ananyo writes "By analysing the chemical structure of a drug, researchers can see if it is likely to bind to, or 'dock' with, a biological target such as a protein. Researchers have now unveiled a computational effort that used Google's supercomputers to assesses billions of potential dockings on the basis of drug and protein information held in public databases. The effort will help researchers to find potentially toxic side effects and to predict how and where a compound might work in the body. 'It's the largest computational docking ever done by mankind,' says Timothy Cardozo, a pharmacologist at New York University's Langone Medical Center, who presented the project at the US National Institutes of Health's High Risk–High Reward Symposium in Bethesda, Maryland. The result, a website called Drugable, is still in testing, but it will eventually be available for free, allowing researchers to predict how and where a compound might work in the body, purely on the basis of chemical structure."
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An anonymous reader writes "The Xeon Phi co-processor requires a Xeon CPU to operate... for now. The next generation of Xeon Phi, codenamed Knights Landing and due in 2015, will be its own CPU and accelerator. This will free up a lot of space in the server but more important, it eliminates the buses between CPU memory and co-processor memory, which will translate to much faster performance even before we get to chip improvements. ITworld has a look."
An anonymous reader writes "As Nicole Hemsoth over at HPCwire reports 'In a nutshell, the Automata processor is a programmable silicon device that lends itself to handing high speed search and analysis across massive, complex, unstructured data. As an alternate processing engine for targeted areas, it taps into the inner parallelism inherent to memory to provide a robust and absolutely remarkable, if early benchmarks are to be believed, option for certain types of processing.'" Basically, the chip is designed solely to process Nondeterministic Finite Automata and can explore all valid paths of an NFA in parallel, hiding the whole O(n^2) complexity thing. Micron has a stash of technical documents including a paper covering the design and development of the chip. Imagine how fast you can process regexes now.
dcblogs writes "In the global race to build the next generation of supercomputers — exascale — there is no guarantee the U.S. will finish first. But the stakes are high for the U.S. tech industry. Today, U.S. firms — Hewlett-Packard, IBM and Intel, in particular — dominate the global high performance computing (HPC) market. On the Top 500 list, the worldwide ranking of the most powerful supercomputers, HP now has 39% of the systems, IBM, 33%, and Cray, nearly 10%. That lopsided U.S. market share does not sit well with other countries, which are busy building their own chips, interconnects, and their own high-tech industries in the push for exascale. Europe and China are deep into effort to build exascale machines, and now so is Japan. Kimihiko Hirao, director of the RIKEN Advanced Institute for Computational Science of Japan, said Japan is prepping a system for 2020. Asked whether he sees the push to exascale as a race between nations, Hirao said yes. Will Japan try to win that race? 'I hope so,' he said. 'We are rather confident,' said Hirao, arguing that Japan has the technology and the people to achieve the goal. Jack Dongarra, a professor of computer science at the University of Tennessee and one of the academic leaders of the Top 500 supercomputing list, said Japan is serious and on target to deliver a system by 2020."
alphadogg writes "A network researcher at the U.S. Department of Energy's Fermi National Accelerator Laboratory has found a potential new use for graphics processing units — capturing data about network traffic in real time. GPU-based network monitors could be uniquely qualified to keep pace with all the traffic flowing through networks running at 10Gbps or more, said Fermilab's Wenji Wu. Wenji presented his work as part of a poster series of new research at the SC 2013 supercomputing conference this week in Denver."
Nerval's Lobster writes "Scientists have been using everything from supercomputing clusters to 3D printers to virtually recreate dinosaur bones. Now another expert is trying to do something similar with the ancient imperial villa built for Roman emperor Hadrian, who ruled from 117 A.D. to 138 A.D. Hadrian's Villa is already one of the best-preserved Roman imperial sites, but that wasn't quite good enough for Indiana University Professor of Informatics Bernie Frischer, who trained as a classical philologist and archaeologist before being seduced by computers into what evolved into the academic discipline of digital analysis and reproduction of archaeological and historical works. The five-year effort to recreate Hadrian's Villa is based on information from academic studies of the buildings and grounds, as well as analyses of how the buildings, grounds and artifacts were used; the team behind it decided to go with gaming platform Unity 3D as a key part of the simulation."
dcblogs writes "At this year's supercomputing conference, SC13, there is worry that supercomputing faces a performance plateau unless a disruptive processing tech emerges. 'We have reached the end of the technological era' of CMOS, said William Gropp, chairman of the SC13 conference and a computer science professor at the University of Illinois at Urbana-Champaign. Gropp likened the supercomputer development terrain today to the advent of CMOS, the foundation of today's standard semiconductor technology. The arrival of CMOS was disruptive, but it fostered an expansive age of computing. The problem is 'we don't have a technology that is ready to be adopted as a replacement for CMOS,' said Gropp. 'We don't have anything at the level of maturity that allows you to bet your company on.' Peter Beckman, a top computer scientist at the Department of Energy's Argonne National Laboratory, and head of an international exascale software effort, said large supercomputer system prices have topped off at about $100 million 'so performance gains are not going to come from getting more expensive machines, because these are already incredibly expensive and powerful. So unless the technology really has some breakthroughs, we are imagining a slowing down.'" Although carbon nanotube based processors are showing promise (Stanford project page; the group is at SC13 giving a talk about their MIPS CNT processor).
MojoKid writes "The supercomputing conference SC13 kicks off this week and Nvidia is kicking off their own event with the launch of a new GPU and a strategic partnership with IBM. Just as the GTX 780 Ti was the full consumer implementation of the GK110 GPU, the new K40 Tesla card is the supercomputing / HPC variant of the same core architecture. The K40 picks up additional clock headroom and implements the same variable clock speed threshold that has characterized Nvidia's consumer cards for the past year, for a significant overall boost in performance. The other major shift between Nvidia's previous gen K20X and the new K40 is the amount of on-board RAM. K40 packs a full 12GB and clocks it modestly higher to boot. That's important because datasets are typically limited to on-board GPU memory (at least, if you want to work with any kind of speed). Finally, IBM and Nvidia announced a partnership to combine Tesla GPUs and Power CPUs for OpenPOWER solutions. The goal is to push the new Tesla cards as workload accelerators for specific datacenter tasks. According to Nvidia's release, Tesla GPUs will ship alongside Power8 CPUs, which are currently scheduled for a mid-2014 release date. IBM's venerable architecture is expected to target a 4GHz clock speed and offer up to 12 cores with 96MB of shared L3 cache. A 12-core implementation would be capable of handling up to 96 simultaneous threads. The two should make for a potent combination."
An anonymous reader writes "In honor of Doc Brown, Great Scott! Ars has an interesting article about a 1.21 PetaFLOPS (RPeak) supercomputer created on Amazon EC2 Spot Instances. From HPC software company Cycle Computing's blog, it ran Professor Mark Thompson's research to find new, more efficient materials for solar cells. As Professor Thompson puts it: 'If the 20th century was the century of silicon materials, the 21st will be all organic. The question is how to find the right material without spending the entire 21st century looking for it.' El Reg points out this 'virty super's low cost.' Will cloud democratize access to HPC for research?"
Nerval's Lobster writes "Scientists at the University of Manchester in England figured out how the largest animal ever to walk on Earth, the 80-ton Argentinosaurus, actually walked on earth. Researchers led by Bill Sellers, Rudolfo Coria and Lee Margetts at the N8 High Performance Computing facility in northern England used a 320 gigaflop/second SGI High Performance Computing Cluster supercomputer called Polaris to model the skeleton and movements of Argentinosaurus. The animal was able to reach a top speed of about 5 mph, with 'a slow, steady gait,' according to the team (PDF). Extrapolating from a few feet of bone, paleontologists were able to estimate the beast weighed between 80 and 100 tons and grew up to 115 feet in length. Polaris not only allowed the team to model the missing parts of the dinosaur and make them move, it did so quickly enough to beat the deadline for PLOS ONE Special Collection on Sauropods, a special edition of the site focusing on new research on sauropods that 'is likely to be the "de facto" international reference for Sauropods for decades to come,' according to a statement from the N8 HPC center. The really exciting thing, according to Coria, was how well Polaris was able to fill in the gaps left by the fossil records. 'It is frustrating there was so little of the original dinosaur fossilized, making any reconstruction difficult,' he said, despite previous research that established some rules of weight distribution, movement and the limits of dinosaurs' biological strength."
hypnosec writes "Quantum computers are currently available in very few labs, usually bankrolled by major organizations like Google and NASA. However, a new project called 'Qcloud' aims to break those barriers by making quantum computing available to everyone. The University of Bristol announced the launch of Qcloud today at the British Science Festival 2013, with the goal of making quantum computing resources available to researchers across the globe. Claimed to be the first open-access system of its kind, the quantum chip is located at the Center for Quantum Photonics at the University of Bristol. Researchers can remotely access the processor over the internet for their computational needs. Those looking to test their ideas on the processor would be required to first practice and hone their skills using an online simulator. The university has made tutorials available to researchers so they can learn how to tune the processor and change its output as required. Once they are confident in their skills, researchers can ask for permission to access the real quantum photonic chip."
alphadogg writes "Following up on work commissioned by the U.S. Defense Advanced Research Projects Agency (DARPA), IBM has developed a programming paradigm, and associated simulator and basic software library, for its experimental SyNAPSE processor. The work suggests the processors could be used for extremely low-power yet computationally powerful sensor systems. 'Our end goal is to create a brain in a box,' said Dharmendra Modha, and IBM Research senior manager who is the principal investigator for the project. The work is a continuation of a DARPA project to design a system that replicates the way a human processes information." Also at SlashBI.
dcblogs writes "The Director of National Intelligence is soliciting help to develop a superconducting computer. The goal of the government's solicitation is 'to demonstrate a small-scale computer based on superconducting logic and cryogenic memory that is energy efficient, scalable, and able to solve interesting problems.' The NSA, in particular, has had a long interest in superconducting technology, but 'significant technical obstacles prevented exploration of superconducting computing,' the government said in its solicitation. Those innovations include cryogenic memory designs that allow operation of memory and logic in close proximity within the cold environment, as well as much faster switching speeds. U.S. intelligence agencies don't disclose the size of their systems, but the NSA is building a data center in Utah with a 65 MW power supply."
Nerval's Lobster writes "Just in time for hurricane season, the National Weather Service has finished upgrading the supercomputers it uses to track and model super-storms. 'These improvements are just the beginning and build on our previous success. They lay the foundation for further computing enhancements and more accurate forecast models that are within reach,' National Weather Service director Louis W. Uccellini wrote in a statement. The National Weather Service's 'Tide' supercomputer — along with its 'Gyre' backup — are capable of operating at a combined 213 teraflops. The National Oceanic and Atmospheric Administration (NOAA), which runs the Service, has asked for funding that would increase that supercomputing power even more, to 1,950 teraflops. The National Weather Service uses that hardware for projects such as the Hurricane Weather Research and Forecasting (HWRF) model, a complex bit of forecasting that allows the organization to more accurately predict storms' intensity and movement. The HWRF can leverage real-time data taken from Doppler radar installed in the NOAA's P3 hurricane hunter aircraft."
knorthern knight writes "Most major weather services (US NWS, Britain's Met Office, etc) have their own supercomputers, and their own weather models. But there are some models which are used globally. A new paper has been published, comparing outputs from one such program on different machines around the world. Apparently, the same code, running on different machines, can produce different outputs due to accumulation of differing round-off errors. The handling of floating-point numbers in computing is a field in its own right. The paper apparently deals with 10-day weather forecasts. Weather forecasts are generally done in steps of 1 hour. I.e. the output from hour 1 is used as the starting condition for the hour 2 forecast. The output from hour 2 is used as the starting condition for hour 3, etc. The paper is paywalled, but the abstract says: 'The global model program (GMP) of the Global/Regional Integrated Model system (GRIMs) is tested on 10 different computer systems having different central processing unit (CPU) architectures or compilers. There exist differences in the results for different compilers, parallel libraries, and optimization levels, primarily due to the treatment of rounding errors by the different software systems. The system dependency, which is the standard deviation of the 500-hPa geopotential height averaged over the globe, increases with time. However, its fractional tendency, which is the change of the standard deviation relative to the value itself, remains nearly zero with time. In a seasonal prediction framework, the ensemble spread due to the differences in software system is comparable to the ensemble spread due to the differences in initial conditions that is used for the traditional ensemble forecasting.'"
Nerval's Lobster writes "Astrophysicists at MIT and the Pawsey supercomputing center in Western Australia have discovered a whole new role for supercomputers working on big-data science projects: They've figured out how to turn a supercomputer into a router. (Make that a really, really big router.) The supercomputer in this case is a Cray Cascade system with a top performance of 0.3 petaflops — to be expanded to 1.2 petaflops in 2014 — running on a combination of Intel Ivy Bridge, Haswell and MIC processors. The machine, which is still being installed at the Pawsey Centre in Kensington, Western Australia and isn't scheduled to become operational until later this summer, had to go to work early after researchers switched on the world's most sensitive radio telescope June 9. The Murchison Widefield Array is a 2,000-antenna radio telescope located at the Murchison Radio-astronomy Observatory (MRO) in Western Australia, built with the backing of universities in the U.S., Australia, India and New Zealand. Though it is the most powerful radio telescope in the world right now, it is only one-third of the Square Kilometer Array — a spread of low-frequency antennas that will be spread across a kilometer of territory in Australia and Southern Africa. It will be 50 times as sensitive as any other radio telescope and 10,000 times as quick to survey a patch of sky. By comparison, the Murchison Widefield Array is a tiny little thing stuck out as far in the middle of nowhere as Australian authorities could find to keep it as far away from terrestrial interference as possible. Tiny or not, the MWA can look farther into the past of the universe than any other human instrument to date. What it has found so far is data — lots and lots of data. More than 400 megabytes of data per second come from the array to the Murchison observatory, before being streamed across 500 miles of Australia's National Broadband Network to the Pawsey Centre, which gets rid of most of it as quickly as possible."
hypnosec writes "Adapteva has started shipping its $99 Parallella parallel processing single-board supercomputer to initial Kickstarter backers. Parallella is powered by Adapteva's 16-core and 64-core Epiphany multicore processors that are meant for parallel computing unlike other commercial off-the-shelf (COTS) devices like Raspberry Pi that don't support parallel computing natively. The first model to be shipped has the following specifications: a Zynq-7020 dual-core ARM A9 CPU complemented with Epiphany Multicore Accelerator (16 or 64 cores), 1GB RAM, MicroSD Card, two USB 2.0 ports, optional four expansion connectors, Ethernet, and an HDMI port." They are also releasing documentation, examples, and an SDK (brief overview, it's Free Software too). And the device runs GNU/Linux for the non-parallel parts (Ubuntu is the suggested distribution).
aarondubrow writes "Researchers reported results in Nature Communications on a new way of sculpting tailor-made fluid flows by placing tiny pillars in microfluidic channels [abstract; article is paywalled]. The method could allow clinicians to better separate white blood cells in a sample, increase mixing in industrial applications, and more quickly perform lab-on-a-chip-type operation. Using the Ranger and Stampede supercomputers, the researchers ran more than 1,000 simulations representing combinations of speeds, thicknesses, heights or offsets that produce unique flows. This library of transformations will help the broader community design and use sculpted fluid flows."
UT Austin tends not to do things by half measures, as illustrated by the Texas Advanced Computing Center, which has been home to an evolving family of supercomputing clusters. The latest of these, Stampede, was first mentioned here back in 2011, before it was actually constructed. In the time since, Stampede has been not only completed, but upgraded; it's just successfully completed a successful six months since its last major update — the labor-intensive installation of Xeon Phi processors throughout 106 densely packed racks. I visited TACC, camera in hand, to take a look at this megawatt-eating electronic hive (well, herd) and talk with director of high-performance computing Bill Barth, who has insight into what it's like both as an end-user (both commercial and academic projects get to use Stampede) and as an administrator on such a big system.
aarondubrow writes "Researchers at The University of Texas at Austin developed a fundamentally new way of simulating fabric impacts that captures the fragmentation of the projectiles and the shock response of the target. Running hundreds of simulations on supercomputers at the Texas Advanced Computing Center, they assisted NASA in the development of ballistic limit curves that predict whether a shield will be perforated when hit by a projectile of a given size and speed. The framework they developed also allows them to study the impact of projectiles on body armor materials and to predict the response of different fabric weaves upon impact." With thousands of known pieces of man-made space junk, as well plenty of natural ones, it's no idle concern.