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InTheLoop | 06.16.2008

The weekly newsletter for Berkeley Lab Computing Sciences

June 16, 2008

All-Hands Safety Meetings Scheduled for NERSC and CRD


A mandatory safety meeting has been scheduled to provide a refresher on safety issues relevant to Computing Sciences and to discuss Berkeley Lab’s new Job Hazards Analysis (JHA). All NERSC and CRD staff should plan to attend one of the following two meetings:

  • Wednesday, June 18, 1:30–2:30 p.m. at OSF (with videoconference to 50B-2222)
  • Thursday, June 26, 2:30–3:30 p.m. in the 50B Auditorium.

Juan Meza to Receive 2008 SACNAS Distinguished Scientist Award


Juan Meza, head of CRD’s High Performance Computing Research Department, has been named recipient of the 2008 SACNAS Distinguished Scientist Award. The award will be presented during the 2008 SACNAS National Conference in Salt Lake City, Utah, on Thursday, October 9.

On hearing the news, ALD Horst Simon wrote, “Juan, Congratulations (again)! That’s a wonderful recognition at the national level for both your scientific accomplishments and your mentoring and outreach efforts.”

The mission of SACNAS (Society for Advancement of Chicanos and Native Americans in Science) is to encourage Chicano/Latino and Native American students to pursue graduate education and obtain the advanced degrees necessary for science research, leadership, and teaching careers at all levels. The organization is celebrating its 35th anniversary this year. For more information, go to SACNAS.


Simon, Strohmaier, Shalf, and Collins Will Speak at ISC’08 in Dresden


Four Berkeley Lab scientists will be panelists and presenters this week (June 18–20) at the International Supercomputing Conference (ISC’08), in Dresden, Germany:

  • Erich Strohmaier from CRD will present “Highlights of the 31st TOP500 List.”
  • Bill Collins of the Earth Sciences Division will present “Computational Challenges for Dynamic Earth System Models.”
  • Strohmaier and Associate Lab Director Horst Simon will participate in a panel discussion on “RoadRunner — The First Petaflop/s System in the World and Its Impact on Supercomputing.”
  • Strohmaier will co-chair “On the Hot Seat: Grilling the Leading HPC Vendors with Tough Questions, Part 2.”
  • Simon will chair a panel discussion on the topic “Is HPC Going Green?” John Shalf from NERSC will be one of the panelists.

Abstracts of the sessions can be found at http://www.supercomp.de/isc08/content/index_eng.html.

You can read a preview article for the panel discussion “Is HPC Going Green?” which Simon wrote for the May/June issue of Scientific Computing magazine at "Green HPC Podcast Episode 1: Sifting Through The Hype".


Berkeley Lab Scientists Contributing to SciDAC 2008 Conference and Tutorials


The SciDAC 2008 conference agenda has been posted to the web at http://hpcrd.lbl.gov/SciDAC08/files/agenda.html. The conference will be held July 13–17 in Seattle. DOE SciDAC Director Michael Strayer will give an update on the program at the opening session.

Presentations by Berkeley Lab scientists will include:

  • Embedded Boundary Algorithms and Software for Partial Differential Equations, Brian Van Straalen, CRD
  • Computational Studies and Optimization of Wakefield Accelerators, Cameron Geddes, Accelerator and Fusion Research Division (AFRD)
  • Sunfall: A Collaborative Visual Analytics System for Astrophysics, Cecilia Aragon, CRD
  • Moving Applications to Extreme Parallelism, Session Chair: Kathy Yelick, NERSC
  • Large-Scale Linear Scaling Electronic Structure Calculations for Nanosystems, Lin-Wang Wang, CRD

A number of LBNL scientists will present posters:

  • SciDAC Advances in Beam Dynamics Simulation: From Light Sources to Colliders, Ji Qiang, AFRD
  • New Eigensolvers and Preconditioners for Large-Scale Nanoscience Simulations, Andrew Canning, CRD
  • Evaluation of SuperLU on Leading Multicore Architectures, Sherry Li, CRD
  • Embedded Boundary Grid Generation Using the Divergence Theorem, Implicit Functions, and Constructive Solid Geometry, Terry Ligocki, CRD
  • Optimizing SN Ia Follow-up in Future Dark Energy Surveys, Peter Nugent, CRD
  • Interaction of Turbulence and Chemistry in a Low-Swirl Burner, John Bell, CRD

The tutorial sessions, organized by NERSC’s David Skinner, who is also head of the SciDAC Outreach Center, will be held July 18 in Redmond, Washington. Three Computing Sciences staff will be leading tutorial sessions:

  • Accelerating Data Selection for Online Analysis with FastBit Indexing, John Wu, CRD
  • An Introduction to the Cray XT4 for Application Scientists, Richard Gerber, NERSC
  • Advanced CompuTational Software (ACTS) Collection Tutorial, Tony Drummond, CRD

Submissions Still Open for SciDAC 2008 Visualization Night


Anyone involved in DOE Office of Science research, such as SciDAC, INCITE, and core-funded projects, is encouraged to submit an image or animation to be shown at the electronic visualization and poster night (Monday, July 14) at the SciDAC 2008 conference. As a benefit to both your project and the program offices, all submissions will be provided to the program offices for future publicity. The submission deadline is July 3. For submission guidelines, see SciDAC Visualization Night.


Register Now for Workshop on Algorithms for Modern Massive Data Sets


The 2008 Workshop on Algorithms for Modern Massive Data Sets (MMDS 2008) will be held June 25–28 at Stanford University, and will address algorithmic, mathematical, and statistical challenges in modern statistical data analysis. The goals of MMDS 2008 are to explore novel techniques for modeling and analyzing massive, high-dimensional, and nonlinearly structured scientific and internet data sets, and to bring together computer scientists, statisticians, mathematicians, and data analysis practitioners to promote cross-fertilization of ideas. Jim Demmel of CRD and UC Berkeley will be one of the speakers.

The registration deadline is this Wednesday, June 18. For further information and to register online, please see the conference web page, MMDS.


Latest Issue of NERSC News Is Now Online


The Summer 2008 issue of NERSC News can be read at NERSC News. Feature stories in this issue include 6,500 user publications in five years, the creation of a benchmark data set for modeling combustion physics, and how NERSC is helping STAR researchers find elusive phenomena in mountains of experimental data.


Memorial Web Email Address for George Michael


As reported last week, the HPC community is mourning the passing of George Michael, chair of the first-ever SC conference 20 years ago. A memorial has been set up on the SC08 home page at SC08 for those wishing to send electronic messages to George’s family. Clicking on that link brings up a mail form addressed to in.memoriam.gm@info.supercomputing.org, where memories can be shared and messages can be sent to George’s family.


This Week’s Seminar Schedule

Fast Deterministic Sparse Fourier Transform Methods

Friday, June 20, 11:00 a.m.–noon, 50B-6208
Mark Iwen, University of Michigan, Dept. of Mathematics
http://www-personal.umich.edu/~markiwen/

I will discuss a recently proposed deterministic sublinear-time sparse Fourier transform algorithm (hereafter called DSFT). DSFT is directly related to a newly emerging signal processing paradigm, called “compressed sensing,” which attempts to exploit signal sparsity under a well chosen (potentially adaptive) basis. Here we consider frequency-sparse signals: DSFT can exactly reconstruct the Fourier transform (FT) of an N-bandwidth signal f, consisting of B << N non-zero frequencies, using O(B2 log4(N)) time and O(B2 log3(N)) f-samples. Hence, DSFT’s runtime and sampling requirements are polynomial in the signal’s “information content.” As a consequence, a new computationally efficient sampling theorem for the interpolation of sparse/compressible trigonometric polynomials is established. Applications to numerical methods for multiscale problems will be discussed.


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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.