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InTheLoop | 07.01.2013

The Weekly Newsletter of Berkeley Lab Computing Sciences

July 1, 2013

Arie Shoshani Delivers Keynote at BigData 2013 Conference

Arie Shoshani, leader of CRD’s Scientific Data Management Group, gave a ke<ynote talk on “Managing the Data Flood in Scientific Domains” at BigData 2013, the IEEE 2nd International Congress on Big Data. The June 27-July 2 conference is in Santa Clara.

In his talk on Saturday, June 29, Shoshani discussed:

  • What do we mean by Big Data in scientific domain?
  • Emerging challenges with Big Data in scientific domains
  • The role of indexing for scientific data

Shoshani, who leads DOE’s Scientific Data Management, Analysis, and Visualization (SDAV) institute, also described SDAV’s organization and technologies and gave examples of current approaches and solutions in SDAV.


ESnet Hosts July 17-18 Workshop on Network Issues for Life Sciences Research

ESnet and Internet2 will host a workshop on “Network Issues for Life Sciences Research,” at Berkeley Lab on Wednesday and Thursday, July 17 and 18. This meeting will bring together network experts involved in life sciences to discuss their most pressing network-related issues and requirements. Registration is now open at: http://events.internet2.edu/2013/ftw-life-sciences/register.cfm

 The workshop will include keynotes from Jay Keasling, Berkeley Lab’s associate laboratory director for Biosciences and chief executive officer of the Joint BioEnergy Institute; George Komatsoulis, chief information officer of the National Institutes of Health’s National Cancer Institute; and Adam Arkin, computational biologist and director of Berkeley Lab's Physical Biosciences Division, and principal investigator for the Kbase project. The full agenda is at: http://events.internet2.edu/2013/ftw-life-sciences/agenda.cfm?types=&details=on

Four main topics will be explored within the context of life sciences:

  • Workflow Engines, Portals and Gateways
  • Data Movement Architecture and Tools
  • Public and Private Cloud Architectures
  • Network Infrastructure Issues and Architectures

House Committee Hearing on Exascale Cites Critical Role of NERSC

(Editor’s note: This is an excerpt from FYI: The AIP Bulletin of Science Policy News)

A May 22 hearing of the House Science, Space and Technology’s Subcommittee on Energy demonstrated bi-partisan enthusiasm for advanced computing technology. Members were interested in learning about developments and challenges faced by researchers as they relate to exascale computing. They acknowledged that high performance computing has played a role in many scientific disciplines and that it has revolutionized how many economic sectors operate.

During the hearing Representative Randy Hultgren (R-IL) exemplified that support for computing research as he described his discussion draft of The American High-End Computing Leadership Act. The bill would modify the Department of Energy (DOE) High-End Computing Revitalization Act of 2004 to authorize increased funding for the DOE Office of Science to develop exoscale computing systems at national laboratories. The bill establishes national laboratory - industry partnerships that would allow industry, institutions of higher education, and Federal agencies to work jointly on the development of exascale computer systems. Furthermore, the bill calls for the DOE to submit an integrated strategy and program management plan to Congress which would outline the execution of the Exascale Computing Program. That plan would address the prioritization of programs during times of tight fiscal climates.

Ranking Member Eric Swalwell (D-CA) was eager to learn more about DOE computing partnerships with industry and national laboratories. He called attention to the vast examples of industrial and academic research that has benefited from advanced computing including energy research, pharmaceutical development, and nuclear reactor design.

Swalwell noted that “while Lawrence Livermore, Argonne, and Oak Ridge National Laboratories are three of the most powerful supercomputers in the world, and they are addressing incredibly important scientific issues that really require their advanced computing capabilities, Lawrence Berkeley’s National Energy Research Scientific Computing Center actually serves thousands of more users with only a fraction of those leadership machines’ computing power. The point is, not every computational research effort requires the two fastest, most sophisticated system we can possibly build, and I think we also need to do more to make what’s sometimes called ‘capacity’ supercomputing more accessible to both the academic and industrial research communities that could benefit.”

Read the full posting at: http://www.aip.org/fyi/2013/109.html


NERSC Simulations Indicate Thriving Tundra Bushes Add Fuel to Northern Thaw

Carbon-gobbling plants are normally allies in the fight to slow climate change, but in the frozen north, the effects of thriving vegetation may actually push temperatures higher. In a series of climate simulations performed at NERSC, a group of researchers found that the spread of bushes, taller ones especially, could exacerbate warming in northern latitudes by anywhere from 0.6°C to 1.8°C per year.

What’s more, taller species have the potential to warm tundra soil more deeply, threatening to thaw permafrost in some areas. That means more of the greenhouse gases now locked up by a year-round freeze could be released into the atmosphere, increasing warming even more. Their results were published in Environmental Research Letters.

“Until now, most climate model studies have only focused on the climate effects induced by a complete tundra-to-forest conversion,” said Celine Bonfils, a scientist at Lawrence Livermore National Laboratory (LLNL) and principal investigator in this study. While warming could eventually lead to northward forest expansion, “we don’t expect a full-scale conversion of tundra to forest anytime in the next century,” said Tom Phillips, one of Bonfils’s collaborators on the study, also of LLNL. “More likely you’ll see shorter shrubs or new species that are taller moving in gradually.

»Read more.


A Note on InTheLoop Submissions

With the June 27 retirement of InTheLoop editor John Hules, news items for the weekly Computing Sciences staff newsletter should be sent to Jon Bashor at jbashor@lbl.gov.



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.