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InTheLoop | 01.12.2009

The weekly newsletter for Berkeley Lab Computing Sciences

January 12, 2009

ASCR Discovery Features Lin-Wang Wang and LS3DF

The online magazine ASCR Discovery posted a new feature story last week, “Method enables bigger models of minuscule molecular systems” <http://ascr-discovery.science.doe.gov/feature/wang1.shtml>. The story describes how Lin-Wang Wang, Byounghak Lee, Hongzhang Shan, Zhengji Zhao, Juan Meza, Erich Strohmaier and David Bailey developed new algorithms and the Gordon Bell Prize-winning LS3DF code to simulate the electronic structure of complex nanomaterials such as semiconductors.

Computing Research Initiatives for the 21st Century

The pivotal role of information technology in the United States’ continued leadership in an increasingly competitive world is well documented. Advances in information technology have led to significant improvements in product design, development and distribution for American industry; provided instant communications for people worldwide; and enabled researchers to collaborate across the globe, simulate experiments, visualize large and complex datasets, and collect and manage massive amounts of data.

What does the new government need to know about the value of computing research? What are some of the most promising and exciting research opportunities in the field? What computing capabilities are critical for the nation today and into the future? The Computing Community Consortium has collected a series of short essays on these topics, including one by CRD’s David Patterson on “The Future of Computer Architecture.” You can find them at <http://www.cra.org/ccc/initiatives.php>.

Budget Year 2011 Deadlines Are Approaching

PIs of continuing projects can find detailed instructions for filling out their Field Work Proposals (FWPs) for FY11 at <http://www.lbl.gov/CS/staff/business/BY11main.html> (accessible only on the Lab network). Here are the key due dates:

  • January 16: All budgets for ongoing proposals are finalized. (PIs need to contact their area/function financial analyst in advance of this date.)
  • January 23: All proposals must be submitted to respective departments for review and coordination.
  • February 2: All proposals due to Division Directors Horst Simon (Computing Sciences, CRD, ESnet) and Kathy Yelick (NERSC) for final signature.


Building 50 Seismic Upgrade Construction Begins Tomorrow

Construction for the Building 50 Seismic Phase I Project will commence on Tuesday, January 13, when the contractor will begin installing the perimeter fencing as well as other mobilization activities. The current parking areas around Bldg. 50 will be revised this evening (Monday, January 12), according to the site laydown plan <http://www.lbl.gov/Workplace/siteconstruction/assets/docs/Sph1_laydown.pdf>. This plan shows that the entrance near the Bldg. 50 Auditorium may be interrupted. The fourth floor corridor entrance and the entrance on the south side of the auditorium will remain accessible.

The Project Management Team has established a website with construction information: <http://www.lbl.gov/Workplace/siteconstruction/>. For questions about the project, please contact Jack Heffernan at x5993 or Doug Brunkow at x6252.

Elsevier ComNet Issues Call for Papers for Special Edition

The Elsevier Journal on Computer Networks has issued a call for papers for a special issue on Performance-Sensitive Security for Very Large Scale Collaboration. Performance sensitivity here refers both to traditional computer performance measures as well as the usability of the security solution being proposed — collaboration should be supported, rather than hindered, by the security solutions. The journal is looking for work that contributes towards all three elements of interest: performance, usability, and security for very large scale collaboration. Topics of interest include, but are not limited to:

  • Security for very large datasets (petascale through exascale), where very large scale data sets can be shared without loss of important security properties, such as integrity, confidentiality.
  • Secure remote access to unique instrumentation; e.g., where scientists and the computer-based instrumentation they use are geographically and organizationally dispersed.
  • Security validation techniques that can provide some measure of assurance that a shared infrastructure meets the collaboration’s and the individual organization’s security requirements.
  • New architectures and methods supporting shared intrusion detection/prevention, situational awareness, threat containment and/or response needed to defend geographically and organizationally dispersed shared computational resources, including shared code.
  • User privilege and user trust negotiation within very large federated environments, both for brief access (minutes) and for long term access (years).

Submissions should be between 15 and 20 pages, and provided electronically in Word format using the instructions located at <http://www.editorialmanager.com/comnet/> on or before the deadline, March 18, 2009. All submissions must be in excellent English. Submissions must not substantially duplicate work that any of the authors has published elsewhere or has submitted in parallel to any other venue. The full papers must list all authors and their affiliations; in case of multiple authors, the contact author should be indicated.

Each submission will be acknowledged by an e-mail. If acknowledgment is not received within ten days, please contact one of the co-editors: Deborah Frincke <Deborah.frincke@pnl.gov>, Frank Siebenlist <franks@mcs.anl.gov>, or Mine Altunay <maltunay@fnal.gov>.

Cray User Group Issues Call for Papers

The Cray User Group (CUG) 2009 conference, “Compute the Future,” will bring together people who define and drive the future of high performance and technical computing. CUG 2009 will be held May 4–7 at the Omni Hotel in Atlanta, Georgia. Nick Cardo of NERSC is the Vice-President and Program Chair.

Participants are encouraged to submit papers in the areas of Applications & Programming Environments, User Services, Systems Support, and Legacy Systems. On Wednesday, May 6, during the General Session, CUG will recognize the conference’s Best Paper. The Call for Papers with submission details is posted at <http://www.cug.org/1-conferences/CUG2009/pages/2-CallForPapers/index.php>.

Conference details are available at <http://www.cug.org/1-conferences/CUG2009>. Here are some key dates:

Abstracts Due January 18, 2009
Abstract Acceptance   February 11, 2009
Early Registration Until: March 25, 2009
Registration Until: April 22, 2009
Late Registration After: April 22, 2009
Papers Due May 1, 2009


Sixtieth Birthday Symposium for Steven Louie Set for March 21–22

“Frontiers in Condensed Matter Physics and Nanoscale Materials” is a two-day Scientific Symposium in honor of Steven Louie’s 60th birthday, co-sponsored by the UC Berkeley Physics Department, the Berkeley Lab Molecular Foundry, NERSC, and the Center of Integrated Nanomechanical Systems (COINS). The Symposium will take place March 21–22, 2009 at UC Berkeley and will focus on Steve’s many important contributions to condensed matter physics, electronic structure theory, and nanoscience. The Symposium will consist of two full days of invited talks from some of Steve’s esteemed colleagues, former students, and postdocs; two poster sessions during lunch; and a banquet dinner including a lighthearted after-dinner program at the Bancroft Hotel.

The deadline for registration and abstract submission is February 13. For more information, see <http://nanotheory.lbl.gov/Symposium2009/>.

DOE CIO Covers Fees for SANS Cyber Security Training

The DOE CIO is paying for SANS training this year (the SANS Institute presents a wide variety of cyber security courses at different levels). This includes the entire course fee, but not the travel expenses. If you are interested, updated information is now available on the Lab’s Computer Protection Program website <https://www.lbl.gov/ITSD/Security/Training/sans.html> (requires authentication). More information about the courses is available at <www.sans.org>.

Dates that may be of interest include April 2009 SANS at the RSA Conference in San Francisco and May 2009 SANS in San Diego. New dates appear throughout the year, so if you don’t immediately see a date you like, check back.

Summer 2009 Paid Internships for Underrepresented Students

The CRA-W/CDC Distributed Research Experiences for Undergraduates (DREU) Program is a highly selective program that matches promising undergraduates with a faculty mentor for a summer research experience at the faculty member’s home institution. The objective of the DREU is to increase the number of women and students from underrepresented groups entering graduate studies in the fields of computer science and engineering. The DREU experience is invaluable for students who are considering graduate school, providing them with a close-up view of what graduate school is really like and also increasing their competitiveness as an applicant for graduate admissions and fellowships.

Funding for the student consists of $6000 for the summer (10 weeks), plus relocation travel assistance when appropriate. Additional funds may be available to support student conference travel, either during the summer or afterward, and for outreach activities promoting the DREU.

An on-line application for students and faculty mentors, more information about DREU, and web pages authored by previous participants are available at <http://parasol.tamu.edu/dreu/>. The application deadline is February 15, 2009, and awards will be announced in mid-March.

NERSC Brown Bag Seminar on Optimizing Compilers

Programming Distributed Memory Computers with Sequential Programming Abstractions: High Level Optimizing Compilers
Richard Lethin, Reservoir Labs, Inc. and Yale University
Wednesday, Jan. 14, noon–1:30 pm, OSF 238 (video to 50B-2222)

New representations of linear algebra kernels in a high level optimizer expand the scope of programs that can be optimized and the range of hardware targets for such optimizations. Programs that conform to an extended static control form are expressed to the compiler in sequential C. A polyhedral abstraction exposes parallelism to a greater degree than available using previous high-level compiler abstractions, and allows ILP formulations of optimizations that balance parallelism with locality of reference. The resulting form can be rendered to emerging architectures with accelerators, explicitly managed communication and local memories, as well as to classic SMP abstractions/OpenMP. The R-Stream compiler provides an implementation of these optimizations linked to a powerful C-language infrastructure to allow using this tool with a conventional programming language without special extensions. This seminar will discuss the polyhedral abstractions, the implementation, current results, challenges, limitations and opportunities enabled by this new compiler technology.

Link of the Week: Mathematician Is the Best Job

According to the Wall Street Journal <http://online.wsj.com/article/SB123119236117055127.html>, mathematician has landed at the top spot on a new study ranking the best and worst jobs in the U.S. The study evaluates 200 professions to determine the best and worst according to five criteria inherent to every job: environment, income, employment outlook, physical demands, and stress.

According to the study, mathematicians fared best in part because they typically work in favorable conditions — indoors and in places free of toxic fumes or noise — unlike those toward the bottom of the list like sewage-plant operator, painter, and bricklayer. They also aren’t expected to do any heavy lifting, crawling or crouching — attributes associated with occupations such as firefighter, auto mechanic, and plumber. The study also considers pay, which was determined by measuring each job’s median income and growth potential.

Other rankings of interest:

 4. Biologist
 5. Software Engineer
 6. Computer Systems Analyst
13. Physicist
18. Computer Programmer
23. Web Developer
57. Chemist
60. Technical Writer
95. Computer Service Technician

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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 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.