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InTheLoop | 09.24.2012

September 24, 2012

NY Times Contrasts Data Center Wastefulness with NERSC Efficiency

In a story titled “Power, Pollution and the Internet,” the New York Times reports that most data centers, by design, consume vast amounts of energy in an incongruously wasteful manner, wasting 90 percent or more of the electricity they pull off the grid. Worldwide, the digital warehouses use about 30 billion watts of electricity, roughly equivalent to the output of 30 nuclear power plants. The article compares the 7 to 12 percent computer utilization typical at data centers with the 96.4 percent utilization NERSC achieved in July. Read more.

A commentary in Slate’s Future Tense blog include links to rebuttals of the Times article.

CASTRO Code Now Publicly Available

As part of the SciDAC-II Computational Astrophysics Consortium, members of the Computational Research Division’s Center for Computational Sciences and Engineering (CCSE), with contributions from several collaborators, developed CASTRO, a multi-dimensional Eulerian AMR radiation-hydrodynamics code that includes several equations of state, nuclear reaction networks, and self-gravity. There are currently three code papers describing CASTRO, and CASTRO has been used in a number of science publications by collaborators for simulations of Type Ia and Type II supernovae as well as pair-instability supernovae.

CCSE has now made CASTRO publicly available via Git at the CCSE Downloads page. CASTRO is based on the BoxLib software framework, which is also available at the CCSE Downloads page.

“Flying Through the Known Universe” Screens at 3D Film Festival in L.A.

A 3D movie flight through hundreds of thousands of galaxies at considerably faster than the speed of light had its world-premiere screening at the 3D Film Festival last weekend (Sept. 20–22) in Los Angeles. Created by Yushu Yao of NERSC, with Prabhat of Computational Research and David Schlegel of Physics, the movie’s Sloan Digital Sky Survey data includes photos of some of the actual galaxies. A 2D peek — the view from the left eye — is temporarily available here, but for the 3D version you’ll have to check out the 3D Festival in Hollywood or attend Berkeley Lab’s Open House on October 13.

Safety Reminder for Long Airplane Flights

Many of us take long plane flights, either for work or personal travel. One of the risks associated with such flights is pulmonary embolism.

ESnet Division Director Greg Bell reports that a young and healthy member of the global networking community recently suffered a serious embolism after a 13-hour flight from Australia to London. He believes his risk was increased by dehydration, by having a drink or two on the flight (which contributed to dehydration), and by the fact that he slept much of the way with his legs crossed. He survived, but an untreated embolism can be fatal.

The Mayo Clinic gives the following advice for preventing blood clots while traveling:

  • Take a walk. Move around the airplane cabin once an hour or so. If you’re driving, stop every hour and walk around the car a couple of times. Do a few deep knee bends.
  • Exercise while you sit. Flex, extend and rotate your ankles or press your feet against the seat in front of you, or try rising up and down on your toes. And don’t sit with your legs crossed for long periods of time.
  • Wear support stockings. The firm, even pressure these stockings exert helps keep blood from pooling in deep veins. You can use a device called a stocking butler to help you put on support stockings.
  • Administer a dose of heparin, if recommended by your doctor. If you have a history of deep venous thrombosis or venous thromboembolism, talk with your doctor before a long trip. He or she may tell you to self-inject a long-acting dose of heparin just before traveling. Your doctor will also tell you whether you need to repeat the dose for your return trip.
  • Drink plenty of fluids. Water is the best liquid for preventing dehydration, which can contribute to the development of blood clots. Avoid alcohol and caffeine, which contribute to fluid loss.

Berkeley and Stanford Announce Data, Society and Inference Seminars

UC Berkeley and Stanford University are proud to announce a new, joint speaker series: Data, Society and Inference Seminars. This cross-disciplinary seminar series will feature speakers tackling social science questions with big data and cutting-edge computation, data analysis, and inference techniques. Talks will alternate between Berkeley and Stanford, with live streaming between sites. Lunch will be provided.

The seminars will be held on Mondays from 1:00 to 2:30 pm in 330 Blum Hall on the Berkeley campus. Go here for the schedule.

This Week’s Computing Sciences Seminars

Par Lab Seminar: Trends in FPGA Systems and Programming
Tuesday, Sept. 25, 1:00–2:30 pm, 430 Soda Hall (Wozniak Lounge), UC Berkeley
Kees Vissers, Xilinx

The FPGA technology has seen an amazing scaling, tracking the best of the ITRS Semiconductor roadmap. In this talk we show that the combination of modern ARM based A9 processors combined with an affordable amount of FPGA fabric can achieve the compute requirements for modern video processing. We will show the C/C++ programs for a simple Sobel Filter at HDTV rate, that are the input for High-Level Synthesis based programming of these FPGAs. We will show the performance results using this methodology in medical applications using floating point, that leverages the tight integration of processors and accelerators via the caches. The complete system consists of AXI based DMA subsystems, dedicated accelerators and linux based processor subsystems. We will discuss future parallel programming constructs in the context of these architectures and their memory subsystems.

Insights Gained From Mathematical Modeling of HER2 Positive Breast Cancer
Tuesday, Sept. 25, 4:00–5:00 pm, 977-141
Claire Tomlin, UC Berkeley/LBNL Life Sciences Division

As the understanding of cellular regulatory networks grows, system dynamics and behaviors resulting from feedback effects have proven to be sufficiently complex so as to prevent intuitive understanding. In this talk, we describe the process of modeling treated regulatory networks in breast cancer. We demonstrate the use of the mathematical models in both understanding the system, and in suggesting new treatments. The talk will conclude with experimental results on HER2 positive cell lines. This is joint work with Soulaiman Itani, Young Hwan Chang, Jim Korkola, and Joe Gray.

Bragg Resonance of Water Waves and its Applications
Wednesday, Sept. 26, 4:00–5:00 pm, 939 Evans Hall, UC Berkeley
Reza Alam, UC Berkeley/Berkeley Lab

Free propagating water waves traveling over bottom ripples may be significantly altered if certain conditions between wave characteristics and the topography are satisfied. This phenomenon is referred to as Bragg resonance, a name taken from the analogy to its close cousin in solid state physics of X-ray diffraction in periodic crystals. Bragg resonance of water waves contributes to the development of coastal wave spectrum, modifies bottom features, and may explain the generation of internal gravity waves in stratified fluids. I will present recent results on oblique and high-order nonlinear Bragg resonance of water waves in homogenous and stratified waters and discuss its effect on the ocean spectral evolution. These results may have a number of practical applications in the area of ocean engineering. Specifically I will briefly talk about how Bragg Resonance can help protecting offshore structures (such as offshore wind farms) against ocean waves, can transfer tidal current energy to the surface, and can focus ocean wave energy for high-efficiency wave energy absorption.

OSF Brown Bag: Cloud Storage Assessment
Friday, Sept. 28, 12:00–1:00 pm, OSF 943-238
Jason Hick, NERSC

VCL Lunch Talk: Adaptive Anisotropic Remeshing for Cloth Simulation
Friday, Sept. 28, 12:00–1:00 pm, 510 Soda Hall, UC Berkeley
Rahul Narain, UC Berkeley

We present a technique for cloth simulation that dynamically refines and coarsens triangle meshes so that they automatically conform to the geometric and dynamic detail of the simulated cloth. Our technique produces anisotropic meshes that adapt to surface curvature and velocity gradients, allowing efficient modeling of wrinkles and waves. By anticipating buckling and wrinkle formation, our technique preserves fine-scale dynamic behavior. Our algorithm for adaptive anisotropic remeshing is simple to implement, takes up only a small fraction of the total simulation time, and provides substantial computational speedup without compromising the fidelity of the simulation. We also introduce a novel technique for strain limiting by posing it as a nonlinear optimization problem. This formulation works for arbitrary non-uniform and anisotropic meshes, and converges more rapidly than existing solvers based on Jacobi or Gauss-Seidel iterations.

Link of the Week: Expanding Knowledge through Social Networks

How can knowledge be spread rapidly across large populations using social media? To explore this question, researchers at the University of California, Berkeley, have launched a new that allows visitors to spread the word quickly about important issues. The key is a novel “influence score” that quantifies the role each participant plays and illustrates each user’s social graph through a unique visualization.

The UC Berkeley group is developing a general-purpose system that can be used for a wide variety of issues. The system will be tested on a timely and important issue: Proposition 30 on the November 2012 California ballot. Visitors to the project website can learn about Prop. 30 and receive a custom web link to share with their friends and family using email, Facebook or Twitter. Visitors can return at any time to view a visualization of their “influence” and track their influence score. After the election, the website will list the 50 “most influential people.”

Influence is computed using a variant of the Kleinberg and Raghavan algorithm, where each visitor’s influence increases for each person he or she recruits, by half a point for every person those people recruit, and so on down the line. The project, from the UC CITRIS Data and Democracy Initiative, emphasizes awareness and is careful to be unbiased. 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.