Entries filed under “Computing Research”

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

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.

Read the Full Story.

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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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Gordon Supercomputer Powers Battle against Autism

Researchers are using the unique capabilities of the flash-powered Gordon supercomputer at SDSC to find transcription factors that could be used to treat mental disorders such as autism.

We live in the unique time when huge amounts of data related to genes, DNA, RNA, proteins, and other biological objects have been extracted and stored,” said lead author Igor Tsigelny, a research scientist with SDSC as well as with UC San Diego’s Moores Cancer Center and its Department of Neurosciences. “I can compare this time to a situation when the iron ore would be extracted from the soil and stored as piles on the ground. All we need is to transform the data to knowledge, as ore to steel. Only the supercomputers and people who know what to do with them will make such a transformation possible,” he said.

Last month, a team of researchers from SDSC, the United States and the Institute Pasteur in France reported in the journal Genes, Brain and Behavior that they used Gordon to devise a novel way to describe a time-dependent gene-expression process in the brain that can be used to guide the development of treatments for mental disorders such as autism-spectrum disorders and schizophrenia. The researchers identified the hierarchical tree of coherent gene groups and transcription-factor networks that determine the patterns of genes expressed during brain development. They found that some “master transcription factors” at the top level of the hierarchy regulated the expression of a significant number of gene groups.

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Video: Amazing DigiCortex Engine Maps the Brain with GPUs

In this video from the 2013 GPU Technology Conference, Ivan Dimkovic and Ana Balevic describe the ground-breaking DigiCortex Engine. Recently ported to CUDA, the application has seen huge speedups with GPU computing.

DigiCortexis my hobby project implementing large-scale simulation and visualization of biologically realistic cortical neurons, synaptic receptor kinetic, axonal action potential propagation delays as well as long-term and short-term synaptic plasticity. Current version of DigiCortex is heavily optimized for Intel CPUs (including Sandy Bridge AVX instruction set). The first CUDA-enabled version with GPU acceleration (CUDA optimizations done by Ana Balevic) is available as of v0.95

The simulation footage in this video is really gorgeous, so be sure to watch it in HD mode. Read the Full Story.

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Nvidia to Stack DRAM on Future ‘Volta’ GPUs

Over at The Register, Timothy Prickett Morgan writes that Nvidia has announced plans to stack up DRAM on future ‘Volta’ GPUs to deliver over 1TB/sec of memory bandwidth. Due sometime around 2016, Volta’s memory technology will bring memory closer to the GPU, increasing bandwidth while reducing latency.

Volta is going to solve one of the biggest issues with GPUs today, which is access to memory bandwidth,” explained Huang. “The memory bandwidth on a GPU is already several times that of a CPU, but we never seem to have enough.” So with Volta, Nvidia is going to get the memory closer to the GPU so signals do not have to come out of the GPU, onto a circuit board, and into the GDDR memory. This current approach takes more power (you have to pump up the signal to make it travel over the board), introduces latencies, decreases bandwidth.

In related projects, Micron, Intel, and IBM are partnering on an effort to stack up DRAM, with hopes to commercialize something in the next few years. Read the Full Story.

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Day 2 Keynote from GTC: Parallel Processing of the Genomes



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At insideHPC, we are very pleased to bring you live streaming keynotes from the GPU Technology Conference this week in San Jose.

In this video, Erez Lieberman Aiden from the Baylor College of Medicine presents a keynote talk entitled: Parallel Processing of the Genomes, by the Genomes and for the Genomes.

The human genome is a sequence of 3 billion chemical letters inscribed in a molecule called DNA. Famously, short stretches (~10 letters, or “base pairs”) of DNA fold into a double helix. But what about longer pieces? How does a 2 meter long macromolecule, the genome, fold up inside a 6 micrometer wide nucleus? And, once packed, how does the information contained in this ultra-dense structure remain accessible to the cell? This talk will discuss how the human genome folds in three dimensions, a folding enables the cell to access and process massive quantities of information in parallel. To probe how genomes fold, we developed Hi-C, together with collaborators at the Broad Institute and UMass Medical School. Hi-C couples proximity-dependent DNA ligation and massively parallel sequencing. To analyze our data and reconstruct the underlying folds, we, too must engage in massively parallel computation. I will describe how we use NVIDIA’s CUDA technology to analyze our results and simulate the physical processes of genome folding and unfolding.


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Record Simulations Conducted on Lawrence Livermore Supercomputer

Over at Lawrence Livermore, Breanna Bishop writes that researchers at LLNL have performed record simulations using all 1,572,864 cores of the Sequoia supercomputer. As the first supercomputer to exceed one million computational cores, Sequoia is also is No. 2 on the TOP500 with 16.3 petaflops of performance.

SIRIS simulation on Sequoia of the interaction of a fast-ignition-scale laser with a dense DT plasma.

The simulations were performed by Frederico Fiuza, a physicist and Lawrence Fellow at LLNL. Designed to study the interaction of ultra-powerful lasers with dense plasmas in a proposed method to produce fusion energy, the project is part of the U.S. Department of Energy’s Office of Fusion Energy Science Program.

Using the OSIRIS code, Fiuza demonstrated excellent scaling in parallel performance to the full 1.6 million cores of Sequoia. By increasing the number of cores for a relatively small problem of fixed size, what computer scientists call “strong scaling,” OSIRIS obtained 75 percent efficiency on the full machine. But when the total problem size was increased, what is called “weak scaling,” a 97 percent efficiency was achieved.

This means that a simulation that would take an entire year to perform on a medium-size cluster of 4,000 cores can be performed in a single day. Alternatively, problems 400 times greater in size can be simulated in the same amount of time,” Fiuza said. “The combination of this unique supercomputer and this highly efficient and scalable code is allowing for transformative research.”

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Grand Challenges Déjà Vu

In this special guest feature, Doug Black from The Exascale Report writes that, while the idea of Grand Challenges is not new, the need for powerful computational tools to solve these global issues remains unchanged.

Flash back to 1992. Do you remember the ‘Blue Book’ and the HPCC program? If this is your first exposure to the ‘Grand Challenges’ you may find this quite interesting. On November 7, 2012, senior representatives of the DOE labs sent a letter to Secretary of Energy, Steven Chu to report on a Grand Challenges Workshop on Advanced Computing for Energy Innovation held in late July – early August 2012.

While the workshop recommendations focused on what it called Technical, Structural and Incentive ‘Grand Challenges’, one of its final recommendations was to establish an Advanced Computing for Energy (ACE) program within the Department of Energy. When I read this letter, I had an intense sense of déjà vu – one of those ‘here we go again’ feelings. But in a good way.

For a moment, it felt like 1992 all over again, a year of unusually high energy and high promise in the HPC community. It’s the year we really sank our teeth into the teraFLOPS challenge. It seemed the entire community rallied in support of what the first President Bush’s science advisor, Alan Bromley, labeled the Grand Challenges – referring to high performance computing and communications. Those Grand Challenges were the challenges of science.

It was the beginning of a period of powerful government and private industry collaboration referred to as the HPCC program. I pulled this quote from the program’s overview documentation: The HPCC Program is driven by the recognition that unprecedented computational power and capability is needed to investigate and understand a wide range of scientific and engineering “grand challenge” problems.

The program’s famous “Blue Book” also made this point:

The HPCC Program is the result of several years of effort on the part of senior government, industry, and academic scientists and managers to design a research agenda to extend U.S. leadership in high performance computing and networking technologies.

So, in many ways, nothing has really changed. Again, I mean this in a good way. The 2012 appeal to address the world’s ‘Grand Challenges’ is eerily similar to what we addressed 20 years ago. HPC is an ever widening circle that keeps coming around. Twenty years ago, the Grand Challenges included climate prediction and genome mapping. Today, the great need is energy innovation and saving the environment. Tomorrow, it may be food. This is HPC and that’s how HPC works, tackling as ever the need for funding and the need for urgency to apply extreme computational resources on the greatest scientific challenges of our time.

Download the Story (PDF).

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Building the Massive Simulation Sets Essential to Planck Results

Using NERSC supercomputers, Berkeley Lab scientists are generating thousands of simulations to analyze the flood of data from the Planck mission. As a project of the European Space Agency, the Planck satellite mission has been collecting trillions of observations of the sky since the summer of 2009.

The sheer volume of the Planck data, with about a trillion observations of a billion points on the sky, means that the techniques of exact analysis we used in the past for the data from balloon flights are no longer tractable,” says Julian Borrill of the Computational Research Division. “Instead we have to use approximate methods, and because they’re approximate, we have to worry about their possible uncertainties and biases. The only way to be sure of the Planck analysis is to compare it with a huge suite of Monte Carlo simulations, long known to be the most challenging aspect of the computation. In preparation, Borrill’s group at C3 has gradually built up their simulation capability for over a decade, tuning it to each new generation of NERSC supercomputers. The result is a suite of massively parallel codes running on NERSC’s 150,000-core Cray XE6 Hopper.

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Interview: How Supercomputers Power Graphene Research

Over at HPC Wales, Biagio Lucini from Swansea University describes how essential supercomputing resources are to his research in the “miracle material” that is graphene.

Our work involves characterising Graphene from its theoretical properties. The material has enormous potential but is not in use on a large scale as of yet, as we don’t know enough about its characteristics. Using supercomputers we will be able to develop an understanding of its theoretical properties using numerical simulations.

Lucini goes on to say that there is a lot of confusion in the outside world about what HPC is and what it is not, and that seeking the right expertise is essential. Read the Full Story.

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TACC Supercomputers Help Researchers Design Useful Organisms

Can scientists enlist bacteria to help save the planet? University of Texas professor Jeffrey Barrick is using TACC supercomputers to understand radical mutations and design artificial organisms.

As described in the September 2012 issue of Nature, Barrick’s research studied the rapid evolution of E. coli to trace key changes that lead to an evolutionary innovation. Using next-generation DNA sequencers and the powerful Lonestar and Ranger supercomputers at TACC, he was able to test 40 genomes from the population and trace the key changes that potentiated the mutation and showed the role of promoter capture and altered gene regulation in evolutionary innovations.

I think a lot about the engineering aspect: making bacteria do useful things,” Barrick said. “I would like bacteria to solve our energy crisis, whether that means making biofuels or something crazy like putting molecular motors in algae that push water to run a generator.”

Across the field, advanced computing is allowing researchers like Barrick to analyze genomes, develop and test synthetic organisms, and experiment with artificial populations, all of which help scientists explore evolution on a far finer-grained level.

When this E. coli experiment started, all they could measure was fitness. They had no clue why certain E. coli strains were better,” Barrick said. “Now we can understand at the molecular level what’s going on, and that’s really powerful.”

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Federal Budget Cuts Threaten Illinois Research Labs

Over at Crain’s Blogs, Joe Cahill writes that the current Federal budget impasse imperils cutting-edge work at the Chicago area’s biggest scientific centers including Fermilab, Argonne National Laboratory and NCSA in Champaign-Urbana.

Funding cuts to DOE’s basic science mission would be severe,” Energy Secretary Steven Chu warned earlier this month in a letter to Sen. Barbara Mikulski, D.-Md., who leads the Senate Appropriations Committee. Mr. Chu said sequestration would squeeze research funding, delay construction projects and generally curtail operations at DOE facilities around the country, including the national laboratories. That would come on top of cuts Fermilab already has made as a result of President Barack Obama’s proposed fiscal 2013 budget, which would reduce the lab’s funding by 8 percent. In response, the lab eliminated 49 jobs, or about 3 percent of its staff.

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HPC Midlands to Host Open House for Research & Industry

The HPC Midlands supercomputing facility will host their launch event in the U.K. on March 20. As a provider of state-of-the-art e-infrastructure for research and industry, HPC Midlands features a 3,000 core supercomputer combined with HPC expertise from Loughborough University and the University of Leicester.

Since establishing HPC Midlands with the financial backing of the Engineering and Physical Sciences Research Council, we have worked closely with academic colleagues and a range of industrial partners to refine the service to ensure that it meets business as well as academic needs,” said Dr Steven Kenny, Director of HPC Midlands. “Now we are ready to invite small and large businesses with specialist computing requirements to come along and see how they can benefit from this world-class facility.”

The launch event will give delegates the chance to meet the team behind HPC Midlands and explore opportunities for collaboration. Case study presentations will showcase how company’s like Tata Steel, E.ON, and Rolls Royce already benefit from working closely with HPC Midlands. Read the Full Story.

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