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InTheLoop | 01.30.2012

January 30, 2012

ESnet Policy Board to Hold First Meeting This Week

The ESnet Policy Board, created last summer, will hold its first meeting on Feb. 2 here at Berkeley Lab. The Policy Board will provide scientific and executive-level advice to the Berkeley Lab Director regarding the overall ESnet program. Meeting annually, the ESnet Policy Board will also focus on specific issues such as resource utilization to maximize the present and future scientific impact of ESnet, and long-range planning for the program, including the research and development necessary for future capabilities. Policy Board members are:

  • Larry Smarr, founding Director of the California Institute for Telecommunications and Information Technology at the University of California San Diego and UC Irvine. Previously Smarr was the founding director of the National Center for Supercomputing Applications at the University of Illinois, Urbana-Champaign.
  • Vinton Cerf, Vice President and Chief Internet Evangelist for Google. Widely known as one of the “Fathers of the Internet,” Cerf is the co-designer of the TCP/IP protocols and the architecture of the Internet.
  • Kristin Rauschenbach is Vice President and Department Head of the Disruptive Information Processing Technologies group at BBN Technologies, and serves as the Substrate Architect for the GENI (Global Environment for Network Innovations) Project Office. She was previously co-founder and CEO of PhotonEx and Associate Division Head at MIT’s Lincoln Laboratory.
  • Jagdeep Singh is the Executive Chairman and Co-Founder of Infinera, where he also served as President, Chief Executive Officer, and Director. He is a member of the Advisory Council at Stanford Graduate School of Business and was previously president and general manager of CIENA Corporation’s Core Switching Division.
  • David Clark is a Senior Research Scientist at the MIT Computer Science and Artificial Intelligence Laboratory (CSAIL). Since the mid 1970s, Clark has been leading the development of the Internet.
  • Cees de Laat is Professor and leader of the System and Network Engineering Science group at the University of Amsterdam in the Netherlands. He is co-founder and organizer of several of the past meetings of the Global Lambda Integrated Facility (GLIF) and founding member of CineGrid.org.
  • David Foster is head of the Communications and Network Group at CERN, the European Organization for Nuclear Research, where he is responsible for all the electronic communications of the laboratory. Educated as a physicist, he also holds an MBA and has been widely published in computer science journals and related publications.

Annual Meeting of the NERSC Users Group This Week

NUG 2012, the annual meeting of the NERSC Users Group, will be held Wednesday through Friday, February 1–3, at NERSC’s Oakland Scientific Facility. The first two days will be training sessions, covering “Getting Started at NERSC” on Wednesday and “Advanced Topics” on Thursday. The NUG Business Meeting will be held Friday, with presentations by NERSC’s ASCR Program Manager Yukiko Sekine as well as by NERSC management and staff. The agenda is available here.


An Energy Storage Record for Lithium Air-Batteries

Using supercomputers at NERSC and electron microscopy, a team of researchers from the Pacific Northwest National Laboratory and Princeton University recently built a novel graphene membrane that could produce a lithium-air battery with the highest-energy capacity to date. Read more.


A Database of Billions of Genes and Counting!

With support from NERSC, the IMG/M data management system, which supports the analysis of microbial communities sequenced by the Joint Genome Institute, crossed the boundary of 1 billion genes recorded in the system—more than any other similar system in the world. Read more.


The Great Gas Hydrate Escape

For some time, researchers have explored flammable ice for low-carbon or alternative fuel or as a place to store carbon dioxide. Now, a computer analysis at NERSC of the ice and gas compound, known as a gas hydrate, reveals key details of its structure. The results show that hydrates can hold hydrogen at an optimal capacity of 5 weight-percent, a value that meets the goal of a Department of Energy standard and makes gas hydrates practical and affordable. Read more.


Computing Steps Up to Capture, Keep Carbon Dioxide Underground

Many of the ideas underlying carbon capture and sequestration are either in laboratory tests or pilot studies. Using traditional scale-up processes to commercialize new research ideas in the power industry has historically taken 20 to 30 years. But DOE supports several computational projects to accelerate this process.

Researchers such as CRD’s Maciej Haranczyk use supercomputers to speed designs for new materials that sponge up carbon dioxide and systems that facilitate its large-scale capture. Other scientists use computation to better understand the geological and physical processes and lay the groundwork for approaches that will sequester gas underground. Read more in ASCR Discovery.


LDRD FY 2013 Call for Proposals

On January 24, Berkeley Lab Director Paul Alivisatos issued the Laboratory Directed Research and Development (LDRD) FY 2013 Call for Proposals. The LDRD program constitutes one of the principal means to seed innovative science and new research directions.

An important factor in judging proposals will be their support of competencies aligned with the Laboratory’s and DOE’s strategic directions. Multi-investigator and multi-divisional initiatives are particularly encouraged. Topics of special significance include projects that address the use of large-scale computation and data science. All projects should have a clearly stated problem (addressing a challenging scientific question, DOE mission, or national need); coherent objectives; and a well considered plan for leadership, organization, and budget.

The complete call, schedule, guidance, and forms are available here. Proposals should be put into the submission system by Friday, March 23, 2012.


Computing Sciences Helps Inspire Careers in Science Research

In an effort to expose high school students to careers in research, the Berkeley Lab Computing Sciences Diversity Outreach Program partnered with San Francisco’s Lowell High School Science Research Program, an after school program that aims to give highly motivated juniors and seniors a chance to develop research projects with professional guidance, with the intent to have the students enter the Intel Science Talent Search, a competition sponsored by Intel that offers college scholarships for outstanding scientific work. As part of this collaboration, 32 Lowell students got a tour of NERSC. Read more.


Wednesday Talk on Role of Networking Infrastructure in Advancing Science

Prof. Cees de Laat, chair of the System and Network Engineering research group at the University of Amsterdam and internationally recognized networking expert, will give a talk on “Mastering Complex Infrastructure” at 10 a.m. Wednesday, Feb. 1 in Bldg. 50B, Room 4205. This talk will cover the use of state-of-the-art networking in support of e-science and the great benefit of networking and e-infrastructure to researchers in many disciplines. Examples will include projects in high-energy physics, radio astronomy, dike engineering, medical research, and other areas. The talk will show how networking innovations enable research collaborations on a new scale with novel capabilities.


Employees Invited to Meet UC Regents Staff Advisors

Penelope Herbert of UC Davis and Kevin Smith of UCLA — the current Staff Advisors to the UC Regents — will visit the Lab on Thursday, Feb. 2, from 8 to 10 a.m. in Perseverance Hall. They will discuss how they work with staff assemblies and the Board of Regents, and explain how staff can share their concerns through them. Other topics will include how to become a staff advisor, results of a recent climate survey, tuition benefits for UC staff at the Lab, and the creation of a Lab staff assembly. All employees are invited to attend. If you have any questions regarding this event, please contact the Lab’s CUCSA delegates, Elizabeth Bautista or Victor Chan.


Safety Note: When Is Noise Hazardous?

Everyone knows that exposure to high noise levels can cause hearing loss, but how do you know when noise levels are in the range that might be detrimental to your hearing? In general, noise may be at a hazardous level anytime that you must raise your voice to communicate with someone three feet away.

The best way to protect your hearing is to consistently use hearing protection whenever noise levels are above 85 decibels, irrespective of exposure duration. Hearing protection must be used all the time when working in high noise areas to get the full benefit.

Though noise levels in most LBNL computer rooms do not exceed 85 decibels, employees may prefer to wear earplugs or earmuffs when working for long periods of time in these areas. Noise-cancelling headphones require special approval from EHS, because not all of them are acceptable.

Here are some hearing safety resources:


This Week’s Computing Sciences Seminars

Cloud Seminar: Storm: Distributed and Fault-Tolerant Real-Time Computation
Monday, January 30, 11:00 am–12:00 pm, 480 Soda Hall, UC Berkeley
Nathan Marz, Twitter.com

Storm makes it easy to write and scale complex real-time computations on a cluster of computers, doing for real-time processing what Hadoop did for batch processing. Storm guarantees that every message will be processed. And it’s fast — you can process millions of messages per second with a small cluster. Best of all, you can write Storm topologies using any programming language. Storm was open-sourced by Twitter in September of 2011 and has since been adopted by many companies around the world.

Storm has a wide range of use cases, from stream processing to continuous computation to distributed RPC. In this talk I will introduce Storm and show how easy it is to use for real-time computation.

NERSC Brown Bag: Large-Scale Nanostructure Simulations from X-Ray Scattering Data on Graphics Processor Clusters
Tuesday, January 31, 12:00–1:00 pm, OSF 943-238
Sherry Li, LBNL/CRD

X-ray scattering is a valuable tool for measuring the structural properties of materials used in the design and fabrication of energy-relevant nanodevices (e.g., photovoltaic, energy storage, battery, fuel, and carbon capture and sequestration devices) that are key to the reduction of carbon emissions. Although today’s ultra-fast X-ray scattering detectors can provide tremendous information on the structural properties of materials, a primary challenge remains in the analyses of the resulting data. We are developing novel high-performance computing algorithms, codes, and software tools for the analyses of X-ray scattering data.

In this paper we describe two such HPC algorithm advances. Firstly, we have implemented a flexible and highly efficient Grazing Incidence Small Angle Scattering (GISAXS) simulation code based on the Distorted Wave Born Approximation (DWBA) theory with C++/CUDA/MPI on a cluster of GPUs. Our code can compute the scattered light intensity from any given sample in all directions of space, thus allowing full construction of the GISAXS pattern. Preliminary tests on a single GPU show speedups over 125x compared to the sequential code, and almost linear speedup when executing across a GPU cluster with 42 nodes, resulting in an additional 40x speedup compared to using one GPU node. Secondly, for the structural fitting problems in inverse modeling, we have implemented a Reverse Monte Carlo simulation algorithm with C++/CUDA using one GPU. Since there are large numbers of parameters for fitting in the X-ray scattering simulation model, the earlier single CPU code required weeks of runtime. Deploying the AccelerEyes Jacket/Matlab wrapper to use GPU gave around 100x speedup over the pure CPU code. Our further C++/CUDA optimization delivered an additional 9x speedup.

Joint work with Abhinav Sarje, Jack Pien, Slim Chourou, Alex Hexemer, and Elaine Chan

Mastering Complex Infrastructure
Wednesday, February 1, 10:00–11:00 am, 50B-4205
Cees de Laat, System and Network Engineering Research Group, University of Amsterdam

This talk will cover the use of state-of-the-art networking in support of e-Science and the great benefit of networking and e-Infrastructure to researchers in many disciplines. With experience from projects in high-energy physics, radio-astronomy, dike engineering, medical research, and more. The talk will show how networking innovations enable research collaborations on a new scale with novel capabilities.

LAPACK Seminar: Application of the Voronoi Tessellation for High-Throughput Analysis of Crystalline Porous Materials
Wednesday, February 1, 12:00–1:00 pm, 380 Soda Hall, UC Berkeley
Chris Rycroft, UC Berkeley and LBNL/CRD

Crystalline porous materials, such as zeolites, contain complex networks of void channels that are exploited in many industrial applications. Since the 1950s, they have been employed in common applications such as chemical catalysts and water softeners, and more recently there has been interest their use for new technologies such as carbon capture and storage. A key requirement for the success of any nanoporous material is that the chemical composition and pore topology must be optimal for a given application. However, this is a difficult task, since the number of possible pore topologies is extremely large: thousands of materials have been already been synthesized, and databases of millions of hypothetical structures are available.

We have developed tools for rapid screening of these large databases to automatically select materials whose pore topology may make them most appropriate for a given application. Many of the methods are based on computing the Voronoi network, which provides a map of void channels in a given structure. This is carried out using the free software library Voro++, which has been modified to properly account for three-dimensional non-orthogonal periodic boundary conditions.

Open Source Robotics
Wednesday, February 1, 12:00–1:00 pm, 310 Sutardja Dai Hall (Banatao Auditorium), UC Berkeley
Steve Cousins, President and CEO, Willow Garage

Over the next 10 years, personal robots (as opposed to industrial robots) have the potential to improve people’s lives by taking automation to a new level. Like personal computers of 30 years ago, the personal robotics industry will take off and become an economic engine. But robotics is a complex, multidisciplinary field, and fielding successful applications requires expertise ranging from hardware (mechanical and electrical) to social science. By working together on an open source software platform, we can accelerate progress in the field and more quickly field successful applications. Willow Garage has partnered with Stanford University and many other top robotics laboratories around the world to create such an open source code base. The robot operating system, ROS, is quickly becoming the de facto platform for robotics research. I will argue that most if not all robotics companies should join the ROS bandwagon, as a way to move the entire industry forward quickly.

EECS Colloquium: Exploring the Universe with Interactive Art
Wednesday, February 1, 4:00–5:00 pm, 306 Soda Hall (HP Auditorium), UC Berkeley
Scott Snibbe, media artist, filmmaker, and researcher in interactivity, Scott Snibbe Studio

San Francisco artist and entrepreneur Scott Snibbe will present selections from twenty years of interactive exhibits, interactive art, and interactive music. He will show many examples of interactive media with technologies including computer vision, haptics, multitouch, and iPads, including recent work creating the first app album with Björk, Biophilia, and the recent interactive exhibits for James Cameron’s movie Avatar. He will discuss the educational and societal benefits of interactivity; and the joys, challenges, and research involved in the creation and distribution of interactive media on the cutting edge of interactive technology.

DREAM Seminar: Why Discrete Is Faster Than Continuous in Computational Finance
Thursday, February 2, 4:00–5:00 pm, 540 Cory Hall, UC Berkeley
Stephen Weston, JP Morgan

Working across multiple asset classes using discrete mathematics, results are reported from an ongoing project to create dataflow computational engines that employ fine-grained parallelism to accelerate complex financial models for trading and risk management.



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.