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Primeur weekly 2011-06-06

EuroFlash

Christliches Jugenddorfwerk Deutschlands chooses Altair's HiQube business intelligence solution to manage and analyze its enterprise business information

From dusk to dawn: Ship's bridge simulation reaches a new level with projectiondesign

Quantum knowledge cools computers

PRACE offers access to Europe's fastest supercomputers - third call launched

Record breaking data centre for genome sequencing opened in Norwich

Panaya named Red Herring Top 100 Europe Tech Startup

USFlash

Team solves decades-old molecular mystery linked to blood clotting

Virtual Prairie results published

New IBM Cloud services to address education challenges

Petaflops power to NERSC

ALICE supercomputer runs computationally intensive research with Panasas high performance storage

High-performance computing cluster is University of Iowa's largest 'supercomputer' ever

NCSA deploys new high-performance cluster dedicated to industrial use

Chameleon magnets: Ability to switch magnets 'on' or 'off' could revolutionize computing

MASSIVE supercomputer open for general use in Australia

University of Toronto scientist leads international team in quantum physics first

SGI names Praveen K. Mandal Senior Vice President of Engineering

Platform Computing cited positively in industry report on private Cloud market

Supermicro shapes the future with MicroCloud and multi-GPU SuperServers at Computex Taipei 2011

Mellanox introduces ConnectX-3, the industry's first FDR 56Gb/s InfiniBand and 10/40 Gigabit Ethernet multi-protocol adapter

SDSC researchers co-author and co-edit new book on Geoinformatics

HP brings greater simplicity, flexibility and intelligence to client virtualization portfolio

Oracle Insurance Policy Administration for Life and Annuity delivers superior performance on Oracle Exadata Database Machine X2-2

Dubuque, Iowa and IBM combine analytics, Cloud computing and community engagement to conserve water

Petaflops power to NERSC

31 May 2011 Berkeley - The US National Energy Research Scientific Computing Center (NERSC) recently marked a major milestone, putting its first petascale supercomputer into the hands of its 4,000 scientific users. The flagship Cray XE6 system is called "Hopper" in honour of American computer scientist Grace Murray Hopper; it is capable of more than one quadrillion floating point operations per second, or one petaflops, and is currently the second most powerful supercomputer in the United States, according to the TOP500 list.

Before this milestone, several pioneering users put the machine through its paces while making scientific discoveries in a broad set of areas, from fundamental science to clean energy alternatives and severe storm modelling.

"We are very excited to make this unique petascale capability available to our users, who are working on some of the most important problems facing the scientific community and the world", stated Kathy Yelick, NERSC Director. "With its 12-core AMD processor chips, the system reflects an aggressive step forward in the industry-wide trend toward increasing the core counts, combined with the latest innovations in high-speed networking from Cray. The result is a powerful instrument for science. Our goal at NERSC is to maximize performance across a broad set of applications, and by our metric, the addition of Hopper represents an impressive five-fold increase in the application capability of NERSC."

Peter Ungaro, president and CEO of Cray, emphasized the collaboration between the two organizations in tailoring the machine for NERSC. "Our partnership with NERSC has been important in further increasing these capabilities in our Cray XE6 supercomputer, not only for NERSC but for all our customers around the world. We worked together to improve the functionality and performance of our external services offerings from our Custom Engineering organisation, as well as put our new Gemini system interconnect to use across an amazingly broad set of scalable applications that needed all the performance they could get to achieve their scientific goals. We're proud that Hopper is the first petascale system at NERSC and I'm convinced it will be a great tool for their users as they strive toward the next scientific breakthroughs."

"Uptake of the Hopper system by early science users was quite impressive", stated Jonathan Carter, Computer Sciences Deputy and lead on the Hopper procurement project. "We started with a select set of users and gradually opened the system up to all interested users as the testing period progressed. From the earliest access, the system was heavily utilized and very popular."

Here is a selection of their stories:

  • Hopper paves the way for understanding DNA replication. Our DNA is damaged every day from exposure to the sun's ultraviolet light, secondhand smoke, toxins released by mold, and various other factors. Fortunately, nature has equipped us all with genes that repair and replicate DNA. But when these repair systems go awry, the result may be fatal cancerous tumours or degenerative diseases. A team of researchers from Georgia State University ran simulations on Hopper to understand the basic mechanisms of repair, which could lead to new preventions and treatments.

"My group has been very pleased with our experience running on Hopper", stated Ivaylo Ivanov, an assistant professor of chemistry at Georgia State University who is part of the team. "Our parallel jobs seem to scale much better on Hopper compared to similar systems. I suspect it has to do with the better processor interconnect network", he stated. "This makes it possible to run on many more processor cores and make quicker progress on our simulations."

  • Improving the accuracy of storm surge forecasts: In the event of a hurricane, storm surges are the greatest threat to life and property along the coast. In fact, experts estimate that most of the 1500 deaths caused by Hurricane Katrina were the result of a surge that occurred when winds that moved cyclonically around the storm in the Gulf of Mexico pushed water toward the shore. The ability to simulate these events on a computer is a powerful tool for evaluating risk, designing hurricane protection systems, planning evacuations and analyzing the physics of a storm.

Today, supercomputers built on parallel architectures with fast networks allow researchers to get these simulations with a fast turnaround. But their codes need to run at peak efficiency on tens of thousands of processors to get detailed results as fast as possible. After all, emergency planners typically need to get anywhere from two to four days of storm simulations in an hour of computer time to plan for human safety.

Researchers Seizo Tanaka and Patrick Kerr of the University of Notre Dame's Department of Civil Engineering and Geological Sciences, and Jay Ratcliff of the US Army Corps of Engineers tested the scalability of their high-resolution storm surge code using Hopper pre-acceptance time. "Advance time on Hopper has helped greatly in the scaling benchmarks as well in the simulations I've been performing related to hurricane modelling and sea level rise impacts", stated Jay Ratcliff.

  • Harnessing wind power with Hopper: Although wind power technology is close to being cost-competitive with fossil fuel plants for generating electricity, wind turbine installations still provide less than one percent of all U.S. electricity. Because scientists don't have detailed knowledge about how unsteady flows interact with wind turbines, many turbines underperform, suffer permanent failures or break down sooner than expected.

Since standard meteorological datasets and weather forecasting models do not provide detailed information on the variability of conditions needed for the optimal design and operation of wind turbines, researchers at the National Center for Atmospheric Research (NCAR) developed a massively parallel large-eddy simulation (LES) code for modelling turbulent flows in the planetary boundary layer - the lowest part of the atmosphere, which interacts with the shape and ground cover of the land.

With approximately 16,000 processor cores on Hopper, the NCAR team simulated the turbulent wind flows over hills in unprecedented resolution and increased the scalability of his code to ensure that it will be able to take advantage of peta- and exascale computer systems.

"The best part of Hopper is the ability to put previously unavailable computing resources toward investigations that would otherwise be unapproachable", stated Ned Patton of NCAR, who heads the investigation. "We seriously couldn't make the progress we have been without NERSC's support. We find NERSC's services to be fantastic and truly appreciate being able to compute there."
Source: NERSC

Back to Table of contents

Primeur weekly 2011-06-06

EuroFlash

Christliches Jugenddorfwerk Deutschlands chooses Altair's HiQube business intelligence solution to manage and analyze its enterprise business information

From dusk to dawn: Ship's bridge simulation reaches a new level with projectiondesign

Quantum knowledge cools computers

PRACE offers access to Europe's fastest supercomputers - third call launched

Record breaking data centre for genome sequencing opened in Norwich

Panaya named Red Herring Top 100 Europe Tech Startup

USFlash

Team solves decades-old molecular mystery linked to blood clotting

Virtual Prairie results published

New IBM Cloud services to address education challenges

Petaflops power to NERSC

ALICE supercomputer runs computationally intensive research with Panasas high performance storage

High-performance computing cluster is University of Iowa's largest 'supercomputer' ever

NCSA deploys new high-performance cluster dedicated to industrial use

Chameleon magnets: Ability to switch magnets 'on' or 'off' could revolutionize computing

MASSIVE supercomputer open for general use in Australia

University of Toronto scientist leads international team in quantum physics first

SGI names Praveen K. Mandal Senior Vice President of Engineering

Platform Computing cited positively in industry report on private Cloud market

Supermicro shapes the future with MicroCloud and multi-GPU SuperServers at Computex Taipei 2011

Mellanox introduces ConnectX-3, the industry's first FDR 56Gb/s InfiniBand and 10/40 Gigabit Ethernet multi-protocol adapter

SDSC researchers co-author and co-edit new book on Geoinformatics

HP brings greater simplicity, flexibility and intelligence to client virtualization portfolio

Oracle Insurance Policy Administration for Life and Annuity delivers superior performance on Oracle Exadata Database Machine X2-2

Dubuque, Iowa and IBM combine analytics, Cloud computing and community engagement to conserve water