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InTheLoop | 08.13.2012

August 13, 2012

Big Data Means Big Issues for Exascale Visualization

When exascale computers begin calculating at a billion, billion operations each second, gaining insights from the massive datasets generated by the simulations they run will be a huge challenge. Scientists may be tempted to pause the simulation, effectively “holding the machine hostage” as they scramble to create meaningful portrayals of the data barrage, says Hank Childs, a computer systems engineer in Berkeley Lab’s Computational Research Division (CRD). Childs, a recent recipient of a $2.5 million Department of Energy Early Career Research Program award, is out to prevent that. Read more.


In the News: A Big Data Revolution in Astrophysics

Datanami, the big data news portal, has posted a presentation by Peter Nugent, co-leader of Berkeley Lab’s Computational Cosmology Center, on “The Big Data Revolution in Astrophysics: A Case Study of the Palomar Transient Factory.” Nugent is Realtime Transient Detection Lead for the PTF. The Datanami post begins with a summary and commentary by Ian Foster of Argonne National Laboratory. Read more.


CRD's Julian Borrill Helps Unveil Cambridge’s Cosmology Supercomputer

Julian Borrill, co-leader of the Computational Cosmology Center, gave an invited talk on “Big Bang, Big Data, Big Iron: High Performance Computing and the Cosmic Microwave Background” at the Numerical Cosmology 2012 conference held July 17–20 at Cambridge University in England.

Borrill also chaired the session in which the university’s new supercomputer, COSMOS—the most powerful shared-memory supercomputer in Europe—was officially launched. Professor Stephen Hawking participated in the ceremony inaugurating COSMOS. Read more.


DOE ACTS Collection Software Workshop This Week

The Workshop on the DOE Advanced Computational Software (ACTS) Collection, Scalable and Robust Computational Libraries and Tools for High-End Computing, will be held at Sutardja Dai Hall on the UC Berkeley campus Tuesday through Friday this week, August 14–17, 2012. This is the thirteenth workshop in a series organized by Tony Drummond and Osni Marques of CRD. The NSF-funded XSEDE partnership will again broadcast the ACTS Workshop tutorials to member HPC sites.

The workshop will include a range of tutorials on the libraries and tools currently available in the collection, discussion sessions aimed to solve specific computational needs by the workshop participants, and hands-on practice using supercomputers at NERSC. On-site attendance this year is full, so there will be no walk-ins, but webcasts can be viewed at mms://media.citris.berkeley.edu/ACTS.

This year there are 45 attendees—graduate students, postdoctoral fellows, faculty, and research scientists from academia and industry—as well as 15 speakers, mostly from DOE national laboratories. Presentations and hands-on sessions led by CS staff include an introduction to the ACTS Collection and SLEPc by Tony Drummond, SuperLU and ScaLAPACK by Osni Marques, VisIt by Harinarayan Krishnan, and an invited talk on Programming Models for Exascale by Kathy Yelick.

Over the years, more than 500 computational scientists have participated in the ACTS Workshops, teaching them how to fast-track the development of efficient, high-performance applications. Workshop participants also have an opportunity to engage with tool developers and eventually add functionality to the tools.


CRD Staff Invited to Speak at Numerical Methods Workshop in China

Xiaoye Sherry Li and Ming Gu of CRD have been invited to speak at the Workshop on Efficient Numerical Methods for Partial Differential Equations being held this week, August 13–18, in Urumqi, China. Li will speak on “Fast and Memory-Efficient Approximate Sparse Factorizations Using Hierarchically Semi-Separable Matrix Structures,” and Gu will present “Low-Rank Matrix Approximations and Randomized Sampling.”


NERSC’s Cody Rotermund Receives EHS Safety SPOT Award

NERSC Computer Operations and ESnet Support Group member Cody Rotermund was awarded an EHS Safety SPOT award for his good response to an employee complaint.

An employee reported to the Oakland Scientific Facility Control Room complaining of dust from under the computer floor and asked for a tissue. NERSC control room operator Rotermund remembered that a tissue is not recommended for use in the eye, and that the first aid kit was stocked with mini-size 200 mL eyewash bottles. He provided this eyewash to the employee and requested a re-stock of the first aid kit.

Go here to see other recent EHS safety spot awards.


Registration Deadline Today for Par Lab Boot Camp

The 2012 Pab Lab Boot Camp—Short Course on Parallel Programming, which is being held Wednesday through Friday this week (August 15–17) in the Banatao Auditorium, Sutardja Dai Hall at UC Berkeley, is intended to offer programmers a practical introduction to parallel programming techniques and tools on current parallel computers, emphasizing multicore and manycore computers. Participants can choose to attend on campus or online. Presenters include UCB/CRD faculty researcher Jim Demmel, Associate Lab Director Kathy Yelick, and David Skinner of NERSC.

The course will provide an introduction to parallel architectures and programming issues, a thorough exposure to languages and tools for shared memory programming, including hands-on experience, a presentation of high level programming parallel programming patterns and libraries that can greatly simplify programming, an overview of programming on other important parallel architectures (GPUs, clouds, and distributed memory machines), and in-depth discussions of a variety of exciting parallel applications from image recognition, computer music, and other areas. See the preliminary agenda.

Registration is free to anyone affiliated with Berkeley Lab. Register here today.


Female Engineers Needed for Exploratorium Event

The Exploratorium in San Francisco is seeking female engineers to serve as role models and to help facilitate hands-on activities on one day, or multiple days, during the “Girl Science Institute: Engineering Thermodynamics” from 9:30 am–3:30 pm on August 20–23, 2012.

This four-day workshop for sixth and seventh grade girls explores engineering thermodynamics—the difference between heat and temperature, how heat flows, and the types and uses of heat engines. Volunteers from any engineering discipline will help facilitate hands-on activities, share their lives and work with the girls, and serve as role models to the girls.

If you are a female engineer who is interested in sharing your love for your work with young girls and helping to encourage the next generation of female engineers, please contact Cassie Byrd at cbyrd@exploratorium.edu or by phone at 415-674-2824.


This Week’s Computing Sciences Seminars

Making Effective Use of Compilers at NERSC
Wednesday, August 15, 11:00 am–12:00 pm, OSF 943-238 and WebEx online
Michael Stewart, NERSC User Services Group

This talk will describe and compare compilers available on Hopper. The strengths and weaknesses of each will be described and a set of best practices presented. There will also be a shorter description of the Carver compiling environment and a preview of the NERSC-7 compiling environment.

Please register here (no fee).


Link of the Week: How Apple and Amazon Security Flaws Led to Epic Hacking

In Wired magazine, Mat Honan reports:

In the space of one hour, my entire digital life was destroyed. First my Google account was taken over, then deleted. Next my Twitter account was compromised, and used as a platform to broadcast racist and homophobic messages. And worst of all, my AppleID account was broken into, and my hackers used it to remotely erase all of the data on my iPhone, iPad, and MacBook.

This incident exposes vital security flaws in several customer service systems. The very four digits that Amazon considers unimportant enough to display in the clear on the web are precisely the same ones that Apple considers secure enough to perform identity verification. 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.