and I was grateful to him for that opportunity to work on the book with him,” Mellander said. “He was a very, very kind person who was loyal to his friends, and I was fortunate to count myself as one of them. Even after he left the lab, we stayed in touch. I have wonderful memories of visiting him at his vacation home in Twain-Harte and smoking cigars together, which Gene loved.”

Turning Grass into Gas for Less

Pull up to the pump and chances are your gas will be laced with ethanol, a biofuel made from corn. But with growing populations and shrinking farmland, there will never be enough corn to both feed and fuel the world. So researchers are working on “grassoline,” liquid biofuels made from hardy, high yielding, non-food crops, like switchgrass. But the sugars needed to make biofuels are locked up tight in cellulose, and researchers have to figure out an economical, scalable way to break them loose. Recent simulations carried out at NERSC by Jhih-Wei Chu, a chemical and biomolecular engineering professor at the University of California Berkeley, could help scientists do just that. Learn more.

Improvements Continue to MyESnet Portal

A new version of the MyESnet Portal has been rolled out. Improvements include:

  • The graphing widget used on the site summary, flow and site interface pages has been significantly improved.
  • A frequently asked questions section was added under the Help tab.
  • A site updates page was added under the Help tab.
  • Duplicate site peering entries were removed (although the speed is still wrong in some cases).

The development roadmap for future improvements is available for user comments. Read more.

Michael Wehner to Give Invited Talk at Climate Change Beijing

Michael Wehner, a staff scientist in Berkeley Lab’s Computational Research Division, will give an invited talk called “Projections of Extreme Weather in a Changing Climate: Balancing Confidence and Uncertainty” at Climate Change Beijing, an international climate change conference hosted by the Chinese Academy of Sciences, the National Science Foundation of China and CSIRO, Australia.

As part of this conference, the world’s leading climate scientists, industry leaders, government representatives, students and members of the general public will meet in Beijing, China from October 18-20 to discuss the most important environmental issues of our time. The Chinese Academy of Sciences has established the conference to promote information sharing and action, with eminent speakers catalyzing scientific advances and collaboration between national and international participants.

Wehner’s current research concerns the behavior of extreme weather events in a changing climate, especially heat waves, intense precipitation, drought and tropical cyclones. He has been selected as a lead author for the upcoming Fifth Assessment Report of the Intergovernmental Panel on Climate Change and was also a member of the lead author team for the 2009 White House report “Global Climate Change Impacts in the United States.”

“QUEST Lab: Engineering Fire” Features John Bell and Robert Cheng

Fire is one of humankind’s first technologies. We have been staring into the proverbial campfire for thousands of years. Yet, surprisingly there seems to be much more to learn. And now it’s becoming even more important to our collective future that we know as much as we can about fire. In a dark lab at Lawrence Berkeley National Laboratory, engineers and mathematicians are developing new burners and studying different flames in hopes of better understanding the power of fire and how to make the most efficient flame possible.

Robert Cheng, John Bell and the other team members have come together from different scientific disciplines—from mechanical engineering and mathematics to physics and chemistry—to develop these innovative burners and amazing three-dimensional combustion simulations that take advantage of some of the largest supercomputers in the world. The story aired last Wednesday, September 28, on KQED channel 9, and can be seen online.

Computing Sciences Volunteers Needed for Open House

Berkeley Lab’s Open House will be held Saturday, October 15, and Computing Sciences is hosting an exhibit in conference room 50B-4205 called “Believe It or Not: The Computing Odditorium.” The room will be set up like a science fair, with tables that showcase Green Flash, scientific networking, and a variety of visualizations.

We need people to help hang out by these exhibits and answer questions, and a few volunteers who will go to the welcome table and bring guests on a guided tour of our room. Go here for more information and to sign up.

This Week’s Computing Sciences Seminars

Recent Advances in Petascale Kinetic Simulations and Analysis Techniques
Tuesday, October 4, 3:00–4:00 pm, 50F-1647
Homa Karimabadi, University of California, San Diego

Recent advances in simulation technology and hardware are enabling breakthrough science where many longstanding problems can now be addressed for the first time. In this talk, we focus on kinetic simulations of magnetic reconnection which is the key mechanism that breaks the protective shield of the Earth’s dipole field, allowing the solar wind to enter the Earth’s magnetosphere. This leads to the so-called space weather where storms on the Sun can affect space-borne and ground-based technological systems on Earth. Magnetic reconnection is an exascale problem. Using 200 K cores on Jaguar, our largest simulations involve over 3 trillion particles, 15 billion cells, and generate over 200 TB.

Knowledge discovery from these massive and complex multivariate data sets remains a challenge. Similar challenges are faced in observational space physics, where 90% of the data collected from various spacecraft missions remain unexplored. We discuss our approach, called Physics Mining, to effective analysis of large data sets from both simulations and spacecraft data. Physics mining entails combining data mining and computer vision algorithms with scientific visualization to extract physics from the resulting massive data sets. One novel aspect of our data mining algorithms is that the solution is always in analytical form rather than the blackbox models obtained from artificial neural nets. This enables one to derive insight from the solution and explore the role of various terms affecting the output. We highlight the power of this approach through several key examples of high interest in space sciences.

Using Hadoop for HPC Applications
Wednesday, October 5, 10:00 am–2:00 pm, OSF 943-238 and webcast
Lavanya Ramakrishnan, NERSC Technology Integration Group

The MapReduce programming model and its open source implementation Hadoop is gaining traction in the scientific community for addressing the needs of data focused scientific applications. The requirements of these scientific applications are significantly different from the web 2.0 applications that have traditionally used Hadoop. The tutorial will provide an overview of Hadoop technologies, discuss some use cases of Hadoop for science, and present the programming challenges with using Hadoop for legacy applications. Participants will access the Hadoop system at NERSC for the hands-on component of the tutorial.

Registration is requested to assist in planning the event.

Cloud Seminar: Transactional Storage for Geo-Replicated Systems
Wednesday, October 5, 3:00–4:00 pm, 380 Soda Hall, UC Berkeley
Marcos K. Aguilera, Microsoft Research Silicon Valley

We describe the design and implementation of Walter, a key-value store that supports transactions and replicates data across distant sites. A key feature behind Walter is a new property called Parallel Snapshot Isolation (PSI). PSI allows Walter to replicate data asynchronously, while providing strong guarantees within each site. PSI precludes write-write conflicts, so that developers need not worry about conflict-resolution logic. To prevent write-write conflicts and implement PSI, Walter uses two new and simple techniques: preferred sites and counting sets. We use Walter to build a social networking application and port a Twitter-like application.

EETD Distinguished Lecture: Advances in Global Climate Modeling for Scientific Understanding and Predictability
Friday, October 7, 12:00–1:00 pm, Bldg. 50 Auditorium
Venkatachalam “Ram” Ramaswamy, Director, NOAA Geophysical Fluid Dynamics Laboratory

The Earth’s climate system presents an array of complex scientific challenges that range from unresolved gaps in knowledge to uncertainties in the understanding of the past, present, and future changes in the system. Additionally, there are demands to advance the frontiers of climate modeling and science arising from the needs of several sectors to obtain trusted information on Earth’s climate. These needs include information about regional and local climate, robust explanations of observed phenomena, quantified trends in key climate variables, and determining the predictability of the climate system from the seasonal to the centennial timescales, including extremes. The consequences of a growing world population, the associated energy demands and accompanying societal concerns regarding atmospheric composition, pollution, and climate make it necessary that climate modeling provide a credible scientific underpinning for understanding past climate changes and enabling reliable predictions. In this talk, we will explore central aspects of the climate challenges and examine the prospects offered by recent developments in climate modeling research and applications.

Building Electronics from Solution: Materials, Device Integration and Application Development
Friday, October 7, 2:00–3:00 pm, 390 Hearst Memorial Mining Building, UC Berkeley
Ana Claudia Arias, UC Berkeley, EECS

Solution-processed electronic materials have the potential to create a new manufacturing paradigm and applications domains beyond those now dominated by silicon technology.

These materials can be deposited and patterned with tools commonly used in the graphics design and printing businesses. Over the past 10 years, solution-processed semiconducting materials have been studied largely for incremental application in information display. However, combining derivatives of these semiconductors with emerging solution-dispersible metal and metal oxide nanoparticles and nanowires enables the fabrication of electronic devices that are fully built from solution.

This establishes a new device-processing platform, which in turn allows device form factors and integration of functionality in systems not feasible in any conventional semiconductor technology. Examples of novel applications and systems enabled by this include: large-area, ultralight and flexible power harvesting, logic-integrated sensing and memory technologies.

In this talk, I will discuss the development of a flexible integrated blast dosimeter to illustrate and demonstrate the challenges and advantages of using solution-processed electronic materials for flexible and disposable applications. The blast dosimeter tapes developed at PARC are used to detect the occurrence of events that cause traumatic brain injury (TBI). TBI is a medical condition that is cumulative and triggered by events such as blast pressure waves, noise, acceleration and extremely bright light. The sensor tape has integrated sensors, signal conditioning electronics, non-volatile memory and a thin film battery. The electronic circuits are based on digitally printed organic semiconductors and integrated with pressure, acoustic, acceleration and temperature sensors based on piezoelectric polymers such as PVDF or PVDF-TrFE. Piezoelectric polymers were chosen based on their ability to meet low-power, low drift and simple fabrication constraints. Active regions formed with distribute interface semiconductor networks based on polymer/polymer and polymer/small molecule systems were used in the fabrication of the printed light sensors. Polarizable solution-processed dielectrics and polymer semiconductors were integrated in the fabrication of non-volatile analog memory arrays. Memory device characteristics were monitored to understand the limiting factors to data retention time. Combined together, these elements demonstrate an integrated sensing, logic and memory system that begins to demonstrate the potential of this approach.

In this talk I will also discuss the main challenges for flexible printed electronics: materials performance, TFT operation voltage, and printing as a manufacturing technology.

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.