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InTheLoop | 05.05.2014

May 5, 2014

NERSC, Cray, Intel Collaborate on Next-Gen Supercomputer

The U.S. Department of Energy’s (DOE) National Energy Research Scientific Computing (NERSC) Center and Cray Inc. announced last week that they have signed a contract for a next generation of supercomputer to enable scientific discovery at the DOE’s Office of Science (DOE SC).

Lawrence Berkeley National Laboratory (Berkeley Lab), which manages NERSC, collaborated with Los Alamos National Laboratory and Sandia National Laboratories to develop the technical requirements for the system. Scheduled for delivery in mid-2016, the new system will deliver 10x the sustained computing capability of NERSC’s Hopper system, a Cray XE6 supercomputer.

NERSC is the DOE SC’s primary high performance computing (HPC) facility, supporting more than 5,000 scientists working on 700 projects each year. The $70 million plus contract represents the DOE SC’s ongoing commitment to enabling extreme-scale science to address challenges such as developing new energy sources, improving energy efficiency, understanding climate change, developing new materials and analyzing massive data sets from experimental facilities around the world. »Read more.

NERSC Sponsors Nobel Lecture Series

In honor of its 40th Anniversary, NERSC is sponsoring a series of lunchtime lectures describing the research behind four Nobel Prizes. The featured Laureates are long-time users of NERSC’s supercomputing resources. Starting May 20 and running through June 11, the weekly lectures start at noon and run until 1:30pm. The first three talks will be held in the Lab's Building 66 auditorium. The final lecture (June 11) will take place in Lab's Building 50 auditorium.

UC Berkeley staff and students may ride the Lab shuttle to the lectures with a valid Cal ID. Please be prepared to tell the driver which building you are visiting, as well. »Get bus schedules and stops.

Tuesday, May 20: John Kuriyan, UC Berkeley

Member of Martin Karplus’ team – 2013 Nobel Prize in Chemistry
“Molecular Dynamics Simulations and the Mechanisms of Protein Complexes”
Berkeley Lab, Bldg. 66 auditorium, 12 noon to 1:30 p.m.

Wednesday, May 28: Warren Washington, National Center for Atmospheric Research (NCAR)

2007 Nobel Prize as a member of the Intergovernmental Panel on Climate Change
“The Brief History and Future Development of Earth System Models: Resolution and Complexity”
Berkeley Lab, Bldg. 66 auditorium, 12 noon to 1:30 p.m.

Tuesday, June 3: George Smoot, Lawrence Berkeley National Lab and UC Berkeley

2006 Nobel Prize in Physics
“Mapping the Universe”
Berkeley Lab, Bldg. 66 auditorium, 12 noon to 1:30 p.m.

Wednesday, June 11: Saul Perlmutter, Lawrence Berkeley National Lab and UC Berkeley

2011 Nobel Prize in Physics
“Data, Computation and the Fate of the Universe”
Berkeley Lab, Bldg. 50 auditorium, 12 noon to 1:30 p.m.

CRD's Michael Wehner a Lead Author on White House's 'Third National Climate Assessment'

Michael Wehner, a climate scientist in the Computational Research Division, is a lead author for the "Third National Climate Assessment" report, which the White House has announced will be released tomorrow, May 6. Wehner was also a member of the lead author team for the 2009 White House report, “Global Climate Change Impacts in the United States” and is a lead author for the "Fifth Assessment Report of the Intergovernmental Panel on Climate Change."

D-Wave Representatives to Discuss Quantum Computing in May 6 Presentation

Representatives from D-Wave, the first commercial quantum computing company, will discuss the company’s technologies in a talk beginning at 9:30 a.m. Tuesday, May 6, in Bldg. 50A-5132. The presentation will briefly review D-Wave which claims to have built the world’s first commercial quantum computing systems. D-Wave has created a unique quantum computer that uses superconducting circuits to create systems with up to 500 qubits today in a “quantum annealing” architecture.  They will discuss the hardware, architecture, programming models and some applications. Also attending will be Bo Ewald, President, D-Wave U.S., and Steve Empedocles.

Founded in 1999, the company released its first commercial system, the D-Wave One quantum computer in 2010.  In 2013, D-Wave shipped its 512-qubit D-Wave Two system. Another focus of the company is developing different layers of software to make the systems easier to use and more accessible to users.
 

Atomic Switcheroo Explains Origins of Thin-Film Solar Cell Mystery

Scientists have known since the 1980s that treating cadmium-telluride (CdTe) solar cell materials with cadmium-chloride improves efficiency, but the underlying physics have remained a mystery until now. Combining electron microscopy with computer simulations run at the Department of Energy’s National Energy Research Scientific Computing Center (NERSC), researchers have put this decades long debate to rest. Their findings could lead to a less-expensive, more easily fabricated, thin-film alternative to silicon-based photovoltaics. »Read more.

CS Staff to Speak at May 4-8 Cray Users Group Annual Meeting

Staff from CRD, ESnet and NERSC will be among the presenters this week at the Cray Users Group meeting hosted by the Swiss National Supercomputing Centre in Lugano, Switzerland. CUG 2014 will look at all emerging supercomputing platforms. Users, developers and administrators will have opportunities to discuss and debate the impending future of supercomputing, in which the architectures for exascale computing are beginning to emerge.

  • Tina Butler of NERSC will chair a technical session and give a talk on “Using Resource Utilization Reporting to Collect DVS Usage Statistics.
  • Andrew Canning of CRD will discuss “A Hybrid MPI/OpenMP 3D FFT for Plane Wave Ab-intio Materials Science Codes.”
  • Shane Canon, Nick Cardo, Jason Hick and David Skinner, all of NERSC, and ESnet’s Eli Dart will be part of a discussion on “HPC’s Pivot to Data.
  • Tina Declerck of NERSC will give talk on “Using Robinhood to Purge Lustre Filesystems” and will join NERSC’s Zhengji Zhao in a discussion on “I/O performance on Cray XC30.
  • Xiaoye “Sherry” Li of CRD will give a talk on “Scalable Hybrid Programming and Performance for SuperLU Sparse Direct Solver on Cray's Manycore Architectures.”

CRD’s Sherry Li to Give Invited Talk at KAUST Workshop on Extreme Computing Algorithms

Sherry Li, a member of CRD’s Scientific Computing Group, will give a talk on “Towards an optimal-order approximate sparse factorization exploiting hierarchically semi-separable structure” at the Second Scalable Hierarchical Algorithms for eXtreme Computing (SHAXC-2) workshop. The workshop will be held May 4-6 will be held at King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
 
The second workshop on Scalable Hierarchical Algorithms for eXtreme Computing (SHAXC-2) focuses international expert attention on prospects for mapping major hierarchical algorithms of scientific computing onto emerging computer architectures. The workshop is sponsored by KAUST’s Strategic Initiative for Extreme Computing.
 
On her return trip, Li will attend part of the Cray Users Group meeting in Lugano, Switzerland, where she will present “Scalable Hybrid Programming and Performance for SuperLU Sparse Direct Solver on Cray's Manycore Architectures” on Thursday, May 8.
 

CRD’s Andrew Canning to Give Three Talks in Switzerland This Week

Andrew Canning of CRD’s Scientific Computing Group will give three talks over the coming week, starting with a presentation on “A Hybrid MPI/OpenMP 3D FFT for Plane Wave Ab-intio Materials Science Codes” on Thursday, May 8 at the Cray Users Group meeting at the Swiss National Computing Center (CSCS). Friday, Canning will give an invited talk at CSCS on “A Hybrid MPI/OpenMP approach for Plane Wave Ab-intio Materials Science Codes on the Cray XC30 and XE6.” The following Monday, Canning will give an invited talk at ETH Zurich, the Swiss Federal Institute of Technology. Canning’s presentation will be on “A Hybrid MPI/OpenMP approach for Plane Wave Ab-intio Materials Science Codes and Applications to Photovoltaic and Detector Materials.”

This Week's CS Seminars

Using the D-Wave Quantum Computer

Tuesday, May 6, 9:30am - 10:30am, Bldg. 50A, Room 5132
Denny Dahl and Aaron Lott, D-Wave Inc.

This presentation will briefly review D-Wave and its products - the world’s first commercial quantum computing systems. D-Wave has created a unique quantum computer that uses superconducting circuits to create systems with up to 500 qubits today in a “quantum annealing” architecture. We will describe the hardware, architecture, programming models and some applications.

Computing the asymptotic spectrum for networks representing energy landscapes

Wednesday, May 7, 3:30PM–4:30PM, 939 Evans Hall, UC Berkeley Campus
Maria Cameron, University of Maryland

The concept of metastability has garnered a lot of interest in recent years. The spectral decomposition of the generator matrix of a stochastic network exposes all of the transition processes in the system while it evolves toward the equilibrium. I discuss an efficient way to compute the asymptotics for eigenvalues and eigenvectors starting from the low lying group for networks representing energy landscapes. I apply this algorithm to Wales's Lennard-Jones-38 stochastic network with 71887 states and 119853 edges whose underlying potential energy landscape has a double-funnel structure. The result turns out to be surprising at the first glance. The concept of metastability should be applied with care to this system.

Tactical High Throughput Computing at NERSC and Beyond

Wednesday, May 7, Noon–1:00PM, NERSC-OSF, Room 238
Stephen Bailey, Berkeley Lab

NERSC has traditionally excelled at high performance computing, where a relatively small number of batch jobs use a large number of cores each.  An increasingly important contrasting case is high throughput computing, where analyses need to perform a very large number of independent tasks, each of which uses only a few cores.  Managing these workflows via traditional batch jobs is inefficient for both humans and the batch queuing system.  I will describe our "Tactical High Throughput Computing" LDRD and the "qdo" toolkit designed to simplify high throughput computing at NERSC and beyond.  qdo scales to millions of tasks within existing batch systems while maintaining a simple lightweight user interface.  It supports task dependencies, priorities, management of tasks in aggregate, and flexibility such as adding additional tasks to a queue even after the batch worker jobs have started.  Even for small workflows, qdo enables scientists to focus on their data analysis rather than the management of boilerplane batch scripts or complicated config files to define a workflow.  This will be an informal, hands on talk — bring your laptop to try out qdo in realtime and offer your feedback on our features, usability, and roadmap.

NWChem: quantum chemistry across spatial, energy, and time (to solution) scales

Thursday, May 8, 1pm - 2pm, Bldg. 50F, Room 1647
Karol Kowalski, WR Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory (PNNL)

In this presentation we will discuss the development of scalable and unique computational chemistry capabilities for modeling and simulation in NWChem, and we will demonstrate its performance on large scale computing platforms. NWChem is DOE’s premier quantum chemistry software developed at the Environmental Molecular Science Laboratory at Pacific Northwest National Laboratory, and is available to the scientific community through the open-source Educational Community License. We will discuss several new parallel algorithms for many-body methodologies, which are capable of taking advantage of existing peta-scale architectures. Special emphasize will be given to the novel algorithms which can utilize the aggregate power of heterogeneous computer architectures.

Link of the Week: The 'Cosmos' Connection

"Science is no longer the wallflower who doesn’t get asked to the dance," physicist and DOE-SC program manager Glen Crawford asserted in a recent essay about science outreach. Making his case in Symmetry, the physics magazine jointly produced by the SLAC National Accelerator Laboratory and Fermilab, Crawford reflects on the flowering popularization of science in the four decades between the launch of Carl Sagan's "Cosmos" television series on PBS and the recent relaunch of the series with celebrity scientist Neil deGrasse Tyson. The fact that it's even possible to say "celebrity scientist" with a straight face is all down to Sagan, who was sometimes ridiculed by fellow researchers for his common touch. Today, scientists don't need a nationally syndicated TV show to join the conversation. The Internet's powerful grip on the public's imagination, Crawford argues, gives scientists more opportunity, and more responsibility, than ever to share their passion. "So I ask my science colleagues: When the music starts, are you going to stare at the floor and shuffle your feet, or are you going to show ‘em what you’ve got?" he asks. »Read more.