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InTheLoop | 07.26.2010

July 26, 2010

Simulations Show That “Sweaty” Flowers Cool the World

The world is a cooler, wetter place because of transpiring flowers, say University of Chicago researchers who ran more than a million lines of code on NERSC’s IBM Power5 “Bassi” system last year. They found that this effect is especially pronounced in the Amazon basin, where 80 percent of ever-wet rainforest area would not exist without flowering plants. These findings were published online on June 16, 2010 in Proceedings of the Royal Society B. Read more.

The Trouble with Multicore

In IEEE Spectrum, UC Berkeley professor and CRD researcher David Patterson writes:

The semiconductor industry threw the equivalent of a Hail Mary pass when it switched from making microprocessors run faster to putting more of them on a chip—doing so without any clear notion of how such devices would in general be programmed. The hope is that someone will be able to figure out how to do that, but at the moment, the ball is still in the air. Why take such a gamble? In short, because there wasn't much of an alternative.

In this essay, Patterson gives an easy-to-read overview of the many ways researchers, including his Par Lab team, are trying to respond to the multicore problem, and he assesses their chance of success. His forecast is cautiously optimistic. Read more.

NERSC Systems Will Be Down for a Power Upgrade This Week

As previously announced, there will be a NERSC-wide outage July 27-30 for a 3 MW power upgrade to the NERSC computer room. All NERSC systems will be taken down at 7 am Pacific Time, Tuesday, July 27. All systems should be back in service by noon Friday, July 30; some may return to service earlier. During the outage you will be able to view status updates at www.nersc.gov. The power upgrade will provide a total of 9 MW of capacity to the NERSC computer room.

Lab Wins Two “OASCRs” at SciDAC 2010 Visualization Night

On Wednesday, July 14, at the SciDAC 2010 conference in Chattanooga, two “OASCR” awards were won by Prabhat and Hank Childs of the NERSC Analytics Team and CRD Visualization Group.

Prabhat’s entry, “Hurricane Season,” joint work with Michael Wehner of CRD, also won the “People’s Choice” award. Here is a description of the science behind the movie:

Global warming will likely change the statistics of tropical cyclones and hurricanes. In this high resolution simulation, using the finite volume version of NCAR’s Community Atmosphere Model, we are studying how well the model can reproduced observed tropical cyclone statistics. The simulated storms seen in this animation are generated spontaneously from the model’s simulated weather conditions long after the memory of initial conditions have been forgotten. The structure of these simulated tropical cyclones is surprisingly realistic with the strongest storms rating as Category 4 on the Sapphir-Simpson scale. The animated field is the total vertical column integrated water vapor.

“Type Ia Supernova: Turbulent Combustion at the Grandest Scale” was produced for the SciDAC Computational Astrophysics Consortium by the NERSC Analytics Team and VACET, with Hank Childs in the lead. Calculations using the CASTRO code were run on Franklin at NERSC and Jaguar at OLCF by Haitao Ma and Stan Woosley of UC Santa Cruz, and John Bell, Ann Almgren, and Andy Nonaka of CCSE. Here is a summary:

Deep inside a dying star in a galaxy far, far away, a carbon fusion flame ignites. Ignition may happen in the middle or displaced slightly to one side, but this simulation explores the consequences of central ignition. In a localized hot spot, represented here by a deformed sphere with an average radius of 100 km, carbon is assumed to have already fused to iron, producing hot ash (~10 billion K) with a density about 20% less than its surroundings. As the burning progresses, this hot buoyant ash rises up and interacts with cold fuel. Rayleigh-Taylor fingers give rise to shear and turbulence, which interacts with the flame, causing it to move faster. In about 2 seconds, the energy released blows the entire white dwarf star up, leaving nothing behind but a rapidly expanding cloud of radioactive nickel, iron, and other heavy elements. A Type Ia supernova is born.

CS Introduces High Schoolers to Careers in Computing, Networking

Beginning today, Computing Sciences is hosting 14 local high school students as part of an outreach program to introduce students to various career options in scientific computing and networking. The sessions will be held at both the main Lab and the Oakland Scientific Facility from July 26–29 and will include presentations, hands-on activities, and tours of various facilities. The program was developed with input from computer science teachers at Berkeley High, Albany High, Kennedy High (in Richmond), and Oakland Tech. Teachers referred students they thought would most benefit from such a program. Staff from NERSC, CRD, ESnet, and the IT Division will present a wide range of topics including assembling a desktop computer, cyber security war stories, algorithms for combustion and astrophysics, the role of applied math, networking, science portals, and Green Flash.

ASCR HQ Posts Job Vacancies for Scientists and Mathematicians

The DOE Office of Advanced Scientific Computing Research (ASCR) has posted announcements of ten job vacancies for physical scientists, computer scientists, and mathematicians at their headquarters in Germantown, MD. Click on the links for details and application instructions.

CRD Researchers to Speak at International Combustion Symposium

Researchers in Berkeley Lab’s Center for Computational Sciences and Engineering will present three papers and co-authored a fourth at the 33rd International Combustion Symposium to be held August 1-6 at Tsinghua University in Beijing, China. Sponsored by the Combustion Institute, the International Symposium on Combustion is held every two years and attracts members of the Combustion Institute as well as others interested in combustion from around the world. LBNL papers are:

  • “Characterization of Low Lewis Number Flames” by Andrew Aspden, Marcus Day and John Bell
  • “Lewis Number Effects in Distributed Flames” by Andrew Aspden, Marcus Day and John Bell
  • “Numerical Simulation of Nitrogen Oxide Formation in Lean Premixed Turbulent Flames” by Marcus Day, John Bell, and Xinfeng Gao, with Peter Glarbor of the Technical University of Denmark
  • “Gas Dynamic Model of Turbulent Combustion in TNT Explosions” by Allen L. Kuhl of Lawrence Livermore National Laboratory with John Bell and Vincent Beckner of LBNL


LBNL Staff Contribute to CScADS Summer Workshops

The SciDAC Center for Scalable Application Development Software (CScADS) is holding four weeks of workshops in Snowbird, Utah, to engage the community in the challenges of leadership computing and foster interdisciplinary collaborations. In last week’s workshop (July 19–22), “Leadership-Class Machines, Petascale Applications and Performance Strategies,” Zhengji Zhao of NERSC presented an “Overview of NERSC Facilities and Usage,” and Paul Hargrove of CRD presented “Introduction to UPC.”

This week’s workshop (July 26–29) is “Scientific Data and Analytics for Extreme Scale Computing.” Hanks Childs of CRD and NERSC is presenting “Introduction to VisIt” and “IDAV View.”

UC Discovery Grant Request for Proposals

The University of California Office of Research and Graduate Studies is pleased to announce the 2010–2011 Cycle 1 UC Discovery Grant request for proposals. The UC Discovery Grant (UCDG) promotes collaborations between UC researchers and industry partners in the interest of supporting UC researchers and trainees, strengthening the state’s economy, and serving the public good. The UCDG is a matching grant mechanism; research projects are jointly funded by a UCDG and a required industry matching contribution.

All applicants must submit a Notice/Letter of Intent (LOI) between July 27 and September 8, 2010. Full proposals are due on November 3. LOIs and proposals must be submitted using the online proposal system proposalCENTRAL. Please refer to the program website for the most up-to-date information. Detailed LOI and application submission instructions will be available at the website and on proposalCENTRAL by July 27.

This Week’s Computing Sciences Seminars

Adaptive Mesh Refinement Based on High Order Finite Difference WENO Scheme
Thursday, July 29, 10:00–11:00 am, 50F-1647
Chaopeng Shen, Michigan State University

We combine the adaptive mesh refinement (AMR) framework with the high order finite difference weighted essentially non-oscillatory (WENO) method in space and the TVD Runge-Kutta (RK) method in time (WENO-RK) for hyperbolic conservation laws. Our goal is to realize mesh adaptivity in the AMR framework, while maintaining very high (higher than second) order accuracy of the WENO-RK method in the finite difference setting. We use high order prolongation in both space (WENO interpolation) and time (Hermite interpolation) from the coarse to fine grid, and at ghost points. The resulting scheme is high order accurate, robust and efficient, due to the mesh adaptivity and high order in both space and time.

We have experimented with both a third and fifth order AMR-finite difference WENO-RK scheme. The accuracy of the scheme is demonstrated by smooth test problems, and the quality and efficiency are demonstrated by several 1D and 2D nonlinear hyperbolic equations with different challenging initial conditions. The AMR solution matches well with, and sometimes even performs better than, the corresponding uniform grid solution. We conclude a significant improvement of the fifth order AMR-WENO over the third order one, not only in accuracy for smooth problems, but also in its ability in resolving complicated solution structures, which we think is due to the very low numerical diffusion of high order schemes. In our work, we found that it is difficult to design a robust AMR-WENO scheme that is both conservative and high order (higher than second order), due to the mass inconsistency of coarse and fine grids for a finite difference scheme. Resolving these issues constitutes our future research.

Link of the Week: Obama Urges Federal Workers to Commute Less

President Obama wants federal workers to take a bike, bus or subway to work more often, according to the Washington Post. The Federal government is the single largest energy consumer in the US economy. Obama signed orders last Tuesday requiring the government to cut its carbon dioxide and other greenhouse gas emissions from indirect sources, including employee commutes and travel, by 13 percent in 2020.

Federal workers should have an easier time changing their commutes now that Congress has passed legislation that jump starts the government’s telework program. A bill approved by the House on July 14 expands work-at-home options and requires agencies to appoint a telework manager, with the goal of setting up a policy that boosts participation. The Senate passed a similar bill in May.

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.