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InTheLoop | 06.02.2008

The weekly newsletter for Berkeley Lab Computing Sciences

June 2, 2008

Orbach Receives Seaborg Memento, Green Flash Briefing

As part of his visit to Berkeley Lab on Friday, May 30, DOE Under Secretary of Science Ray Orbach met with representatives of Computing Sciences. ALD Horst Simon and NERSC Director Kathy Yelick opened the meeting by presenting Orbach with a framed memento from the decommissioned IBM supercomputer Seaborg and thanking him for his support of computational science. The Under Secretary quickly showed his knowledge of computing technology and asked if that was the Power 3 machine, and this led to further discussions. At one point, Simon also pointed out that it was in the same room during a visit to LBNL in spring of 2002 that Orbach first learned about Japan’s Earth Simulator, an event Orbach called one of the most important meetings of his tenure as Director of the Office of Science.

The session also included a presentation by John Shalf on “Green Flash,” the LBNL project to design a specialized supercomputer for solving leading-edge scientific problems, using the same design techniques that result in the highly efficient processors of battery-powered consumer electronic devices such as cell phones. The project was announced in a May 5 press release describing Berkeley Lab’s partnership with Tensilica to create a prototype energy-efficient climate computer "Berkeley Lab Reseachers Proposed New Breed of SuperComputers for Improving Global Climate Predictions", and in a paper published in the May issue of the International Journal of High Performance Computing Applications Table of Contents. The paper by Michael Wehner, Lenny Oliker and John Shalf proposes an innovative architecture for modeling climate change with 1-kilometer resolution.

Berkeley Lab Staff Are Playing Key Roles in MAPD Conference

Scientists and mathematicians from CRD and two other LBNL divisions are playing key roles in this week’s Mathematics for Analysis of Petascale Data (MAPD) conference, sponsored by the DOE Office of Advanced Scientific Computing Research from June 3–5 in Rockville, MD. The goal of this workshop is to engage mathematical scientists and applications researchers to define a research agenda for developing the next-generation mathematical techniques needed to meet the challenges posed by petascale data sets.

Dan Rokhsar of the Genomics Division will speak on “Genomes, Genetics, and Diversity.” Bill Collins of the Earth Sciences Division will speak on “Extreme Climate Change, Scaling Laws, and Scale Invariance.” And Michael Wehner of CRD will speak on “Challenges in the Analysis of Petascale Climate Model Output Datasets.”

CRD’s Peter Nugent and Julian Borrill will be moderator and scribe for the breakout session on astrophysics. Deb Agarwal will moderate a breakout session on earth system modeling. Juan Meza will moderate a session on optimization and be scribe for the breakout session on fusion physics; he is also on the organizing committee for the conference.

Registration Is Still Open for SciDAC 2008 Conference and Tutorials

The SciDAC 2008 conference, July 13–17 in Seattle, is filling up. If you’re planning to attend but haven’t registered yet, now would be a good time to do so. Registration is up to 274, and there is a limit of 300 participants. Hotel rooms at the conference rate of $190+ are selling out fast and may be gone before the official room block release date of June 20. To register, go to http://hpcrd.lbl.gov/SciDAC08/files/registration.html.

Also, please note that the SciDAC Conference (July 13–17) and the SciDAC Tutorials (July 18) are separately organized. If, in addition to the main conference, you plan on attending the SciDAC Tutorials held at the Microsoft Complex in Redmond, please be sure to register yourself separately at https://outreach.scidac.gov/scidac08/tutorials/index.php?registration=Y. This is very important to ensure that the organizers have an accurate head count for transportation, food and seating. Questions regarding the tutorials should be directed to help@outreach.scidac.gov.

This Week’s Seminar Schedule

Early Experiences in “T2K Open Super Computer (Todai Combined Cluster)” with AMD Quad-Core Opteron Processors

Friday, June 6, 1:00–2:00 p.m., 50A-5132
Kengo Nakajima, Supercomputing Division, Information Technology Center, University of Tokyo, Japan

The T2K Open Supercomputer Alliance (http://www.open-supercomputer.org/) was established primarily aiming at collaborative work on the specification design for new supercomputers procured by the following three member universities:
•    Center for Computational Sciences, University of Tsukuba
•    Information Technology Center, University of Tokyo
•    Academic Center for Computing and Media Studies, Kyoto University

This activity is for creative procurements at the initiative of universities based on technology market research, rather than those by choosing machines from product market and at the initiative of system venders. This creative and university-initiative approach results in open specifications, with respect to the architecture, software stack and usage of the new supercomputers, to give an efficient HPC solution with the most advanced technologies to a wide spectrum of users in Japanese academe.

In the end of 2007, all of three universities decided to introduce AMD Quad-Core Opteron (Barcelona) based clusters, and three systems start operation for practical use in June 2008.

“T2K Open Super Computer (Todai Combined Cluster)” at the University of Tokyo by Hitachi Ltd. consists of 952 nodes, where each node has four sockets of Quad-Core Opteron (i.e., 4 x 4 = 16 cores/node). Total peak performance is approximately 140 Tflops, total memory size is 32 TB, and total storage is 1 PB.

In this presentation, a brief overview of the system and preliminary results of GeoFEM benchmarks will be presented.


Link of the Week: Nathan Myhrvold’s Breakthrough Factory

In the May 12 New Yorker, Malcolm Gladwell discusses Nathan Myhrvold’s company Intellectual Ventures, which aims to create large numbers of new ideas, patent them, and license the patents. (Myhrvold was the founder of Microsoft Research.) “The original expectation was that I.V. would file a hundred patents a year,” Gladwell writes. “Currently, it’s filing five hundred a year. It has a backlog of three thousand ideas.” How do they do it? Bring together a large group of smart people with very different backgrounds and viewpoints, and let them brainstorm.

The article also discusses multiple independent scientific discovery, an event so common it is summarized by Stigler’s Law: “No scientific discovery is named after its original discoverer.” Stigler’s Law was, of course, not discovered by the statistician Stephen Stigler, but by the sociologist Robert K. Merton, who concluded that “our romantic notion of the genius must be wrong. A scientific genius is not a person who does what no one else can do; he or she is someone who does what it takes many others to do. The genius is not a unique source of insight; he is merely an efficient source of insight.”

You can read the article at http://www.newyorker.com/reporting/2008/05/12/080512fa_fact_gladwell?currentPage=all.

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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.