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InTheLoop | 03.25.2013

The Weekly Newsletter of Berkeley Lab Computing Sciences

March 25, 2013

Reading the Cosmic Writing on the Wall

Thanks to a sensitive space telescope and some sophisticated supercomputing done at NERSC, scientists from the international Planck collaboration have made the closest reading yet of the most ancient story in our universe: the cosmic microwave background. On March 21 the team released preliminary results based on the Planck observatory’s first 15 months of data. They reveal that the universe is 80 million years older than we thought, with more matter and less dark energy. Read more.

A March 22 front-page San Jose Mercury News story highlighted NERSC’s crucial role in the Planck satellite findings and quoted Julian Borrill, co-leader of the Computational Cosmology Center (C3) in CRD, who described the results as “the baby picture of our universe.” Borrill is also quoted in a NASA news story, and Ted Kisner of C3 is quoted in a Universe Today story, both stories highlighting the role of NERSC’s Hopper Cray XE6 system.


Computer Simulations Yield Clues to How Cells Interact with Surroundings

Your cells are social butterflies. They constantly interact with their surroundings, taking in cues on when to divide and where to anchor themselves, among other critical tasks.

This networking is driven in part by proteins called integrin, which reside in a cell’s outer plasma membrane. Their job is to convert mechanical forces from outside the cell into internal chemical signals that tell the cell what to do. That is, when they work properly. When they misfire, integrins can cause diseases such as atherosclerosis and several types of cancer.

Despite their importance—good and bad—scientists don’t exactly know how integrins work. But now computer models run at NERSC offer a new look at the molecular machinery that enables cells to interact with their environment. Read more.


Kathy Yelick Named ACM Athena Lecturer, Profiled in DOE Women’s History Month Feature

The Association for Computing Machinery’s Council on Women in Computing (ACM-W) has named Katherine Yelick, Berkeley Lab’s Associate Laboratory Director for Computing Sciences, as the 2013–2014 Athena Lecturer. The Athena Lecturer award celebrates women researchers who have made fundamental contributions to computer science. Yelick has improved fundamental understanding and practice of parallel programming. She co-invented two parallel programming languages and developed novel performance tuning, compilation, and runtime systems, which implement the core behavior of computer languages. Read more.

In celebration of Women’s History Month, the Department of Energy is featuring “Women @ Energy,” which showcases talented and dedicated employees at the Energy Department who are helping change the world, ensuring America’s security and prosperity through transformative science and technology solutions. Women @ Energy profiles women across the country who share insights on what inspired them to work in STEM fields (Science, Technology, Engineering and Mathematics). Kathy Yelick is one of eight Berkeley Lab researchers profiled; read her interview here.


HPC Source Meets ESnet Network Innovator Chin Guok

HPC Source, a supplement to Scientific Computing magazine, has posted a feature story about ESnet network engineer Chin Guok, who has been helping lay the foundation for software defined networking since 2004. Guok is the technical lead for OSCARS, ESnet’s On-Demand Secure Circuits and Advance Reservation System. To read the story, go here and click on the bullet “Meet HPC Innovator Chin Guok.”


ESnet’s Greg Bell Taking “Network as Discovery Instrument” Talk to JGI User Meeting

Since ESnet Director Greg Bell began discussing DOE’s high speed network as an instrument for scientific discovery and not just infrastructure, the message has resonated well in the research community. Bell has been invited to give the talk in Europe, in Canada, and at a joint meeting in Hawaii with Asian research and education network representatives.

On March 28, he’ll deliver an iteration of his talk closer to home — at the Joint Genome Institute’s annual user meeting, being held in Walnut Creek. His presentation is entitled “Network as Discovery Instrument: A Quick-Start Guide.” In his talk, Bell will attempt to raise user expectations for networks; explain how they can accelerate scientific workflows; and provide guidance about getting maximum benefit from ESnet and other research networks.

ESnet provides a dedicated 10-gigabit-per-second link between JGI and NERSC for moving large data sets from the sequencing facility in Walnut Creek to NERSC, where the data is stored and made available for analysis by users around the world.


Dan Martin Explains Supercomputers and Antarctic Ice to Kindergartners

Dan Martin of the Applied Numerical Algorithms Group took his research on melting ice sheets to his son’s kindergarten class on March 15, drawing interesting questions and earning mention in the class newsletter. Martin’s son attends Malcolm X School in Berkeley.

He used the occasion to show a number of simulations done using the Chombo AMR (adaptive mesh refinement) software developed by the group. One of those showed the projected melting of ice sheets in Antarctica. Afterwards, the students wrote a sentence about what they learned and drew a picture.

“Based on the kids’ drawings, the most popular one was the movie of interacting shock waves we showed at SC03, which is pretty colorful,” Martin said. “The teacher had them write a sentence about it afterward, and the two most common ones were, ‘Dan makes great movies,’ and ‘Dan uses supercomputers.’”

Among the questions posed by the students about Antarctica were “Can a submarine go there?” and “Can you jump up and down on the ice?” The teacher wrote in the class newsletter, “You see, we can make any job accessible to the kids! They just need lots of visuals and props.”


Kennedy High School Students Look at Careers in Computing and Networking

As part of Berkeley Lab Computing Sciences’ ongoing outreach efforts with the Kennedy High School IT Academy in Richmond, eleven students and two teachers spent half the day March 20 learning about different career opportunities in computing and networking. The event was organized to give the students ideas about career paths beyond the basics of computer science and web design taught in the classroom. Read more.


Free Prescription Computer Glasses Available at Health Services

Free glasses for eye protection or assistance with computer viewing are available to all Lab employees through a Health Services optometrist, who is on site every Thursday. Eyestrain and related headaches are more common among computer users than more widely known problems such as carpal tunnel syndrome. Eyeglasses tuned for monitor use are an effective way to address these issues.

Eye exams are performed Thursdays by Dr. Bernard Hale, by appointment only. Bring in your eyeglass prescription. If an eye exam is needed, the cost is $40, a portion of which may be reimbursable under the Vision Service Plan (VSP). Call Health Services at x6266.


This Week’s Computing Sciences Seminars

Active Measurement of Application Resource Utilization

Thursday, March 28, 12:00–1:00 pm, OSF CR 238
Webinar/telecon info: go here
Marc Casas, LLNL

The high performance and efficiency demands of HPC applications make it critical to develop proactive mechanisms to assign computing work to different hardware components in a way that maximizes performance and efficiency. However, this is extremely difficult in practice because the performance properties of software components cannot be measured accurately, making it hard to predict how long a given task will run on a given piece of hardware or how two different tasks that share resources (e.g. cache, network or file system) may interfere with each other. We present a new approach to measure the performance properties of software components based on their observable behavior.

First, we measure a task’s effective use of any given resource by actively making this resource unavailable to the task and observing the point where its performance degrades as well as measuring the degree of the degradation. We reduce the application’s available resources by using threads running on additional cores to actively utilize shared resources. Second, we measure the amount of each resource that the given task leaves available to other tasks by inferring it from the execution time of small workloads that utilize just the resource in question. These two pieces of information make it possible to predict the performance of multiple software components that share one or more resources. In this talk we will present our work on measuring application utilization of caches and networks and point towards our future work on techniques to measure utilization of more complex resources such as file systems.


Link of the Week: What Will the Sequester Mean to HPC (and Federal) Research?

HPCwire reports: On Friday, March 15, President Obama gave a speech at DOE’s Argonne National Laboratory, and light-heartedly expressed his concerns about the effects of sequestration on budgets at the country’s national laboratories. Noting that some of the employees were standing in the crowded auditorium, he quipped, “I thought [that at] Argonne, one of the effects of the sequester [was that] you had to get rid of chairs!”

People laughed. Outside of that speech, however, nobody in a federal lab is chuckling over the possible impact of sequestration. Prominent heads of national labs, university researchers and technology executives are very concerned about how budget stalemates between the White House and Congress will affect government-funded research across the country. 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.