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InTheLoop | 01.11.2010

January 11, 2010

Molecular Worm Algorithm Navigates inside Chemical Labyrinth

With the passage of a molecule through the labyrinth of a chemical system being so critical to catalysis and other important chemical processes, computer simulations are frequently used to model potential molecule/labyrinth interactions. In the past, such simulations have been expensive and time-consuming to carry out. But now Maciej Haranczyk and James Sethian of CRD’s Mathematics Group have developed a new algorithm that should make future simulations easier and faster to compute, and yield much more accurate results. Read more.


ESnet Gets a Jump on Implementing DNS Security

The Department of Energy (DOE) has finished implementing Domain Name System Security Extensions (DNSSEC) to its high-performance Energy Sciences Network (ESnet) using a commercial appliance to digitally sign Domain Name System records and manage cryptographic keys. The signed records were published last month, in December 2009, ahead of a mandate from the U.S. Office of Management and Budget (OMB) requiring government networks outside of the .gov domain to do so. Read more.


NERSC and CRD Post Job Openings for Postdoc, CSEs

NERSC is searching for a Computational Postdoctoral Fellow who can assist with the DOE Magellan Project, which will research how cloud computing can be used to address the computing needs for the DOE's Office of Science. The project will evaluate cloud computing’s effectiveness to run applications across all areas of science including bioscience, high-energy physics, climate and material science. To perform this work, the fellow will have access to a newly acquired testbed including a 5760-core cluster. The postdoc will also assist in determining how cloud computing models can be adapted to mid-range computing and how these models can be integrated into production computing facilities like NERSC. See job details.

NERSC is also looking for a Computer Systems Engineer 3 to contribute to a short-term team effort in evaluating the performance potential of GPU-based cluster computer architectures for scientific applications. The CSE will assist NERSC in evaluating existing and emerging HPC systems by analyzing the performance characteristics of leading-edge DOE Office of Science application codes. The successful applicant will require knowledge of GPU programming and detailed domain knowledge of underlying applications in the area of high energy physics scientific computing applications. See job details.

The Advanced Computing for Science (ACS) Department in CRD has an opening for a Computer Systems Engineer 2 or 3. This CSE will work on a wide array of problems, including user requirements and systems analysis for monitoring Pegasus-WMS workflows, distributed monitoring data collection and analysis tools (based on NetLogger), database design and tuning for on-line troubleshooting, integration of troubleshooting tools with the perfSONAR framework, and development of techniques for addressing application performance on many-core platforms. See job details.

The Lab’s Employee Referral Incentive Program (ERIP) awards $1,000 (net) to employees whose referral of an external candidate leads to a successful hire.


New Help Request Email Address for CRD

The System Engineering Team for CRD has a new help request email address for everyone to use: crd-help@lbl.gov. The original help@hpcrd.lbl.gov is also still in use. Staff in the High Performance Computing Research Department and the Biological Data Management and Technology Center should direct requests for computer assistance to crd-help@lbl.gov. For LBNL services that are not supported at the division level, such as your LBNL LDAP password, continue to contact the IT Help Desk.


ARPA-E Energy Innovation Summit to Be Held March 1–3

The first ever ARPA-E Energy Innovation Summit, hosted by the U.S. Department of Energy’s Advanced Research Projects Agency – Energy (ARPA-E), will serve as a forum for the nation’s energy leaders to share ideas, collaborate, and begin building the next Industrial Revolution in clean energy technologies. The Summit will be held March 1–3, 2010, at the Gaylord National Hotel and Convention Center, Washington, DC.

The ARPA-E Energy Innovation Summit will bring together the nation’s energy leaders to share ideas, collaborate and identify future technology opportunities and gaps. Participants will include members of the scientific and research communities, venture capital investors, technology entrepreneurs, corporations with an interest in clean energy technologies, policymakers and government officials. The Summit will present ARPA-E’s first round of awardees and, for the first time, showcase many of the 250 additional top-ranking projects — out of nearly 3,700 concept papers submitted — from ARPA-E’s first $150 million solicitation.

For more information and to register, go here. The deadline for hotel reservations is January 18.


Registration Is Open for BEARS 2010 on February 11

The Berkeley EECS Annual Research Symposium (BEARS 2010), sponsored by the Electrical Engineering and Computer Sciences Department at UC Berkeley, will be held at Sibley Auditorium, Bechtel Engineering Center on Thursday, February 11, 2010.

The program will begin with an integrated series of talks on the future of devices, microprocessor-based computation, mobile, and the cloud. Next is a panel on Energy by three members of the National Academy of Engineering—Professors David Culler, Randy Katz, and Eli Yablonovich—led by Greg Papadopoulos, Sun CTO and co-author of the provocative new book Citizen Engineer: A Handbook for Socially Responsible Engineering.

Lunch gives you the chance to talk technology with your favorite Berkeley professor inside their research centers. The afternoon offers poster sessions and demos where you can interact and connect with the next generation of technology leaders, the Berkeley EECS PhD students.

For more information and to register, go here.


Women in Math, Friendship in Math Are Topics of Play and Lecture

Catch an exclusive West Coast performance of NYC writer/performer and “recovering mathematician” Gioia De Cari’s solo show “Truth Values: One Girl’s Romp through MIT’s Male Math Gaze,” winner of the 2009 New York Fringe Festival Overall Excellence Award. The Mathematical Sciences Research Institute (MSRI) is pleased to present this play during the 2010 Joint Mathematics Meetings.

Performances will be on Thursday and Friday, January 14 and 15, at 8:00 pm in the Zeum Theater, 221 Fourth Street, San Francisco (next to the Moscone Center). Discussions on women in mathematics will immediately follow the shows. A portion of the proceeds will benefit the Association for Women in Mathematics. Click here for more information.

The Calculus of Friendship: What a Teacher and a Student Learned about Life while Corresponding about Math, a book by Steven Strogatz, is the story of an extraordinary connection between a teacher and a student, as chronicled through more than thirty years of letters between them. What makes their relationship unique is that it is based almost entirely on a shared love of calculus. For them, calculus is more than a branch of mathematics; it is a game they love playing together, a constant when all else is in flux. Like calculus itself, The Calculus of Friendship is an exploration of change. It's about the transformation that takes place in a student’s heart as he and his teacher reverse roles, as they age, as they are buffeted by life itself.

Strogatz will discuss The Calculus of Friendship in the AMS-MAA-SIAM Gerald and Judith Porter Public Lecture on Saturday, January 16, from 3:00 to 4:45 pm in the Main Lecture Room at Moscone Center. The lecture is free, but preregistration is required. Click here for more information.


This Week’s Computing Sciences Seminars

Mathematical and Statistical Foundations for Computing
Monday, January 11, 9:30–10:30 am, 50B-4205
Larry Wang

Recent graduate and prospective Mathematical Analyst Larry Wang will give an overview of his experience and qualifications. He will discuss his coursework and projects at UC Berkeley and his software development work at LBNL's National Center for Electron Microscopy and Center for X-Ray Optics.

Green In Silico Project: Evolving Scientific Research out of the Lab into the Data Center — Environmental Benefits and Challenges of Scientific Computing
Monday, January 11, 12:15–1:15 pm, 90-3122
Peter James, University of Bradford, UK

Scientific and technical computing is a major element in the energy consumption and carbon emissions of universities and research organisations. Europe’s largest high performance computing (HPC) based research centre has an energy bill approaching $100 million annually. And HPC was found to be 14% of the almost $2 million per annum computing-related electricity bills in a middle-tier, mid-size, UK university, with a similar amount associated with science-related conventional computing. The bills and impacts are also growing rapidly as in silico work expands, driven by new opportunities such as enhanced visualisation, and actual substitution for in vivo and in vitro activity, e.g. replacement of physical manipulation of molecules by computer modelling. Absent radical action to improve computing and cooling efficiency, science-based institutions have growing difficulties in meeting environmental regulations and targets (especially in Europe), and are facing energy bills of a size that will greatly constrain actual research and teaching. More positively, in silico research can also create environmental benefits, e.g. speeding up the development of new biofuel molecules through simulation of protein chemistry reaction pathways; replacement of “bench science” lab activities with computational and robotic processes, controlled by scientists in an adjacent “science studio” (thereby minimising the need for energy-intensive laboratory ventilation to ensure safety).

The UK HEEPI project (see www.goodcampus.org) supports environmental improvement in British universities, and currently has programmes on green IT and sustainable laboratories. Its new Green In Silico Project (which it is hoped will involve LBNL collaboration) is reaching beyond computing specialists to scientific decision-makers and funders by providing them with a strategic analysis of the environmental implications of trends in scientific computing, and the actions they need to take to make them sustainable. In addition to this specific focus, the seminar will also provide an opportunity for comparative discussion of American and European state-of-the-art regulations and other issues with regard to green IT.

Integrating Modeling and Experiment to Understand Actinide Chemistry
Wednesday, January 13, 4:00–5:00 pm, 70A-3377
Bert A. DeJong, Pacific Northwest National Laboratory

Computational chemistry has reached the point where it makes significant contributions to the fundamental understanding of actinide chemistry, and plays an important role in interpretation of experimental data and the prediction of chemical and physical properties of actinide complexes. This presentation will discuss results of (1) understanding chemical bonding by combining sensitive experimental gas-phase measurements on actinides with the interpretative power of ab initio computational chemistry, and (2) modeling the dynamical behavior of actinides in solution and at interfaces using the newly developed and highly scalable heavy-element chemistry software capability in NWChem.


Link of the Week: Trusting Nature as the Climate Referee

John Tierney writes in the New York Times:

Imagine a planet in which global warming was averted without the periodic need for thousands of people to fly around the world to promise to stop burning fossil fuels. Imagine no international conferences wrangling over the details of climate policy. Imagine entrusting the tough questions to a referee: Mother Earth.

That is the intriguing suggestion of Ross McKitrick, an economist at the University of Guelph in Ontario.… He suggests imposing financial penalties on carbon emissions that would be set according to the temperature in the earth’s atmosphere. The penalties could start off small enough to be politically palatable to skeptical voters.

Read more.



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.