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InTheLoop | 02.13.2012

February 13, 2012

Simulations at NERSC Suggest Hydrates Could Be Used to Store Hydrogen Fuel

Heroes of the silver screen seem to have a habit of getting caught in impossible prisons and frozen cages. All hope seems lost until they somehow break free, saving the day (and presumably coming back for a sequel). In a sense, researchers at Pacific Northwest National Laboratory (PNNL), using supercomputers at NERSC, have recently uncovered how other energetic “heroes” escape from their frozen cages, which may lead to lasting energy benefits.

PNNL chemist Sortiris Xantheas and his colleague Soohaeng Yoo Willow studied the icy substances known as gas hydrates. Found in great abundance deep in the ocean, hydrates consist of “cages” of ice surrounding natural gas (methane), which burns cleaner than gasoline and other oil-based fuels. Hydrates look like ice, but can also burn. The trick is breaking the fiery fuel free.

Using supercomputers at NERSC, the two made detailed simulations of the great molecular escape. This was the first time researchers had accurately described the interactions between the water and gas molecules, and it opened new insights and new ideas. While it had been thought that a great amount of energy would be needed to break the cages and free the gas, the simulation showed that the molecules can squeeze through another way, using far less energy. Read more.


Public Affairs Hosts Climate Science Workshop for Journalists

On Tuesday, February 7, Berkeley Lab Public Affairs brought journalists who cover environmental and climate science to the Lab for workshop that looked at recent advances in climate science, the challenges ahead, and tools being used to better understand the changing environment. Speakers included the Lab’s Bill Collins and Margaret Torn of the Earth Sciences Division, Michael Wehner of the Computational Research Division, and Ronnen Levinson of the Environmental Energy Technologies Division, and included a welcome by Associate Lab Director Don DePaolo. A tour of the Advanced Light Source by director Roger Falcone capped off the workshop. Reporters from the New York Times, San Francisco Chronicle, Forbes, San Francisco Business Times, Reuters, KQED, and Dow Jones/Wall Street Journal participated. Public Affairs will use this experience to design similar workshops in the future.


Share Your Passion for Astronomy in a Local Classroom

Project ASTRO is looking for amateur and professional astronomers to work with teachers and students in third- to ninth-grade classrooms. This is a great opportunity to share your love of astronomy with a receptive audience and help kids learn about science.

Bay Area Project ASTRO, part of a national program at the Astronomical Society of the Pacific, pairs you with a local teacher at a school convenient for you. Together, you and your teacher partner attend a two-day summer workshop to learn hands-on, inquiry-based astronomy activities, and then you “adopt” a class for a year.

Astronomer applications are now being accepted for the 2012–2013 school year. There is no cost, but space is limited. All participants are required to attend a two-day workshop held July 27–28, 2012, at the San Mateo County Office of Education in Redwood City. Apply online here by May 29. For more information, go here.


Grace Hopper Conference Issues Call for Participation

The 12th Annual Grace Hopper Celebration of Women in Computing (GHC) has opened its Call for Participation. The annual conference, presented by the Anita Borg Institute for Women and Technology, is the world’s largest gathering of women in computing. The Grace Hopper Celebration will take place from October 3–6, 2012 at the Baltimore Convention Center in Baltimore, Maryland. This year’s theme, “Are We There Yet?” recognizes that technology and the culture of technology are continuously evolving but there are also concrete goals we are striving to achieve.

Leading researchers present their current work, while special sessions focus on the role of women in today’s technology fields, including computer science, information technology, research and engineering. The technical conference features well known keynote speakers and invited technical speakers, panels, workshops, new investigator technical papers, PhD forums, technical posters, birds of a feather sessions, the ACM Student Research Competition, and an Awards Celebration.

The deadline for submission of program abstracts is Friday, March 16, 2012. Learn more.


Six Short Plays Explore “Patterns of Chaos”

Monday Night PlayGround (now in its 18th season) is a monthly presentation of six short plays written on a common theme. On Monday, February 20, at Berkeley Repertory Theatre, the theme will be a mathematical one: “Patterns of Chaos.”

On February 9, a group of mathematicians at the Mathematical Sciences Research Institute (MSRI) met with the PlayGround pool of playwrights to talk about randomness and pattern development, how mathematicians think about them, and the often surprising ways in which patterns emerge in systems that evolve randomly. The playwrights engaged the mathematicians in a discussion of how some models of physical phenomena, such as the Ising model (originally proposed as a model for magnetism) and dimers, show critical behavior changes and phase transitions that lead to the development of striking patterns or regularities, even though the evolution of the model incorporates randomness that on first glance seems to want to destroy any patterns (or even prevent their development). (This topic fit well with MRSI's current spring program, entitled “Random Spatial Processes.”)

The playwrights have five days to write a short play inspired by the topic, and the best six of the resulting plays will be presented on Monday, February 20, at Monday Night PlayGround. The performances start at 8:00 pm, and the pre-show discussion starts at 7:10 pm, featuring a panel of mathematicians and some of the playwrights who wrote the plays that will be performed that night. More information, including where and how to buy tickets, can be found here.


This Week’s Computing Sciences Seminars

Enhancing Locality of Irregular Programs
Monday, February 13, 4:00–5:00 pm, 320 Soda Hall, UC Berkeley
Milind Kulkarni, Purdue

Over the past several decades of compiler research, there have been great successes in automatically enhancing locality for regular programs, which operate over dense matrices and arrays. Tackling locality in irregular programs, which operate over pointer-based data structures such as trees and graphs, has been much harder, and has mostly been left to ad hoc, application specific methods. In this talk, I will describe efforts by my group to automatically improve locality in a broad class of irregular applications, those that traverse trees. The key insight behind our approach is an abstraction of data structure traversals as operations on vectors. This abstraction lets us design transformations, predict their behavior and determine their correctness. I will present two specific transformations we are developing, “point blocking” and “traversal splicing,” and show that they can deliver substantial performance improvements when applied to several real-world irregular kernels.

New Lower and Upper Bounds on Communication and Arithmetic: LAPACK Seminar
Wednesday, February 15, 12:10–1:00 pm, 380 Soda Hall, UC Berkeley
James Demmel, UC Berkeley/LBNL

We present two new approaches to lower and upper bounds in arithmetic and communication. First, we consider dense and sparse linear algebra algorithms: Under reasonable assumptions intended to describe any algorithms that are 3-nested-loop-like, we use geometric arguments to prove lower bounds on the arithmetic required. These bounds are attained for some but not all sparsity patterns, offering the hope of faster algorithms yet to be discovered.

Second, in joint work with Katherine Yelick and Michael Christ, we describe a generalization of our communication lower bounds for 3-nested-loop-like algorithms to any number of nested loops, with any array references that are general affine functions of the loop indices. This lower bound is attained by a new algorithm of Yelick and Edgar Solomonik for the N-body problem.

Phase Transitions and Sampling
Wednesday, February 15, 4:10–5:00 pm, 939 Evans Hall, UC Berkeley
Allan Sly, Department of Statistics, UC Berkeley

I will discuss two recent pieces of work relating phase transitions of spin-systems to questions of sampling their distributions.

(i) For the heat bath Glauber dynamics for the two dimensional Ising model, the growth of the mixing time is now known at all temperatures. The final case was at the critical temperature which was completed using new ideas from the study of SLE.

(ii) The question of what relationships exist between phase transitions in statistical physics and the computational complexity of sampling and counting has been of ongoing interest in theoretical computer science. Recent progress has established the computational complexity of sampling on d-regular graphs for essentially all 2-spin systems. The complexity depends on whether the model has a unique Gibbs measure on the infinite d-regular tree establishing the equivalence of phase transitions and computational thresholds in these cases.

Issues and Perspectives of LHC Computing
Thursday, February 16, 3:00–4:00 pm, 50B-4205
Federico Carminati, CERN

More than two years after the LHC startup, the computing frameworks of the LHC experiments have finally had a substantial field-test after more than ten years of intense preparation, planning and testing. At this point in time it is interesting to attempt a first summary review of the situation. Which assumptions have stood the reality check, which did not? Which new problems have emerged, and which previously identified “risk factors” have turned out to be irrelevant? This talk will review the experience of the first year of operation of the LHC Offline and how well the Computing Models of the LHC experiments are collectively coping with the impact of the real data. The major issues facing data collection, distribution, processing and analysis will be discussed based on the feedback from the LHC experiments. The talk will conclude with an overview on the potential solutions and the new perspectives for LHC computing.


Link of the Week: The Scale of the Universe

“The Scale of the Universe 2” by Cary Huang is an entertaining interactive tour of the universe that shows the sizes of representative samples of every length scale, from quantum foam (1 x 10–35 m) to giant earthworms (3 m) to the Sloan Great Wall (1.3 x 1025 m).



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.