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InTheLoop | 02.18.2014

February 18, 2014

CRD, NERSC Staff Present at SIAM Conference on Parallel Processing for Scientific Computing

Dozens of scientists from Berkeley Lab’s Computational Research and National Energy Research Scientific Computing divisions are presenting their research this week at the Sixteenth Conference on Parallel Processing for Scientific Computing. Sponsored by the Society for Industrial and Applied Mathematics, the conference series has played a key role in promoting parallel scientific computing, algorithms for parallel systems and parallel numerical algorithms. The conference is unique in its emphasis on the intersection between high performance scientific computing and scalable algorithms, architectures, and software. This year’s meeting is being held Feb. 18-21 in Portland, Ore. Lenny Oliker of CRD’s Future Technologies Group was a member of the organizing committee. »Read more

Decoding the Molecular Mysteries of Photosynthesis

 Scientists from the University of California, Berkeley and Berkeley Lab are using simulations performed at NERSC to understand the role certain proteins play in the production of energy via photosynthesis. Their aim is to understand how plants regulate and heal their photosynthetic systems. The work could lead to more robust and efficient solar energy capture using artificial photosynthesis. The team’s paper appeared as the cover story in the September 2013 Biophysical Journal. »Read more

Feb. 19: CS Innovations to be Recognized at Royalties Distribution Ceremony

Every year, Berkeley Lab holds a ceremony to distribute royalty checks and recognize lab researchers for successfully commercialized intellectual property. Typically, over 100 inventors and authors receive royalties; this year will include six honorees from Computing Sciences. All lab employees are invited to the 2014 ceremony and reception held Wednesday, February 19th at 3:00pm in the cafeteria. »Read more.

Feb. 20: ESnet’s Greg Bell to Give Keynote at Event for Government Networking, IT Pros

ESnet Director Greg Bell will deliver the keynote at “Networking for Discovery,” a one-day program organized by Government Computer News, Federal Computer Week and Ciena that is targeted at government network providers and IT staff. The event will be held Thursday, Feb. 20, at the National Press Club in Washington, D.C. 

In this program, technology experts and government leaders will provide their thoughts and strategies on delivering the infrastructure that will enable the future of big data computing. Bell’s talk will focus on ESnet's approach to providing high performance networks to support the growing trend of big science data. He will also discuss ESnet’s work in researching and developing new Internet technologies to support big data growth over time.

Feb. 20: BES Facilties Computing Working Group Technical Meeting

Berkeley Lab is hosting a second technical working meeting regarding collaborations to meet data analysis needs emerging from DOE light sources and neutron facilities. This technical working meeting draws on beamline scientists, facility staff and users to share progress in the design and development of software capable of handling the data deluge from DOE facilities; it is not an official DOE BES or ASCR meeting. Participation is limited and is being coordinated by a lead at each DOE lab. A limited number of slots remain available for qualified participants. »Learn more.

ESnet's Brian Tierney Featured in HPCWire Podcast

Brian Tierney was interviewed for an HPCWire podcast. In the interview Tierney, who leads ESnet’s 100G Network Testbed Project, also addresses progress with the perfSONAR project, which he is helping to drive. »Read more.

NERSC@40: Take a Virtual Stroll Down Memory Lane

As part of its year-long 40th anniversary celebration, NERSC has launched special "NERSC@40" web pages. Read news of the anniversary year celebrations, view photo galleries, and peruse fun facts about the center. Or step back into the past by downloading early brochures, newsletters, articles and more. The content will continue to grow and expand throughout anniversary year. On the way are anecdotes from "old-timers," a historical timeline and more. »Read more.

ESnet Staff Present at LHC Networking Workshop

ESnet’s Patrick Dorn, Bill Johnston, Joe Metzger and Inder Monga were among the 65 participants in an LHCONE workshop on Networking for the Worldwide LHC Computing Grid. The workshop was held Feb. 10-11 at CERN in Geneva, Switzerland. The sessions allowed physicists to communicate with network staff about issues related to moving data generated by LHC experiments, and for network experts to provide infrastructure updates. Johnston, Metzger and Monga were among the presenters. »See the workshop schedule with links to presentations.

SC14 Technical Program Accepting Submissions

Technical program submissions opened February 14th for research papers, posters (regular, education, and ACM Student Research Competition), panels, tutorials, BOF sessions, scientific visualization and data analytics showcase, emerging technologies, and doctoral showcase. »More information.

This Week's Computing Sciences Seminars

The Truth About Diffusion (in liquids)

Wednesday, February 19, 2014, 3:30pm - 4:30pm, 939 Evans Hall - UC Berkeley Campus
Aleksandar Donev, Courant Institute of Mathematical Sciences

We demonstrate that hydrodynamics and fluctuations affect diffusion in liquids in crucial ways, for both molecular diffusion (fluid mixtures), and colloidal suspensions. We study diffusive mixing in the presence of thermal fluctuations when the Schmidt number is large. We obtain a closed equation for the concentration which is amenable to efficient numerical solution. This equation captures both Fick's law for the ensemble-averaged mean and also the long-range correlated giant fluctuations in individual realizations of the mixing process. These giant fluctuations, observed in experiments, are shown to be the result of the long-ranged hydrodynamic correlations among the diffusing particles. Through a combination of Eulerian and Lagrangian numerical experiments we demonstrate that mass transport in liquids can be modeled at all scales, from the microscopic to the macroscopic, not as irreversible Fickian diffusion, but rather, as reversible random advection by thermal velocity fluctuations. Our model gives effective dissipation with a diffusion coefficient that is not a material constant as its value depends on the scale of observation. Our work reveals somewhat unexpected connections between flows at small scales, dominated by thermal fluctuations, and flows at large scales, dominated by turbulent fluctuations. This is joint work with Thomas Fai and Eric Vanden-Eijnden.

Two Case Studies in Accelerating Scientific Code Performance

Friday, February 21, 2014, 10:00am - 11:00am, Room 238 - NERSC (Oakland Scientific Facility)

Accelerating and Scaling a Numerical Model for Thunder - A general nonlinear acoustic model is chosen for simulating the acoustical propagation of thunder in the atmosphere. Multiple techniques for increasing the efficiency when numerically solving the model equations are discussed and the model is ultimately ported to a massively parallel architecture using a software library.

Accelerating the NASA SAGE III Code - Existing serial Fortran code is obtained and its performance analyzed. Performance is then increased by choosing more efficient algorithms and by porting sections of the code to CUDA and OpenMP.

Link of the Week: Public's Scientific Knowledge Low, but Support High, Survey Says

First the bad news: One quarter of Americans surveyed by the National Science Foundation don't know that the Earth rotates around the Sun. Nearly half think that astrology is a science. The good news: About 90 percent think that the good done by science outweighs the risks and agree that scientists "work for the good of humanity." A third think we should increase governmental funding for science. The survey results were prepared as one chapter of the National Science Board's annual report to the president titled "Science and Engineering Indicators 2014."

»Download the Chapter: "Science and Technology: Public Attitudes and Understanding" (PDF | 711KB).

»View links to the entire report.