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InTheLoop | 05.30.2006

The weekly electronic newsletter for Berkeley Lab Computing Sciences employees

May 30, 2006

Berkeley Lab Researchers Analyze Performance, Potential of Cell Processor

Though it was designed as the heart of the upcoming Sony PlayStation3 game console, the STI Cell processor has created quite a stir in the computational science community, where the processor's potential as a building block for high performance computers has been widely discussed and speculated upon.

To evaluate Cell's potential, computer scientists at the U.S. Department of Energy's Lawrence Berkeley National Laboratory evaluated the processor's performance in running several scientific application kernels, then compared this performance against other processor architectures. The results of the group's evaluation were presented in a paper at the ACM International Conference on Computing Frontiers, held May 2-6, 2006, in Ischia, Italy.

The paper, “The Potential of the Cell Processor for Scientific Computing,” was written by Samuel Williams, Leonid Oliker, Parry Husbands, Shoaib Kamil and Katherine Yelick of Berkeley Lab's Future Technologies Group and by John Shalf from NERSC.

“Overall results demonstrate the tremendous potential of the Cell architecture for scientific computations in terms of both raw performance and power efficiency,” the authors wrote in their paper. “We also conclude that Cell's heterogeneous multi-core implementation is inherently better suited to the HPC environment than homogeneous commodity multicore processors.”

The full paper can be read at: http://www.cs.berkeley.edu/~samw/projects/cell/CF06.pdf.

CS Discussion of LDRD Process Set for 2 p.m. Today

Computing Sciences ALD Horst Simon invites anyone who has ever submitted an LDRD proposal, or who is thinking of submitting an LDRD proposal in the future, to a discussion of Computing Sciences' process for reviewing proposals.

“I believe that there are many misunderstandings about what are LDRDs and how the proposal process works,” Horst said. “I would like to clear up any misunderstandings and answer any questions that you might have.”

The meeting is scheduled for 2-4 p.m. Tuesday, May 30, in Bldg. 50A-5132.

Ray Orbach Confirmed as Under Secretary for Science

On Friday, the Senate confirmed the appointment of Ray Orbach as DOE's Under Secretary of Science. Orbach, who served as chancellor of UC Riverside for 10 years before being named to head the Office of Science in 2002, will now oversee all of the department's science activities. The under secretary position is a new one that was established under the Energy Policy Act of 2005 to create a higher profile for science at DOE.

Energy Secretary Samuel Bodman welcomed the confirmations. "President Bush has placed a renewed emphasis on strengthening our nation's basic science research and education as part of the American Competitiveness Initiative," Bodman said in a statement. "Ray will help oversee the expansion of basic science research at the department, including the doubling of the government's basic science budget over the next decade."

Lab's Nonsmoking Policy Ignored, Result Is Burning Deck

Last week, an employee discarded a burning cigarette butt on the redwood deck outside the Bldg. 50B basement level near the stairs leading down to the bus stop. The discarded butt ignited several of the boards forming the deck. The fire was quickly extinguished and no significant damage was caused.

“What is most disconcerting about this event is that the location of this fire was not five feet from a ‘no smoking' sign,” said Bldg. 50 Building Manager John Hutchings. “Crushing one's cigarette out on a dry wooden deck is not a safe behavior, and smoking in this area is not permitted.”

The incident prompted Computing Sciences safety staff and senior management to remind employees about the Lab's Nonsmoking policy, which specifically prohibits smoking within 20 feet of doorways, as well as on decks and stairs. Here's the full policy:


1. Policy

It is the Laboratory's objective to create and maintain an environment as close to smoke-free as practicably possible. In addition, the Laboratory is located in an environment that poses severe hazards from wildland fires and is obliged to ensure that outdoor smoking is restricted to safe areas.

This policy applies to all employees, contractors, guests, and visitors. Accordingly, the Laboratory, in keeping with these obligations and in compliance with State law, has determined that smoking is not permitted:

  • In any Laboratory building
  • In any Laboratory vehicle
  • Within 20 feet of entrances and exits, operable windows, and air intakes
  • On decks or stairs
  • In areas with vegetation
  • In any area posted as "No Smoking"

Smoking is permitted only in outdoor areas that are paved with asphalt, brick, or concrete.

All individuals are responsible for ensuring:

  • That their smoke does not enter buildings
  • The safe disposal of their smoking materials

If the preferences of smokers and nonsmokers conflict, the preference of nonsmokers will prevail. Violations of this policy should be reported to a supervisor, who, if necessary, will consult with Labor/Employee Relations before taking action in accordance with appropriate personnel policies or labor agreements.

Job Posting: EH&S and Facilities Systems Group Lead

The recruitment effort to replace John Pon, who is retiring, as the group lead of EH&S and Facilities Systems has started. The position has been posted and here is the position summary:

"Reporting to the Head of IT Institutional Systems, the group lead is accountable to the directors of the Environmental Health & Safety (EH&S) Division and the Facilities Division for the delivery of information systems support for EH&S and Facilities divisions. The group lead leads the development and implementation of the strategic, tactical and operational systems plans to assure operational stability and achievement of operational goals of the customer organizations. Partnering with management and key staff in customer organizations, the group lead manages the migration from legacy systems to new or upgraded systems consistent with IT technology direction. The group lead advises management and key staff in customer organizations in alternative business process strategies related to the implementation of new systems and technology. The incumbent prepares, controls and manages budget within areas of responsibility, consistent with approved funding and customer objectives."

The complete posting can be found at http://www.lbl.gov/CS/Careers/OpenPositions/IT19043.html.

Call for Workshop Papers: Petascale Computational Biology and Bioinformatics

Organizers of a workshop on Petascale Computational Biology and Bioinformatics, to be held as part of Euro-Par 2006, have issued a call for papers and posters. Euro-Par 2006 (http://www.europar2006.de/) will be held Aug. 29-Sept. 1 in Dresden, Germany.

The workshop will address what bioinformatics or computational biology applications can or should accomplish with petascale computing facilities, and what obstacles must be overcome in order to implement and effectively use these facilities to solve important problems in the life sciences (biology, biochemistry, environmental sciences, etc.). The deadline for submissions is Thursday, June 15.

Suggested topics for papers and posters include:

  • What does it take to create a computational biology or bioinformatics application that achieves a sustained petaflop/s of calculations?
  • What sort of computational biology and bioinformatics applications that exist now can be scaled up to perform useful work and provide new insights on various types of petascale platforms?
  • Given a resource capable of a petaflop/s of sustained performance, what sort of new and novel applications could be written?
  • How will petascale computational biology and bioinformatics applications be organized and accessed so as to have the greatest possible impact on the largest possible community of researchers?
  • What are the I/O and data management requirements of computational biology and bioinformatics applications that will take advantage of petabytes of life sciences data?
  • What evolutionary path of applications and problems will aid the process of moving from the current state of bioinformatics and computational biology to effective petascale applications?

Submissions should include an abstract, keywords, the e-mail address of the principal author (contact person), and must not exceed 15 pages, including tables and figures, with PDF or PostScript. However, short papers of around four pages are encouraged for work-in-progress contributions. Questions and submission of papers can be sent to: bioworkshop@europar2006.de.

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.