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InTheLoop | 01.22.2008

The weekly newsletter for Berkeley Lab Computing Sciences

January 22, 2008

“Berkeley View” Report Makes HPCwire’s Top Stories of 2007 List


Under the title “Manycore Angst,” the December 21, 2007 issue of HPCwire listed the “Berkeley View” report as one of the year’s top stories. Published by UC Berkeley’s Electrical Engineering and Computer Sciences department, the paper was co-authored by NERSC’s Kathy Yelick and John Shalf and CRD’s David Patterson and former staff member Parry Husbands.

Here’s what HPCwire had to say about the report:
“Published a year ago this week, ‘The Landscape of Parallel Computing Research: The View from Berkeley’ became a wake-up call to the computing community about the perils and pitfalls of our manycore destiny. Was anyone listening? Maybe. In the past year, both Intel and Microsoft spent a gazillion dollars for parallel computing R&D and education. Universities like Purdue, LSU, the University of Manchester, MIT and many others are expanding their HPC curriculums for the next crop of students. By the time these kids start to graduate in 2010, the manycore chips will be spilling out of the fabs.”


FY 2008 LDRD Awards Announced, FY 2009 Call for Proposals Issued


The FY 2008 Laboratory Directed Research and Development (LDRD) awards were announced in December. Lead PIs from Computing Sciences and the titles of their funded projects included:

  • Agarwal: On-Demand Overlays for Scientific Applications
  • Bell: Structured, Adaptive Mesh Refinement Method for Multiphase Reactive Transport in Groundwater
  • Bell, Pau: Low Order Models and Numerical Methods for Computational Chemistry
  • Markowitz et al.: Integrated Microbial Community Genomes Data Management System
  • Rotem, Otoo: Energy-Smart Disk-Based Mass Storage System
  • Shalf et al.: Holistic Approach to Energy Efficient Computing Architecture
  • Skinner: Integrated Performance Monitoring of Grid and HPC Workloads
  • Wilkening: Extended First Order System Least Squares Finite Elements

Berkeley Lab Director Steve Chu has issued the call for proposals for the FY 2009 LDRD Program. The complete call, schedule, guidance, and forms are available on the Web. The overall FY 2009 process is similar to last year’s, with proposals submitted to division offices by March 14. If you have questions or need assistance, please contact Todd Hansen in the Office for Planning and Development (x6105, tchansen@lbl.gov).


NERSC to Host Cray Technical Workshop Feb. 26–27 in San Francisco


Registration is now open for the Cray Technical Workshop North America to be held Feb. 26–27, 2008 at the Hotel Nikko in San Francisco. The workshop will feature presentations from users and Cray experts on the latest scientific advancements using Cray supercomputers, as well as advice on how to achieve the optimum performance on Cray systems. Featured speakers include NERSC’s Bill Kramer, Zhengji Zhao, and Katie Anytpas, CRD’s Terry Ligocki and Julian Borrill, as well as NERSC users Zhihong Lin (UC Irvine) and Nick Wright (SDSC). There will be additional user talks on performance and various vendor presentations on state-of-the-art subjects, especially related to quad-core usage and performance.


Seaborg Demolition Proceeds Quickly


Only a week after Seaborg was shut down, all the computer racks have been removed and the computer room floor is passable. Underneath the floor, cable recovery and demolition of the seismic bracing for the frames are under way. Bill Iles has been coordinating the work with the help of Wallace Haynes, the LBNL rigger, moving, and sheet metal teams, and contractors from Doubleday and Trane.


SciDAC Outreach Center Is Soliciting Tutorials for SciDAC08


A day of tutorials will be held in conjunction with this year’s SciDAC08 annual meeting in Seattle. The main meeting is July 13–17 at the Fairmont Olympic Hotel, and the tutorial day will be held in Redmond on Friday the 18th. Transportation will be provided from the Fairmont to the tutorials. Microsoft Research and the SciDAC Outreach Center are sponsoring this year’s tutorials. The audience for the tutorials is expected to include students from the surrounding universities, DOE Computational Science Graduate Fellowship students, and interested parties from industry. Last year there were just under a hundred students participating.

The SciDAC Outreach Center is soliciting ideas for tutorials from the SciDAC PIs. Anyone who would like to give a tutorial is asked to send the proposed topic to David Skinner (DESkinner@lbl.gov), along with any AV or computing requirements your tutorial might require. Projectors, wireless network, etc. will be provided. As they did last year, the SciDAC Outreach Center can provide temporary training accounts and batch queues for tutorials that would benefit from hands-on access to XT4, POWER5, and other HPC architectures.


Security Advisory for Excel Warns of Suspicious Email Attachments


Brent Draney of NERSC’s security team sent this notice to NERSC staff, and we’re passing it on for CRD and CS staff as well:

“Please be aware that a Microsoft advisory for Excel has recently been released. Be extra cautious opening Excel files that you receive in email. If you receive an Excel attachment named okN.xls or something similar, report it to security@nersc.gov [or CPPM@lbl.gov] immediately.”


International Sherwood Fusion Theory Conference Is Accepting Abstracts


The 2008 International Sherwood Fusion Theory Conference will be held in Boulder, CO, from March 31 through April 2, 2008. The abstract submission deadline is February 1, and the registration deadline is February 29.


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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.