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InTheLoop | 01.25.2010

January 25, 2010

ESnet Staff to Share Expertise at Joint Techs Meeting

ESnet projects and expertise will play a central role at the Winter 2010 Joint Techs meeting being held January 31 to February 4 in Salt Lake City. The meeting, an international conference of network engineers, is being hosted by the University of Utah.

Established in 1998, the conference is co-sponsored by the ESnet Site Coordinating Committee (ESCC) and Internet2 and brings together networking expert to share their know-how, present innovative strategies and work toward common solutions to some of the biggest challenges facing research and education networks. Contributions by staff from ESnet and the Advanced Computing for Science (ACS) Department include:

  • Joe Metzger of ESnet will give an update on perfSONAR, a network performance monitoring and diagnostic system co-developed by ESnet.
  • Keith Jackson of ACS will give a talk on Cloud Computing for Science.
  • ESnet’s Brian Tierney will give an overview of the new DOE ARRA-funded 100G Testbed.
  • Kevin Oberman of ESnet will join a panel discussion of national lab experiences in rolling out DNSsec (Domain Name System Security Extensions).
  • ESnet head Steve Cotter will give an update on ESnet.
  • Michael O’Connor of ESnet will discuss the network’s deployment of IPv6 SNMP (Simple Network Management Protocol) management as a production application.
  • ESnet’s Jon Dugan will describe how ESnet has new developed tools and modified some other tools to aid in the monitoring of ESnet 4 and in visualizing network events.
  • Additionally, Paul Grun of the OpenFabrics Alliance will discuss “Storage at Future ESnet Wire Speeds.”

Reaching for the Stars to Create Cosmic Music

Keith Jackson of CRD’s Advanced Computing for Science Department teamed up with Nobel Prize-winning astrophysicist George Smoot of Lawrence Berkeley National Laboratory and Grateful Dead percussionist and Grammy award-winning artist Mickey Hart to “sonify” the universe by translating supernovae light waves into sound.

Hart presented his composition using supernova and other astrophysics data during the Cosmology at the Beach Conference held January 15–20 in Playa del Carmen, Mexico. The conference was cosponsored by the Berkeley Center for Cosmological Physics (BCCP), established by Smoot after he received the Nobel Prize for Physics in 2006. Read more.

John Bell Named Co-Organizer of AMS Von Neumann Symposium

John Bell, head of CRD’s Center for Computational Sciences and Engineering, and longtime collaborator Alejandro Garcia of San Jose State University have been selected as organizers of the 2011 von Neumann Symposium on “Multimodel and Multialgorithm Approaches to Multiscale Problems.” The symposium is sponsored by the American Mathematical Society and held every four years. The symposium will bring groups together in four key areas (fluids, solids, earth sciences, and molecular dynamics) and will enable applied mathematicians and scientists to discuss current practices and future research directions in the development of hybrid methodologies for multiscale phenomena. The AMS von Neumann Symposia are made possible by the generous support of a fund established by Dr. and Mrs. Carrol V. Newsom in honor of the memory of John von Neumann.

ALS/CRD Collaboration Meeting Begins Earlier This Wednesday

The agenda for the Advanced Light Source/Computational Research Division Scientific Computing Opportunities Meeting has expanded, so the event will begin a half hour earlier than previously announced, running from 8:30 am to 3:30 pm Wednesday, January 27, in Perseverance Hall.

During the morning session, ALS researchers will present the mathematical and computational problems they need to solve. In the afternoon, “speed dating” sessions will provide opportunities for CRD and ALS researchers to have one-on-one conversations to explore opportunities for collaboration, followed by group discussions and determination of next steps.

If you are interested in attending, please add yourself to the mailing list als-crd-computing@lists.lbl.gov by subscribing here. The meeting is being organized by Deb Agarwal of CRD and Simon Clark of ALS.

New Version of PEtot Code Is Available

A new version of PEtot, an open-source code developed by Lin-Wang Wang of Berkeley Lab’s Computational Research Division, is available. PEtot, which stands for Parallel total Energy (Etot), is a parallel plane wave pseudopotential program for atomistic total energy calculations based on density functional theory. It is designed for large system simulations to be run on large parallel computers.

PEtot Version3 has more features and is faster, especially for large systems. It has three levels of parallelization: on planewave G-vector, band index, and k-points. It can be scaled to thousands of processors. All three versions of the code are available at https://hpcrd.lbl.gov/~linwang/PEtot/PEtot.html.

Introduction to i4Energy Center on Friday

In the last three decades, information technology has radically changed and created disruptive efficiencies in a wide variety of industries that include international banking, manufacturing, travel, and consumer purchasing. The i4Energy Center will now bring such information technology and smart sensing methods to a broad landscape of energy generation, transmission, distribution, and end-use in, among other places, “smart” buildings and homes.

The i4Energy Center is a collaboration among CITRIS (U.C. Berkeley, Davis, Merced, and Santa Cruz); the California Institute for Energy and Environment (CIEE); and the Lawrence Berkeley National Laboratory (LBNL). The mission of the Center is to facilitate and promote research on system-integrated enabling technologies that will achieve better energy efficiency, improved demand / response, and dramatic improvements in energy distribution.

A public Introduction to i4Energy will begin at noon on Friday, January 29, in the Banatao Auditorium, third floor, Sutardja Dai Hall at UC Berkeley, with a formal presentation about the activities and structure of the new i4Energy Center.

Distinguished CEC visitors, Commissioner Arthur Rosenfeld and Mike Gravely, Manager of Energy Systems Research Office in the PIER Program, will open the meeting with observations about the work of the new Center, followed by a panel of distinguished leaders from CIEE, CITRIS, LBNL, and UC. At 1:00 p.m. they will formally dedicate the new i4Energy space on the fourth floor of Sutardja Dai Hall, followed by a reception and poster session.

As always, these talks are free, open to the public and broadcast live online at mms://media.citris.berkeley.edu/webcast, and questions can be sent via Yahoo IM to username: citrisevents.

GlobusWORLD 2010 Will Be Held March 2–4 at Argonne

Registration and a preliminary program are now available for GlobusWORLD 2010, which will be held March 2-4 at Argonne National Laboratory (near Chicago, Illinois). This year’s GlobusWORLD conference will focus on Globus success stories, including discussions with Globus users about their experiences, technical presentations, and tutorials on using new (and old) Globus software. Registration is now available at www.globusworld.org.

Plasma Theory Symposium Will Be Held March 5-6 in Pleasanton

A Symposium on Plasma Theory will be held on March 5-6, 2010, at the Sheraton Hotel in Pleasanton, CA. This Symposium will have invited talks on diverse topics in laboratory fusion plasmas (both magnetic fusion and inertial confinement), high energy density physics, and plasma astrophysics. Go here for more information.

2010 TeraGrid Conference Issues Call for Papers

Participants can now submit papers and abstracts for the Science, Technology, Gateways, and Education tracks, and abstracts only for all other parts of the TeraGrid’10 conference, to be held August 2-5, 2010 in Pittsburgh, Pennsylvania. Details of the submissions process can be found here. The deadline for all submissions is May 10, 2010.

Grace Hopper Conference Opens Call for Participation

The 10th 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 September 29 to October 2, 2010 at the Hyatt Regency in Atlanta, Georgia. This year’s theme, “Collaborating Across Boundaries,” recognizes the significant role women play in using technology to work together across various borders including gender, scientific, social, geographical, racial or political.

The submission deadline is March 16, 2010. For more information, go here.

Safety Tip: Duck, Cover and Hold in an Earthquake

In the event of an earthquake, the best way to protect yourself is to Duck, Cover and Hold:

  • DUCK or drop down to the floor.
  • Take COVER under a sturdy desk, table or other furniture. If that is not possible, seek cover against an interior wall and protect your head and neck with your arms.
  • If you take cover under a sturdy piece of furniture, HOLD on to it and be prepared to move with it. Hold the position until the ground stops shaking and it is safe to move. When the shaking stops, gather your personal belongings and evacuate.

In computer rooms where desks or tables may not be available, the recommendation is to duck and cover next to a solid wall (no windows). If shaking makes it impossible to get to a sturdy desk or solid wall, the Lab’s seismic safety subject matter expert recommends that you duck and cover in place, with your back to any windows. Protect your head and neck with your arms.

Real-time earthquake information is available on this USGS webpage. For more seismic safety information, see the USGS handbook developed for the Bay Area, Putting Down Roots in Earthquake Country.

This Week’s Computing Sciences Seminars

Numerical Methods for the Chemical Master Equation
Tuesday, January 26, 11:00 am-12:00 pm, 50B-2222
Jingwei Zhang, Virginia Polytechnic Institute and State University

The chemical master equation, formulated on the Markov assumption of underlying chemical kinetics, offers an accurate stochastic description of general chemical reaction systems on the mesoscopic scale. The chemical master equation is especially useful when formulating mathematical models of gene regulatory networks and protein-protein interaction networks, where the numbers of molecules of most species are around tens or hundreds. However, solving the master equation directly suffers from the so called “curse of dimensionality” issue. In this presentation, I will try to give a survey on various numerical algorithms that have been developed to solve the master equation. The focus will be given to the adaptive aggregation method and the radial basis function collocation method that I have proposed. Numerical results are also presented to illustrate the promises and potential problems of these new algorithms.

LAPACK Seminar: Communication-Avoiding Krylov Subspace Methods
Wednesday, January 27, 11:10 am-12 pm, 380 Soda Hall, UC Berkeley
Mark Hoemmen, UC Berkeley

Krylov subspace methods (KSMs) are numerical algorithms for solving large, sparse linear systems of equations and eigenvalue problems. Although they are commonly used and often highly optimized, most KSMs achieve only a small fraction of peak arithmetic performance of the computers on which they are run. This occurs on almost all computers, from workstations to massively parallel supercomputers. The cause is that the performance of most commonly used KSMs is bound by the speed of communication — moving data between processors or between levels of the memory hierarchy — rather than by the speed of arithmetic. Communication is much slower than arithmetic, and is only getting slower relative to arithmetic as hardware evolves.

In my thesis, I propose new communication-avoiding Krylov methods. These require much less data movement between levels of the memory hierarchy, and between processors in parallel, than standard KSMs. Our single-node shared-memory parallel implementation of a communication-avoiding version of GMRES also achieves significant speedups over a parallel version of standard GMRES running on the same number of processors.

In this talk, I will give an overview of these new Krylov methods, which replace the standard versions of Arnoldi iteration, GMRES, symmetric Lanczos, and CG, both with and without preconditioning. I will explain how one makes them numerically stable in practice. Also, I will talk about the computational kernels which make these new KSMs communication-avoiding, and show that they must be tuned simultaneously (“co-tuned”) for best performance.

Bifurcation Properties of a Delay Differential Equation with Two State-Dependent Delays
Thursday, January 28, 10:00–11:00 am, 50F-1647
Orianna DeMassi, McGill University, Montreal

Differential delay equations (DDEs) denote a class of equations which allow the derivative to depend on past states of the system. DDEs generalize ODEs and thus are powerful for modeling physical situations. However, interactions with the delay allow DDEs to have much richer dynamics than ODEs and much more delicate numerical solutions. Interesting behavior develops when the delay is allowed to depend on the current state of the system; we investigate a test equation which has two terms with linearly state dependent delays. Numerical solutions and bifurcation properties are presented. Results include establishing the existence of many bifurcation points and the complexity of dynamics within the system. Further bifurcations are found in the branches of periodic solutions that lead to regions which contain invariant tori. Some aspects of branch shape and interaction are explained and others presented as interesting but unresolved issues.

Energy Efficiency and Renewables: Market and Behavioral Failures
EETD Distinguished Lecture Series
Thursday, January 28, 12:00 pm, Building 50 Auditorium
Jim Sweeney, Director of the Precourt Institute for Energy Efficiency, Stanford University

Policies to promote renewable energy and energy efficiency have been gaining momentum throughout the world, often justified by environmental and energy security concerns. Sweeney will discuss energy efficiency options and delve into the economic motivation for energy efficiency and renewable energy policies by articulating the classes of relevant behavioral failures and market failures. Such behavioral and market failures may vary intertemporally or atemporally; the temporal structure and the extent of the failures are the critical considerations in the development of energy policies. The talk will discuss key policy instruments and assess the extent to which they are well suited to correct for failures with different structures.

Models, Algorithms, and Software: Tradeoffs in the Design of High-Performance Computational Simulations in Science and Engineering
Thursday, January 28, 4:00-5:30 pm, 306 Soda Hall, UC Berkeley
Phil Colella, Berkeley Lab

Phillip Colella is Senior Staff Scientist and Group Leader for the Applied Numerical Algorithms Group in the Computing Sciences Directorate at LBNL, working on high-resolution and adaptive methods for partial differential equations. He has also applied numerical methods in a variety of scientific and engineering fields, including shock dynamics, low-Mach number and incompressible flows, combustion, porous media flows, and astrophysical flows.

Link of the Week: National Lab Day

A coalition of educators, science and engineering associations, philanthropies and other organizations have launched National Lab Day, a new grassroots initiative designed to reinvigorate science and math education in the nation’s schools and after-school programs and lead to increased U.S. competitiveness.

National Lab Day aims to inspire a wave of future innovators and foster U.S. competitiveness by improving the quality STEM (science, technology, engineering, and math) education in America. A collaboration between government and more than 200 public- and private-sector organizations, National Lab Day will connect students in grades 6-12 to hands-on learning experiences and promote tinkering in laboratory settings.

National Lab Day will promote hands-on learning throughout the year and culminate each year with special events the first week of May. Volunteer science and technology professionals and educators will work together with students to improve America’s science labs and offer inquiry-based STEM experiences in classrooms, learning labs, and after-school programs.

The website http://www.nationallabday.org/ invites volunteer science and technology professionals as well as educators and others to sign up to participate. The website will automatically match volunteers to requests from educators to participate on the basis of geography and interests. The website also provides resources and ideas for hands-on learning experiments and invites the public to suggest new materials.

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 7,000-plus 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 Department of Energy 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.