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InTheLoop | 05.6.2013

May 6, 2011

Bert de Jong to Lead CRD’s Scientific Computing Group

Bert de Jong of the Pacific Northwest National Laboratory has been named the new leader of the Scientific Computing Group in Berkeley Lab’s Computational Research Division (CRD). De Jong will join Berkeley Lab on July 1.

“We were very impressed with Bert’s strong research track record in computational chemistry, as well as his excellent management skills as both group leader and acting associate director for molecular science computing,” said CRD Director David Brown. “With his leadership and experience, we are also looking forward to building stronger ties with the Berkeley Lab Chemical Sciences Division.” Read more.

Brain Visualization Prototype Holds Promise for Precision Medicine

Researchers from Berkeley Lab, UCSF, and Oblong Industries presented a prototype of their brain simulation and innovative navigation interface at UCSF’s OME Precision Medicine Summit on Thursday, May 2. Experts believe that this visualization technology holds promise for the field of precision medicine, which will allow future doctors to cross-reference an individual’s personal history and biology with patterns found worldwide and use that network of knowledge to pinpoint and deliver care that’s preventive, targeted, timely, and effective. Read more.

Aided by Simulations, Scientists Observe Atomic Collapse State

Aided by simulations generated at NERSC, scientists have finally confirmed a 70-year-old prediction in quantum mechanics: Electrons in super-heavy atoms can spiral into the nucleus and away again, emitting a positron in the process, an effect known as atomic collapse resonance. This finding holds important implications for new kinds of graphene-based electronic devices, as well as future basic physics research. Read more.

ASCR Discovery: Energy-Materials Research a Test Case for Big-Data Flood

Big data extends far beyond its literal interpretation. It’s more than large volumes of information. It’s also complexity, including new classes of data that stretch the capabilities of existing computers. In fact, analytical algorithms and computing infrastructures must rapidly evolve to keep pace with big data.

“On the science side,” says David Brown, director of the Computational Research Division at Berkeley Lab, “it caught us somewhat by surprise.” Detectors, for example, would improve and provide ever more data, Brown says, “but we didn’t realize that we might have to develop new computational infrastructure to get science out of that data.” Read more.

NERSC Hosting Cray User Group Meeting This Week in Napa Valley

NERSC is hosting the annual Cray User Group meeting, CUG2013, this week, May 6–9, in the Napa Valley. The theme of this year’s conference, “A New Vintage of Computing,” reflects the newest crop of multi-core and many-core computing systems, as well as the growing impact of high end computing. Understanding the climate impacts on agriculture, developing new crops to fuel economic growth, and analyzing carbon mitigation techniques, are just a few of many new and fertile areas that can benefit from computationally driven advances in climate, genetics and systems biology.

Berkeley Lab staff contributions to the conference include:

Julian Borrill: Big Bang, Big Data, Big Iron — Analyzing Data from the Planck Satellite Mission

Suren Byna, Andrew Uselton, Prabhat, and Yun (Helen) He: Trillion Particles, 120,000 cores, and 350 TBs: Lessons Learned from a Hero I/O Run on Hopper

Nicholas Cardo: Sonexion 1600 I/O Performance

Tina Declerck and Iwona Sakrejda: External Torque/Moab and Fairshare on the Cray XC30

Jack Deslippe and Zhengji Zhao: Comparing Compiler and Library Performance in Material Science Applications on Edison

Brent Draney, Tina Declerck, Jeffrey Broughton and John Hutchings: Saving Energy with “Free” Cooling and the Cray XC30

Helen He: Programming Environments, Applications and Documentation SIG

Larry Pezzaglia: Supporting Multiple Workloads, Batch Systems, and Computing Environments on a Single Linux Cluster

Horst Simon: Why We Need Exascale, and Why We Won’t Get There by 2020

Jay Srinivasan and Shane Canon: Evaluation of a Flash Storage Filesystem on the Cray XE-6

Nicholas Wright, Brian Austin, Matthew Cordery, and Harvey Wasserman: Performance Measurements of the NERSC Cray Cascade System

Andrew Uselton and Nicholas Wright: A File System Utilization Metric for I/O Characterization

Yushu Yao and Katie Antypas: Production I/O Characterization on the Cray XE6

Zhengji Zhao, Nicholas J. Wright and Ka tie Antypas: Effects of Hyper-Threading on the NERSC Workload on Edison

James Sethian Elected to National Academy of Sciences

James Sethian, an applied mathematician at Lawrence Berkeley National Laboratory and professor of mathematics at the University of California at Berkeley, was one of 84 new members and 21 foreign associates from 14 countries elected to the National Academy of Sciences in recognition of their distinguished and continuing achievements in original research. At Berkeley Lab, Sethian leads the Mathematics Group in the Computational Research Division.

“James’ election to the National Academy is yet another well-deserved recognition of his innovative research and his commitment to developing future generations of mathematicians and scientists,” said Kathy Yelick, Berkeley Lab’s Associate Laboratory Director for Computing Sciences. “What makes the work of his group so compelling is their use of innovative mathematical models to address problems ranging from new energy sources to environmental remediation to seismic imaging.” Read more.

CRD’s John Shalf Co-Chairing May 5–8 IEEE Optical Interconnects Conference

John Shalf, head of CRD’s Computer and Data Sciences Department, is co-chair of the 2013 IEEE Optical Interconnects Conference being held May 5–8 in Santa Fe, NM. This is the second IEEE Photonics Society Optical Interconnects Conference and builds on 22 years of the Society’s successful Workshop on Interconnections within High Speed Digital Systems. The workshop brings together researchers and engineers from multiple disciplines to discuss advanced interconnect technologies for applications at all levels of computing granularity.

Among the keynote speakers are Berkeley Lab Deputy Director Horst Simon, who will discuss “Why We Need Exascale, and Why We Won't Get There by 2020,” and Intel Corporation’s Shekhar Borkar, who will present “How to Stop Interconnects from Hindering the Future of Computing.”


ESnet’s Greg Bell to Speak at May 13 Science at the Theater

ESnet Director Greg Bell will be one of eight speakers at Berkeley Lab’s next Science at the Theater program to be held from 7:00–9:00 pm on Monday, May 13, at the Berkeley Repertory Theatre.

The evening’s theme is eight Berkeley Lab scientists presenting eight game-changing concepts in eight minutes each. Bell will discuss “Accelerating Science with (Very, Very) Big Data.” Other speakers are Mina Bissell, Bill Jagust, David Schlegel, Blake Simmons, Aindrila Mukhopadhyay, Carolyn Larabell and Ron Zuckermann.

Admission is free, but an RSVP is recommended, either through Eventbrite or by calling 510.486.7292. Berkeley Rep is located at 2015 Addison St. in downtown Berkeley.

Call for Proposals on Network Issues for Life Sciences Research

For over a decade, Internet2 and ESnet have hosted technical meetings that bring together network operators from the university, laboratory, and vendor communities to share best practices, discuss common challenges, and unite around emerging technologies that support improved networking for science. The Focused Technical Workshop series is a spin-off of these successful efforts.

In July 2013, ESnet and Internet2 will host a two-day workshop focusing on Network Issues for Life Sciences Research in Berkeley, CA. As the first of its kind, this meeting will bring together our communities’ technical experts in a smaller, more intimate setting with scientists in the field of life sciences to discuss their most pressing network-related issues and requirements. Four topics will be explored in depth:

workflow engines, portals and gateways

data movement architectures and tools

public and private cloud architectures

network infrastructure issues and architectures.

If you feel that your insight would be valuable to this discussion, please read the call for proposals for more information and to submit an abstract. Proposals are due by May 31.

Funding Available to Attend Grace Hopper Conference

The Grace Hopper Celebration of Women in Computing conference will be held October 2–5, 2013 in Minneapolis, MN. This conference is designed to bring the research and career interests of women in computing to the forefront. Presenters are leaders in their respective fields, representing industrial, academic, and government communities. Leading researchers present their current work, while special sessions focus on the role of women in today’s technology fields, including computer science, information technology, research, and engineering.

The Berkeley Lab Computing Sciences Diversity Working Group is able to pay the travel and registration of a few Lab staff to attend. If you would like to attend the Grace Hopper Conference and would like to have your travel costs sponsored by the Diversity Working Group, please contact Elizabeth Bautista. Send the following information:



Paragraph giving the reason you would like to attend Grace Hopper:

The deadline for submitting applications is May 20, 2013.

This Week’s Computing Sciences Seminars

Workflow Technologies for Science Automation

Tuesday, May 7, 10:00–11:00 am, 50B-2222

Ewa Deelman, University of Southern California, Information Sciences Institute

This talk describes the use of workflows in various science domains including astronomy, bioinformatics, earthquake science, gravitational-wave physics, and others. Scientific workflows allow users to declaratively describe potentially complex applications that are composed of individual components. Workflows include a description of the data and control dependencies between the components. Over the years, various workflow management systems have been developed to manage computations in a variety of domains. This talk will give example applications, describe the various workflow management systems such as Galaxy, Kepler, and Taverna, and focus on the Pegasus Workflow Management System developed at USC/ISI. Pegasus bridges the scientific domain and the execution environment by automatically mapping high-level workflow descriptions onto distributed resources. It automatically locates the necessary input data and computational resource necessary for workflow execution. It also restructures the workflow for performance and reliability reasons. Pegasus can execute workflows on a laptop, a campus cluster, grids, and clouds. It can handle workflows with a single task or millions of tasks and has been used to manage workflows accessing and generating terabytes of data.

Mathematical Models and Experimental Evolution to Study Genetic Interactions and Evolution of Synthetic Microbial Communities

Tuesday, May 7, 4:00–5:00 pm, Rm 141, 717 Potter St.

Christopher Marx, Harvard University

Metabolism offers a great opportunity to frame evolutionary and ecological questions in a quantitative framework. Drawing from both kinetic and constraint-based models, I will discuss our work to try to move toward predicting future behavior from current cell properties. Within cells, we ask how well we can predict the effects of beneficial mutations and the interactions between these changes. Between cells, we attempt to predict the growth of multi-species communities in time and space to ask how various metabolic, cooperative strategies fare under various conditions.

The Hitchhiker's Guide to the Lovász Local Lemma

Wednesday, May 8, 3:00–4:15 pm, 380 Soda Hall, UC Berkeley

Mario Szegedy, Rutgers University

The Lovász Local Lemma (LLL) gives a simple sufficient condition for the satisfiability of sparse constraint systems, and is widely used in combinatorics. According to Knuth, the lemma goes back to the early 1970s, when Lovász circulated his ideas about a Local Lemma in an unpublished note. It was first published by Erdos and Lovász in 1975, in the proceedings of a conference held in 1973, in honor of Erdos's 60th birthday, as a tool by which several theorems about the existence of certain hyper-graphs could be proved. Since its introduction, several variants of the lemma has become known, some proposed by the current speaker and his students. In this talk, we explain the differences between the main variants, touch upon their wide range of applications, and raise a great number of new research questions.

A Pathway-Based Mean Field Model for E. Coli Chemotaxis: The Mathematical Derivation and Keller Segel Limit

Friday, May 10, 11:00 am–12:00 pm, 50F-1647

Xu Yang, University of California, Santa Barbara

In this talk, we give a mathematical derivation of a pathway-based mean-field model for E. coli chemotaxis based on the moment closure in kinetic theory. The pathway-based model incorporate the most recent intracellular chemical dynamics. The derived moment system, under some assumptions, gets to the chemotaxis model proposed in [G. Si, T. Wu, Q. Quyang and Y. Tu, Phys. Rev. Lett., 109 (2012), 048101], especially an important physical assumption made in which can be understood explicitly in this new moment system. We obtain the Keller-Segal limit by considering the moment system in the regime of long time and strong tumbling rate. Numerical experiments are presented to show the agreement of the moment system with (individual based) signaling pathway-based E. coli chemotaxis simulator ([L. Jiang, Q. Ouyang and Y. Tu, PLoS Comput. Biol., 6 (2010), e1000735]).

Link of the Week: Great Scientist ≠ Good at Math

In a Wall Street Journal essay, biologist E. O. Wilson writes:

For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate….

Fortunately, exceptional mathematical fluency is required in only a few disciplines, such as particle physics, astrophysics and information theory. Far more important throughout the rest of science is the ability to form concepts, during which the researcher conjures images and processes by intuition….

Wilson’s Principle No. 1: It is far easier for scientists to acquire needed collaboration from mathematicians and statisticians than it is for mathematicians and statisticians to find scientists able to make use of their equations….

Wilson’s Principle No. 2: For every scientist, there exists a discipline for which his or her level of mathematical competence is enough to achieve excellence.

Read more.


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