Entries filed under “Computing Research”

News of research and the results of research within the high performance computing community.

Researchers Set New Simulation Speed Record on Sequoia Supercomputer

Over at Lawrence Livermore National Laboratory, Donald B Johnston writes that researchers at LLNL and Rensselaer Polytechnic Institute have set a high performance computing speed record that opens the way to the scientific exploration of complex planetary-scale systems.

In a paper to be published in May, the joint team will announce a record-breaking simulation speed of 504 billion events per second on LLNL’s Sequoia Blue Gene/Q supercomputer, dwarfing the previous record set in 2009 of 12.2 billion events per second. Participants included Peter Barnes, Jr. and David Jefferson of LLNL and CCNI Director and computer science professor Chris Carothers and Justin LaPre of Rensselaer. The records were set using the ROSS (Rensselaer’s Optimistic Simulation System) simulation package developed by Carothers and his students, and using the Time Warp synchronization algorithm originally developed by Jefferson.

This is an exciting time to be working in high-performance computing, as we explore the petascale and move aggressively toward exascale computing,” Carothers said. “We are reaching an interesting transition point where our simulation capability is limited more by our ability to develop, maintain and validate models of complex systems than by our ability to execute them in a timely manner.”

The calculations were completed while Sequoia was in unclassified “early science” service as part of the machine’s integration period. The system is now in classified service for the National Nuclear Security Administration’s Advanced Simulation and Computing program for stewardship of the nation’s nuclear weapons stockpile.

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Indiana University Helps NASA Manage Big Data for Operation IceBridge

Indiana University has contributed Big Data expertise and infrastructure to NASA’s Operation IceBridge, a decade-long polar ice monitoring project.

For the past four years, IU Research Technologies, a cyberinfrastructure and service center affiliated with the Pervasive Technology Institute (PTI), has provided IT support for the Center for Remote Sensing of Ice Sheets (CReSIS), a National Science Foundation Science and Technology Center led by the University of Kansas. Kansas scientists provide NASA with the radar technology that measures the physical interactions of polar ice sheets in Greenland, Chile and Antarctica. IU experts bring innovative data management and storage solutions to the missions.

Essentially, IU has built a supercomputer that can fly,” said Rich Knepper, manager of IU’s campus bridging and research infrastructure team within Research Technologies. “During this current mission, our system provided analysis of radar data as the data was collected – in real time — allowing mission scientists to see the ice bed information as the plane flies over the Arctic.”

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Quantum Leaps in Computing

Disruptive changes often originate from science labs, says David Power, head of HPC at Boston LTD.

Path-breaking findings coming from the pure sciences – new materials, chemical or physical properties, methods learnt from biological systems, etc. – often open up game-changing alternatives with the potential to disrupt the smooth flow of technological progress. And in the words of telecommunications expert and faculty at the Illinois Institute of Technology, Dr Suresh Borkar: “For continued progress, cross-disciplinary advances are needed in many areas including materials sciences, physical sciences, chemical sciences, biological sciences and mathematics.”

With this in mind, I have decided to celebrate the contributions of science to the field of computing, by discussing how pure science research could transform technology in the future and bring us closer to quantum computing.

Combining physics, mathematics and computer science, quantum computing has transformed from a visionary idea to one of the most fascinating areas of quantum mechanics in the last two decades. The circuits on a microprocessor will be measured on an atomic scale,’ explains Venkata Ramana, senior vice president, Hinditron-Cray India. ‘Quantum computers will harness the power of atoms and molecules to perform memory and processing tasks significantly faster than any silicon-based computer.”

The word ‘quantum’ is always used to refer to something immeasurably large. So when quantum physics finally meets computer engineering, just imagine what the resulting computer will be like! Today’s conventional computers represent information using two states, ‘0’ and ‘1.’ In contrast, quantum computers operate with more than two states. They encode information as quantum bits, or qubits, which can exist in superposition and because a quantum computer can manipulate information in multiple states simultaneously, it has the potential to be millions of times more powerful than today’s top supercomputers.

The good news is that scientists have already built basic quantum computers that can perform certain calculations, as proof-of-concept. A practical quantum computer is still years away. Most research in this field is still highly theoretical today,’ adds Ramana.

When quantum computing finally comes of age, points out Dr Suresh Borkar, we will have secure quantum computers, quantum routers and quantum Internet based on photonic networks with advanced encoding. He further explains that quantum computers would use quantum particles instead of binary bits – and this includes the use of impurities in materials, rare metal atoms and crystalline structures.

In 2012, a multinational team of researchers built a basic quantum computer inside a diamond. The team, funded by the US Army, tapped the impurities inside diamonds to build their quantum computer. The spins of two stray subatomic particles – a nitrogen nucleus and an electron – were used as the two qubits. Since electronics is susceptible to decoherence, the team also incorporated a level of protection using microwave pulses to continually switch the direction of electron spin rotation.

They also demonstrated the quantum properties of the computer using Grover’s Algorithm – a test developed in 1996 at Bell Labs to show the promise of quantum computing. The test involves searching an unsorted database, akin to searching for a name in a phone book when you have only the phone number. Generally, an average person or computer would find this in X/2 tries, if ‘X’ is the total number of choices. However, with superposition, a quantum computer can do this much faster. The new diamond computer picked the correct choice on first try, 95 per cent of the time.

One of the researchers commented that this demonstration suggests a pathway to increasingly complex quantum machines – ones that use qubit control protocols to circumvent the expected limitations from real materials. Could there be a better example of the progress that Dr Suresh Borkar expects to see from ‘cross disciplinary advances’? In this case, indeed, transcending conventional material sciences.

This story appears here as part of a cross-publishing agreement with Scientific Computing World.

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Video: Applying New Computing Techniques to Numerical Astrophysics

In this video from the HPC User Forum in Tucson, Brant Robertson from the University of Arizona presents: Applying New Computing Techniques to Numerical Astrophysics.

For more presentations, check out the HPC User Forum Video Gallery.

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Study: Extreme Weather to Increase, Doubling Economic Losses by 2050

Extreme weather events like Superstorm Sandy can cost lives and billions of dollars in damages.

Over at Oak Ridge National Labs, Katie Elyce Freeman writes that simulations show that losses from extreme weather damage could double by 2050.

 

A side effect of America’s growth has been the tendency to put more people, infrastructure and assets in harm’s way, and when a storm comes through, that increased exposure drives up economic losses,” said author Benjamin Preston, deputy director of ORNL’s Climate Change Science Institute, who studied historical data from more than 3,000 U.S. counties and used predictive modeling in the assessment.

Preston projected that current annual U.S. disaster losses of $10 billion to $13 billion could increase by a factor of 1.8 to 3.9 by 2050. Read the Full Story.

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GPU-based Brain Research Hits it Out of the Park

The robot’s task is to learn the timing needed to hit a flying ball, mimicking the sort of visual thinking humans use to quickly learn how to navigate through the real world.

Over at the Nvidia Blog, Brian Caulfield writes that researchers in Japan has used GPUs and the CUDA parallel programming model to create a 100,000 neuron simulation of the human cerebellum, one of the largest simulations of its kind in the world. And they’ve put their model to the test by applying this knowledge to teach a robot to learn to hit a ball.

Our physical actions change the environment, which changes the sensory input to human brain our sensation. The brain then processes this changed sensory information and determines what action to take. It is called the ‘sensorimotor loop,’” Igarashi explains. “The brain must continue to choose appropriate actions on the basis of gradually-changing sensory information.”

One of the biggest challenges in modeling neural brain function: simulation speed. Using a CPU alone it took 98 seconds of compute time to figure out how to respond to a stimulus lasting just one second. Using GPUs resulted in a 100x speedup, giving the GPU-based system the speed needed to handle real world tasks.

To show their system in action, the researchers demonstrated their robotic system learning – in real time – how to hit a small plastic ball thrown by a toy pitching machine with a round plastic racket. Yamazaki believes his work could result in robots within 5 years that rely on a silicon cerebellum that will allow them to “think” – that is, they would be able to assess their environment and organize movements autonomously.

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Predicting Twisters with HPC

A simulated radar image of a storm produced by CM1. The hook-like appendage in the southwest corner is an indication of a developing vortex.

Over at the National Institute for Computational Sciences, Scott Gibson writes that researchers are using HPC to enhance tornado prediction capabilities.

We hope that with a more accurate prediction and improved lead time on warnings, more people will heed the warnings, and thus loss of life and property will be reduced,” said Amy McGovern of the University of Oklahoma. McGovern is working to revolutionize the ability to anticipate tornadoes by explaining why some storms generate tornadoes and others don’t, and by developing advanced techniques for analyzing data to discover how the twisters move in both space and time.

To run each of McGovern’s simulations, graduate student Brittany Dahl is using 6,000 processor cores and 10 compute service units (hours) on the Kraken supercomputer. Read the Full Story.

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Video: Tales from the Grid – In Search of the Top Quark

In this video, Marcel Vreeswijk and Hurng-Chun Lee from the NIKHEF National Institute for Subatomic Physics explain how customized grid computing workflows are key to filtering LHC datasets down to a manageable size.

The Large Hadron Collider (LHC) is the world’s largest and most complex experiment, at the cutting edge of High Energy Physics. Particle physicists use the LHC to study variations from the Standard Model and discover potential new laws of physics. The particle known as the top quark is a window to this weird and wonderful world. The LHC produces enormous amounts of data, enough to fill piles of DVDs. Without these tools, it would be impossible to pick out the collision event that could hold the clues to top quark behaviour.

Check out more Tales from the Grid on YouTube.

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Obama Initiative Leverages Big Data to Explore the Brain

This week President Obama announced a research initiative that has the ambitious goal of “revolutionizing our understanding of the human brain,” according to a White House press release.

Know as BRAIN (Brain Research through Advancing Innovative Neurotechnologies), the initiative is being launched in FY 2014 with an initial budget of about $100 million, a modest amount given the project’s goals.

In short, BRAIN is designed to help researchers find “…new ways to treat, cure, and even prevent brain disorders, such as Alzheimer’s disease, epilepsy, and traumatic brain injury.” Included is support for new technologies that will allow researchers to produce dynamic pictures of the brain that show how individual brain cells and complex neural circuits interact in real time.

This is a foray into Big Data. The initiative will let researchers amass and analyze the data needed to “…explore how the brain records, processes, uses, stores, and retrieves vast quantities of information, and shed light on the complex links between brain function and behavior.”

Among the many public and private organizations involved in the effort are the National Institutes of Health (NIH), the Defense Advanced Research Projects Agency (DARPA), and the National Science Foundation (NSF). NSF in particular is leading the charge in applying the technologies and techniques of Big Data to the initiative.

The National Science Foundation will play an important role in the BRAIN Initiative because of its ability to support research that spans biology, the physical sciences, engineering, computer science, and the social and behavioral sciences,” according to the White House release. “The National Science Foundation intends to support approximately $20 million in FY 2014 in research that will advance this initiative, such as the development of molecular-scale probes that can sense and record the activity of neural networks; advances in ‘Big Data’ that are necessary to analyze the huge amounts of information that will be generated, and increased understanding of how thoughts, emotions, actions, and memories are represented in the brain.”

In a story in Information Week posted the same day, senior editor J. Nicholas Hoover, writes, “On a conference call with reporters after the President’s announcement, National Institutes of Health director Francis Collins said that the brain-mapping initiative might eventually require the handling of yottabytes of data. A yottabyte is equal to a billion petabytes.”

That’s Big Data at its mind-boggling best.

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Memory Cube Consensus Reached

More than 100 developer and adopter members of the Hybrid Memory Cube Consortium (HMCC) have announced that they have reached consensus for a global standard that will deliver a “much-anticipated, disruptive memory computing solution’”.

Developed in 17 months, the final specification marks the turning point for designers in a wide range of segments – from networking and high-performance computing, to industrial and beyond – to begin designing Hybrid Memory Cube (HMC) technology into future products.

A major breakthrough with HMC is the long-awaited utilisation of advanced technologies to combine high-performance logic with state-of-the-art dynamic random-access memory. With this first HMC milestone reached so quickly, consortium members have elected to extend their collaborative effort to achieve agreement on the next generation of HMC interface standards.

The consensus we have among major memory companies and many others in the industry will contribute significantly to the launch of this promising technology,’ said Jim Elliott, vice president for memory planning and product marketing at Samsung Semiconductor. ‘As a result of the work of the HMCC, IT system designers and manufacturers will be able to get new green memory solutions that outperform other memory options offered today.”

“This milestone marks the tearing down of the memory wall,’ said Robert Feurle, Micron’s vice president for DRAM Marketing. ‘The industry agreement is going to help drive the fastest possible adoption of HMC technology, resulting in what we believe will be radical improvements to computing systems and, ultimately, consumer applications.”

This story appears here as part of a cross-publishing agreement with Scientific Computing World.

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Hybrid CPU-GPU Chips Plus RDMA and PCI-Express Make for Screamin’ Iron

Over at The Register, Timothy Prickett Morgan writes that a GE presentation at the recent GPU Technology Conference discussed the benefits of Remote Direct Memory Access (RDMA) for InfiniBand and its companion GPUDirect method of linking GPU memories to each other across InfiniBand networks.

On plain old CPUs, RDMA allows CPUs running in one node to reach out through an InfiniBand network and directly read data from another node’s main memory, or push data to that node’s memory without having to go through the operating system kernel and the CPU memory controller. If you prefer 10 Gigabit Ethernet links instead, there is an RDMA over Converged Ethernet, or RoCE, wrapper that lets RDMA run on top of Ethernet – as the name suggests. With GPUDirect, which is something that InfiniBand server adapter and switch maker Mellanox Technologies has been crafting with Nvidia for many years, the idea is much the same. Rather than having a GPU go back to the CPU and out over the network to get data that has been chewed on by another GPU, just let the GPUs talk directly to each other over InfiniBand (or Ethernet with RoCE) and get the CPU out of the loop.

GE's IPN251 hybrid computing card marries a Core i7, a Xilinx FPGA, and an Nvidia Kepler GPU with a PCI switch

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DSSD is Andy Bechtolsheim’s Secret Chip Startup for Big Data

Over at GigaOm, GigaStacey writes that the solution for better and faster storage may lie in DSSD, a stealthy chip startup backed by Andy Bechtolsheim. Founded in 2010 by Sun Alums Jeff Bonwick and Bill Moore, DSSD is trying to build a chip that would improve the performance and reliability of flash memory for high performance computing, newer data analytics, and networking.

My sources tell me the startup is building a new type of chip — they said it’s really a module, not a chip — that combines a small amount of processing power with a lot of densely-packed memory. The module runs a pared-down version of Linux designed for storing information on flash memory, and is aimed at big data and other workloads where reading and writing information to disk bogs down the application. This fits with the expertise of the team, but this is a problem that others are trying to solve as well with faster and cheaper SSDs and targeted software to to optimize the flow of bits to a database. But the proposal here appears to be about designing an operating system that takes advantage of the difference in Flash memory when compared to hard drives to boost I/O.

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GPUs Help Californians Prepare for Earthquakes

Over at the Nvidia Blog, Roy Kim writes that SDSC researchers are using NVIDIA Tesla K20X GPU accelerators to help improve earthquake forecasts, enabling engineers to design safer buildings and save lives. The power of GPUs enabled SDSC to run high-frequency, compute-intensive wave propagation simulations to better understand how a broad range of structures will respond in a major quake.

To meet the needs of the CyberShake 3.0 project, Cui realized they would need 750 million CPU hours on a traditional CPU-based supercomputer, costing over $800,000 just in power cost to support his simulations. That’s when they turned to GPUs for help. AWP-ODC, the research team’s primary seismic application, is more than 5x faster when run with GPUs, allowing researchers to discover insights they would not have been able to before. At the same time, they would save over $600,000 in power costs for their simulations. Less than a month ago, Cui’s team achieved over one petaflop of performance running on over 8,000 GPUs on the Titan supercomputer, shattering their previous record of 220 teraflops of sustained performance on Oak Ridge’s Jaguar supercomputer.

This video from Amit Chourasia at SDSC depicts a magnitude-8 earthquake in the northern San Andreas Fault.

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IU awarded $1.1 million to Advance Supercomputer Programmability

Indiana University’s Center for Research in Extreme Scale Technologies (CREST) is the recipient of a three-year, $1.1 million grant from the US Department of Energy (DOE) to develop software that improves the speed and programmability of supercomputers. This funding is part of a $7.05 million grant for the XPRESS (eXascale PRogramming Environment and System Software) project, led by Sandia National Laboratories as part of the DOE Office of Science Advanced Scientific Computing Research X-Stack programme.

As part of the Pervasive Technology Institute to pioneer research at the frontiers of exascale computing, CREST was created by IU in 2011. Andrew Lumsdaine and Thomas Sterling, both professors in the School of Informatics and Computing at IU Bloomington, lead CREST as director and associate director, respectively. Sterling also serves as CREST’s chief scientist.

We’re writing software that moves execution from static to dynamic, allowing supercomputers to use new information as it is being revealed,’ commented Sterling. ‘By doing so, supercomputers will “think” about how they use their resources, as well as where and when they schedule various concurrent tasks.” He added: “Our goal is to completely redesign the system software in order to produce a revolutionary class of supercomputers. It is exciting that IU will be at the forefront of such research, setting future directions for exascale computing and programming.”

This story appears here as part of a cross-publishing agreement with Scientific Computing World.


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Video: Challenging Large-Data Problems at NASA

In this video from the 2013 National HPCC Conference, Dr. Tsengdar Lee from NASA presents: Challenging Large-Data Problems at NASA.

NASA’s observations from Earth-orbiting satellites and outputs from computational climate models have contributed to one of the most data-intensive scientific disciplines today. The Earth system science tries to analyze the data, turns the data into information, makes sense of the information into knowledge and wisdom, utilize the knowledge and wisdom in decision making processes. In every step of the data life cycle workflow (i.e. curation, discovery, access, and analysis), NASA faces tremendous challenges.”


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