insideHPC » Applied HPC

Conway: Data-Intensive Computing Could Save $Billions

Rich Brueckner — Wed, 20 Apr 2011 00:05:52 +0000

IDC’s Steve Conway has written a nice feature on Big Data in HPC. Once the singular domain of cryptography and weather applications, the data-handling capabilities of supercomputers could potentially have big-dollar effects on our economy:

Oak Ridge National Lab has submitted a proposal to unify all these databases and perform fraud detection using a Cray supercomputer nicknamed “Jaguar” that features 224,000 AMD Opteron™ processor cores. This solution could save $50 billion a year by analyzing the data in near-real time. The same methods could be applied to other criminal behavior, terrorist activities and many of the other applications I mentioned.

Conway goes on to say that recent technology advances have given data-intensive computing much higher potential as a horizontal market. Read the Full Story.

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Supercomputing for a Changing Planet: Simulation and Climate Change

Linda Barney — Tue, 09 Nov 2010 15:00:35 +0000

There are few issues today that capture as much attention as climate change: from policy makers and soccer moms to activists and mathematicians, a great deal of the world’s intellectual capability is focused on understanding, managing, and reversing the damaging climate effects of human activity on planet earth. The scope and complexity of the climate change problem pushes the boundaries of our scientific and engineering capabilities, even as the vast scale of the problem challenges our concepts of governance and the organization of civil society.

Climate scientists examine how elements such as atmosphere, land surface, ocean and sea ice systems interact to create global weather patterns whose statistics compiled over long periods of time define the climate state. They use sophisticated mathematical algorithms and complex calculations on supercomputers to gain a better understanding of climate system processes, and to use that understanding to predict changes in the Earth’s climate.

In fact, computer simulation is one of the few tools available to scientists and policy makers for understanding climate change. Numerical models allow us to validate our evolving understanding of the mechanisms of climate change, but the models are so complex that ordinary computers will not suffice. This is precisely the kind of challenge that supercomputers were designed to address, and supercomputing is a vital part of the climate science tool chest.

Climate Simulation at SC10

Climate science is a major focus area at this year’s Supercomputing Conference (SC10), a reflection of the focus that the HPC community is placing on this important issue. SC10, being held in New Orleans this year, will again attract scientists, researchers, students and businesses from around the world.

“The topic of climate has never been more relevant to a meeting like SC10 given the growing importance of simulation to addressing climate change questions from policy makers and stakeholders,” said James Hack, National Center for Computational Sciences director at Oak Ridge National Laboratory and the SC10 climate simulation thrust co-chair. “HPC will become an even more critical resource to help the broader research community to develop solutions to potential environmental impacts.”

During the conference, attendees will gather to learn from some of the world’s foremost experts in climate change and computation, and participate in exchanges that may shape future solutions. From masterworks sessions on the future of computing in climate science to papers on computational and data analytic issues, SC10 is a must-attend event for anyone working in the intersection of computing and the climate.

“This topic is particularly relevant to SC10, in view of recent extreme weather events, such as the very mild winter in Vancouver for the 2010 Olympics while Washington, D.C. experienced the heaviest snowfall in history. It is an open research question whether extreme weather events are related to climate change, ” said William Sawyer, computational scientist at the Swiss National Supercomputing Centre, and the SC10 climate simulation thrust area co-chair. “HPC is a critical resource to help the broader research community understand the connection between extreme weather events and climate, develop solutions to current climate issues, and help minimize the environmental impact of future events.”

Those who want to learn more will find a rich selection of papers, talks, and learning opportunities in New Orleans this year.

Learn from the masters

SC10 presents a rare opportunity to learn about the latest in climate science — and the latest thinking in the future of climate science — from the best in the world.

Terry Davies from the UK Meteorological Office will give a plenary talk on Thursday morning looking out over the next 20 years of climate prediction research, while the conference Masterworks program will provide even more opportunities to learn from the best in the world. Princeton’s V. Balaji, Richard Rood from the University of Michigan, James Kinter from the Institute of Global Environment and Society, and Mark Govett from NOAA will present during the week in separate sessions on topics ranging from computation and data management to new advances in our approach to science and the potential of GPUs in climate research applications.

Those looking for more interaction will enjoy Robert Jacob’s Birds of a Feather session on the analysis and visualization of large climate data sets, as well as the panel on “Pushing the Frontiers of Climate and Weather Models” with panelists Christiane Jablonowski, David Randall, Terry Davies, William Putman, Shian-Jiann Lin, and Peter Lauritzen.

And, of course, the week features many papers focused on computational technologies and techniques that those interested in climate science will want to keep in their toolbox.

Time to Dig In

The thrust areas at SC10 offer a unique opportunity to dig deep into critical issues driving the supercomputing community. Tune into events in the Climate Simulation thrust area throughout the week to be sure you are well-positioned to understand the issues of today, and to plan well for the science of tomorrow.

Linda Barney owns Barney and Associates, a technical, marketing writing and web firm in Beaverton, Oregon that provides writing and web content for the high tech, government, medical and scientific communities. Readers can reach her at linda@barneyassoc.com.

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FAA uses HPC to make sure planes stay in the air

John West — Wed, 25 Aug 2010 15:00:26 +0000

The staff and resources at TACC were recently part of an effort to add HPC-enabled calculations to the FAA’s operational safety workflow. Here is the outline of the full story which can be found on TACC’s website (complete with cool pics)

…if a crack is detected in an aircraft structure, does the problem affect only one plane, or is the failure systemic to the aircraft model or part? With lives and livelihoods on the line, officials must decide whether to institute a new inspection regime, keep the status quo, or ground the fleet.

Until recently, the FAA had little to go on when making this decision for small airplanes or the general aviation fleet. As a result, Harry Millwater, associate professor of mechanical engineering at The University of Texas at San Antonio (UTSA), working with post-doctoral researcher Gulshan Singh, and graduate student Juan Ocampo, developed a state-of-the-art structural integrity software, called SMART (SMall Aircraft Risk Technology), that in a matter of minutes can run thousands of simulations on a given part of a plane and provide a detailed report of the likelihood of a crack initiating in terms of both “hours and flights to failure”.

The invididual simulations aren’t long, but the FCC wanted to create an ensemble analysis that looks at a range of probable values for the critical variables in each situation. This can mean tens of thousands of runs that need to be completed rapidly in response to a detected failure in a flight system.

For that reason, Millwater approached TACC with the goal of “parallelizing” their code—making it capable of running simultaneously on multiple processing cores—and ultimately speeding up its performance so it could become a valuable, real-world tool.

…Working with Schulz, Millwater was able to make his code run 188 times faster by instituting a new MPI (Message Passing Interface) version that can efficiently distribute the calculations onto 256 processors (or the equivalent of more than 100 PCs).

“Something that took a couple of hours for analysis now took 42 seconds. You can’t beat that,” said Millwater.

The FAA has been using early versions of the code in exercises since last summer, and will take delivery of the final code at the end of this month when it will enter the FAA’s operational workflow.

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Weather Research Forecast Version 3.2.1 Released

John Leidel — Wed, 18 Aug 2010 22:50:20 +0000

The nice folks working on the Weather Research Forecast [WRF] code base announced a bug-fix release this afternoon. Version 3.2.1 includes mostly bug fixes, but a few improvements. They include:

Fixes for producing wrffdda file
Fixes for restart with auxiliary inputs (wrflowinput, wrffdda)
Various fixes for physics, including URBPARM.TBL, MYJ PBL, YSU PBL, and RRTMG_LW
tracer option without WRF-Chem
curvature term correction for rotated lat-lon projection in ARW
more namelist cross-checks

For more detailed updates for WRF-ARW, check out the UCAR website here. For more info on the updates in WRD-NMM, check out the DTCenter website here.

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IBM Super to Compete on Jeopardy

John Leidel — Wed, 18 Aug 2010 01:14:28 +0000

…no word yet what its going to do with the furniture it wins. According to an article in eWeek today, the IBM computer called ‘Watson’ [based on the BlueGene] will officially compete on the long-running television game show Jeopardy!. The Blue-Gene-based machine will utilize technology called DeepQA developed by a research group at IBM Research. Dr. David Ferrucci heads up the lab in charge of the project.

According to the source article, the official contest will occur sometime this Fall. No additional details on the underlying hardware were provided in the article.

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TACC On Memory Performance in a Cluster

John Leidel — Fri, 30 Jul 2010 01:04:53 +0000

Dan Stanzione and Tommy Minyard from the Texas Advanced Computing Center [TACC] posted an article on Dell’s Enterprise Technology Center website about the perils of relying on pure clock frequency for performance comparisons of real applications. As many of you have undoubtedly read the various bi-annual releases of the latest Top500 numbers know that the rankings are based on the High Performance Linpack [HPL] benchmark. While sensitive to issues other than the core silicon, HPL generally delivers a high percentage of peak performance [when configured correctly]. But what about real world applications? How does this compare to my app?

Given that HPL delivers a pretty good fraction of peak performance on most processors, not surprisingly, higher clock rate has meant higher HPL, higher Top 500 number, and the impression that your new cluster is “faster.” The big gotcha here is the not-so-well-kept-secret in the HPC community that *peak* performance and *real* application performance didn’t really have that much to do with one another, and the performance of HPL did not reflect the ability of a cluster to get work done. This has become especially true with the last generation of new quad-core processors. [Minyard, Stanzione]

Stanzione and Minyard make a very important statement in the body of the article: “HPL doesn’t really suffer too much from inadequate memory bandwidth, so the magnitude of the problem hasn’t been quite as obvious.”

The duo from TACC go on to explain a series of benchmark runs performed on an Intel Harpertown [E5450] clocked at 3.0Ghz versus those performed on an Intel Nehalem [E5550] clocked at 2.66Ghz. The benchmark in question was the Weather Research Forecast [WRF] version 3.1.1 application [no specific details on which piece/variant]. The single core performance comparison between the processors was reasonably similar. However, at eight cores, the Nehalem was nearly four times faster than the [higher clocked] Harpertown.

So why the disparity? Its the operand, not the operation! The next comparison made by the duo involves the STREAM memory bandwidth. At this point, its clear who wins the memory argument and eventually crowned king of performance [in these tests].

Minyard and Stanzione do a great job in laying out a simple example of why clock speed is not the cat’s pajamas anymore. One thing I might add to this evaluation is the individual latency of a memory operation. Remember, the Harpertown was a classic Front-Side-Bus [FSB] architecture while a single memory controller handling requests from all devices. The Nehalem is a System-on-Chip [SOC] architecture with an integrated memory controller on each die. Long story short, the Harpertown has to work twice as hard to cover the latency of any given main memory operation.

For more info and some great graphs, check out their full writeup here.

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OSC’s Blue Collar Computing effort goes international

John West — Wed, 30 Jun 2010 15:01:50 +0000

This week the Ohio Supercomputer Center announced that the French consulting computing Sciences Computers Consultants is partnering with the Blue Collar Computing project to bring new applications and expertise to the polymer industry

As part of its Blue Collar Computing offerings, OSC will provide SCC with computational infrastructure and services to test and scale advanced modeling and simulation software for polymer extrusion and mixing on its supercomputers with the intent of developing web portals for polymer industry process modeling. SCC numerical simulations applications are used by companies in high technology fields within the polymer, energy, automotive and food industries.

SCC has procured from OSC a startup package that consists of 2,500 production-level compute cycles and advanced technical support. As part of the biannual agreement, SCC will receive up to 150K CPU hours and 250GB of storage per year, as well as 20 user accounts for each project, outside network connectivity and technical support. SCC intends to install its flagship software product, XimeX, on OSC’s systems for scalability testing and small pilot projects.

The two are now on the lookout, along with trade group PolymerOhio, for companies in the polymer industry to work with them on a pilot project demonstrating the potential of the partnership.

“Partnering with OSC allows us to develop a significant toehold in the U.S. to answer industrial needs for process analysis and validation, material behavior analysis, and other engineering studies,” said Philippe David, general manager of SCC.

Part of the problem with radically growing the user base for HPC (a move that would transform modern society, inundating it with everything from new drugs to cheap ways to get clean water to sub-Saharan African villages) is that most people’s world view doesn’t include any connection to high performance computing apart from some vague ideas from Jurassic Park. A sensible way to evangelize the solution is to partner with software providers, the people who already know what customers could benefit from HPC, and have them reach out to their customers. Building this partnership enables SCC to not only suggest that HPC might help, but to be able to offer its customers a low-barrier path to computing in a short timeframe.

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Making big iron with the help of big iron

John West — Mon, 28 Jun 2010 16:27:08 +0000

NCSA has posted another video briefing from its annual Private Sector Program Annual Meeting, this time about what Caterpillar does with HPC

At the recent NCSA Private Sector Program Annual Meeting, Keven Hofstetter described how Caterpillar uses high-performance computing to enhance product development and outlined a vision for extremely accurate, integrated simulation.

You can watch the movie here.

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Deep space telescope peers back in time, HPC needed to make sense of it all

John West — Wed, 23 Jun 2010 14:00:37 +0000

Earlier this month Jonathan Sievers, of the Canadian Institute for Theoretical Astrophysics, presented early data from the Atacama Cosmology Telescope during HPCS2010

The Atacama Cosmology Telescope is one of the largest telescopes of its kind, and the flood of data from this instrument in Chile in one day is the equivalent of a decade of data from an earlier satellite experiment. This requires the largest computers to make sense of it all — including SciNet’s GPC, the largest computer in Canada. “SciNet is essential for the Atacama Cosmology Telescope (ACT) project. The computer has enabled a new frontier in producing maps of the early universe, and is changing the way cosmologists make sense of the cosmos”, said Professor Lyman Page of Princeton.

The first results have already given cosmologists the first glimpse of the transition from a simple universe to one containing the more complicated structures seen today. As part of the investigation, the team has identified previously unknown clusters of galaxies and is following them up with optical observations to determine their distances and masses.

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HPC plays a role in developing understanding of how we hear

John West — Tue, 22 Jun 2010 23:07:09 +0000

According to news out of TACC recently, Harvard Medical School researchers recently published results from computational studies they’ve been doing of a protein that is crucial to the hearing process

Cadherin-23 is also one of the proteins that malfunctions in individuals with hereditary deafness. Scientists believe one in 1,000 individuals in the U.S. are affected by this kind of disease, and 7.5 percent of hereditary deafness cases are caused by mutations in cadherin-23.

…The Harvard research team, including Sotomayor and Wilhelm Weihofen, and led by Rachelle Gaudet and David P. Corey, used the Ranger supercomputer at the Texas Advanced Computing Center (TACC) to simulate the 3D structure of cadherin-23 obtained from x-ray data. Then, they set the protein in motion, simulating the behavior of each atom as it reacted to forces that mimicked the effect of sound waves.

In simulations that involved up to 355,000 atoms, the team found that these particular proteins aren’t springy, but stiff. And they found a clue about what goes wrong in certain types of hearing loss

The simulations also showed that some deafness-related mutations to the protein do not alter the fold and strength of cadherin-23 directly. Rather, they change the way the protein binds calcium, which ends up weakening its structure.

Nifty application of HPC, and some very common codes (NAMD and VMD).

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HPC simulations helping predict impact, path of gulf oil spill

John West — Mon, 07 Jun 2010 14:16:56 +0000

The gulf oil spill is (justifiably) receiving much of the world’s scientific and engineering attention, so it is no surprise that there are two HPC groups in the news right now working on the problem.

The University of Texas at Austin announced last week that researchers there are using Ranger — a Sun supercomputer that at one time was ranked 7th in the world and which today is still number 11 — to predict impact of oil spilling from the failed BP Deepwater Horizon oil well

With an emergency allocation of one million computing hours from the National Science Foundation TeraGrid project, the researchers are running high resolution models of the Louisiana coast to track the oil spill through the complex marshes, wetlands and channels in the area.

…”What our model can do that a lot of the other models can’t do is track the oil spill up into the marshes and wetlands, because we have fine-scale resolution in those areas,” he said.

This kind of detail will help the scientists determine how the oil may spread in environmentally sensitive areas. The team’s 2-D and 3-D coastal models also will take into account the Gulf of Mexico waves, which may bring the oil closer to the Texas coast.

The researchers are running 72-hour forecasts updated with satellite data about the current location of the spill at 50-meter resolution. UT claims that this is 10-20 times more refined than other simluations being conducted. Each run takes about 3 hours on 4,096 cores.

NCAR is also working together to produce simulations about a likely path for the spill

The computer simulations indicate that, once the oil in the uppermost ocean has become entrained in the Gulf of Mexico’s fast-moving Loop Current, it is likely to reach Florida’s Atlantic coast within weeks. It can then move north as far as about Cape Hatteras, North Carolina, with the Gulf Stream, before turning east. Whether the oil will be a thin film on the surface or mostly subsurface due to mixing in the uppermost region of the ocean is not known.

The code being used is POP, and simulations are being run at the New Mexico Computer Applications Center and at Oak Ridge National Laboratory.

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Stimulus funds development of petascale ocean circulation code

John West — Mon, 10 May 2010 16:16:15 +0000

The JHU Gazette is running an article today on American Recovery and Revitalization Act of 2009 funded research at Johns Hopkins to develop a new petascale ocean model.

The supercomputer model, which will be run by a National Science Foundation–built supercomputer capable of doing a million billion calculations per second, will simulate currents in the Arctic, Antarctic and Atlantic oceans in hopes of shedding light on how small-scale turbulent eddies affect large currents, such as the powerful Gulf Stream.

…“Traditional scientific inquiry is being revolutionized by computing, and scientific computing and numerical simulation are becoming so important that they actually rival laboratory experiments and mathematical theory as tools for new progress,” Haine said. “There is an urgent national interest in designing, building and operating the biggest, fastest computers on Earth, and the group funding us and our circulation project is one element of this race.”

The effort uses $736,000 of ARA money, which seems low so I assume they are aggregating funds to make this happen

“Even though ocean circulation equations have been known since the 1880s, there is still a remarkable opportunity to make discoveries about how turbulent currents interact and evolve,” he explained. “By understanding circulation better, we can understand how other geophysical fluids work, too, like the Earth’s core, or Jupiter’s red spot or the sun’s photosphere.”

King’s College using HPC to study links between genetics and disease [UPDATED]

John West — Thu, 06 May 2010 15:40:02 +0000

My friend Gavin sent me a note by email last week about some recent news out of OCF (the UK-based HPC integrator) and King’s College London. The net net is that King’s College researchers have reduced the time taken to analyse DNA sequencing data by 20-fold, from days to hours. This is the first use at the National Institute for Health Research (NIHR)

“The sequence of the human genome has been known for ten years now so we are using new sequencing technologies to sequence specific regions of the genome in large numbers of people in order to help understand the contributory factors to a variety of common complex disorders and developmental defects,” says Dr. Rebecca Oakey, Reader in Epigenetics, Department of Medical & Molecular Genetics, School of Medicine, King’s College London. “These include skin diseases such as psoriasis, inflammatory bowel disease and the step by step development of vascular disorders, psychiatric disorders, diabetes, infection and immune disease as well as genetic components in cancer development.”

Dr Oakey adds: “To do so we need innovative sequencing technology to generate the data and the processing power to analyse, store and archive the data.”

The system that OCF helped field is an IBM iDataPlex with a 10GbE interconnect.

[UPDATED on 05062010 with details of the system]

The system that King’s College is using has 31 nodes. 30 of those nodes are dual socket quadcore processors, yielding 240 cores total for your run-of-the-mill distributed memory cluster jobs. The cluster also includes one fat node with 4 sockets loaded with six-core processors. The fat compute node operates as a large shared memory environment for those existing codes which either do not scale well on a cluster or require too much work to be economic by KCL to port to a cluster environment.

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NVIDIA announces GPU-optimized version of AMBER

John West — Mon, 03 May 2010 16:59:49 +0000

Last week NVIDIA released its tweak of the MD code AMBER, optimized to perform well on its GPU platform (AMBER is part of NVIDIA’s recently announced Bio Workbench)

AMBER 11, the latest version of one of the most widely used applications for biochemists and others involved in molecular dynamics research, is optimized to run on NVIDIA® graphics processing units (GPUs), which speed up the tool by up to 100-fold over a traditional CPU -based server. GPUs deliver performance from a desktop workstation that previously could only be achieved on a supercomputer, improving productivity as scientists no longer need to wait for time on a shared supercomputer or departmental cluster of servers.

…AMBER 11 is designed to take advantage of NVIDIA Tesla™ 20-series GPUs, which utilize the massively parallel CUDA™ architecture for the specific needs of high performance computing applications. In early trials with the AMBER user community, Dr. Walker received over a dozen reports of speedups over 30-times on a range of bio-molecular simulations.

…Dr. Walker noted that just one Tesla GPU provides as much processing power as a high performance cluster of 512 CPU cores when simulating one nanosecond in the lifetime of a 25,000 atom implicit solvent nucleosome. In a simpler explicit solvent simulation, such as the JAC benchmark, he noted that one Tesla GPU provides the equivalent processing power of 48 cores of the NSF Ranger supercomputer.

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HPC helps solve question of how a cell knows what to be when it grows up

John West — Mon, 03 May 2010 16:00:28 +0000

Ohio State University systems biologist Dan Siegal-Gaskins is using HPC to help answer the question of how a cell knows what to turn into as it develops. To help him, he is studying the plant world’s answer to fruit flies, Arabidopsis thaliana (or mouse-ear cress)

At a specific phase of Arabidopsis leaf development, cells on the surface of the leaf receive genetic instructions to become either one of the majority ‘pavement’ cells or a large hair-like cell known as a trichome. The specific function of trichomes is unclear, although they may be involved in preventing infection, protecting delicate tissues on the underside of the leaf, or reducing the amount of water lost to evaporation.

…The mathematical model Siegal-Gaskins constructed consists of seven differential equations and twelve unknown factors. For his preliminary studies, he turned to OSC to choose random values for the unknowns and solve the equations for millions of different random value sets.

“Due to the large range of possible parameters and the complexity of the problem, we took advantage of OSC’s parallel processing capabilities and the MATLAB computing environment,” Siegal-Gaskins said. “This process was repeated for five million randomly-chosen parameter sets, and the set that gave us the closest agreement with experimentation was kept.”

It’s interesting that the team is using MATLAB for this problem — I’ve seen MATLAB function as a gateway into HPC for many teams of scientists that hadn’t previously used HPC before. I have a sense that its value in that role is seriously underestimated by mainstream HPC centers.

“Our bcMPI software, initially released in 2006, interfaces with HPC cluster technologies like PBS and Infiniband when executing MATLAB scripts on a cluster,” explained David Hudak, director of HPC engineering at OSC. “Over the last year, we have been working to improve the accessibility of parallel MATLAB. We designed Remote MATLAB Services (RMS) to enable our users to transition MATLAB scripts developed on their laptops to HPC resources. Dan was an early adopter of OSC RMS, and we learned a lot from his feedback. It was a very good fit for his needs.”

With the combination of computational modeling, literature-based analyses and laboratory experimentation, Siegal-Gaskins and Morohashi determined that the three cell fate proteins seem to constitute an “incoherent feed forward loop,” a relationship in which a master regulator (MR) triggers expression of two genes involved in the initiation of trichome cell development, one of which (G1) later suppresses expression of the other (G2).

Platform turns its HPC management software up a notch

John West — Wed, 28 Apr 2010 14:00:31 +0000

Platform hopes its HPC Enterprise Edition will encourage commercial adoption of HPC

This week Platform Computing announced that it was turning some of its focus back to HPC, after spending the past year or so aiming at a more traditional large-IT audience. On Monday the company announced the launch of HPC Enterprise Edition, a package of tools that Platform believes will help “enterprise” (I read that as either non-traditional or inexperienced) users in the commercial market ease into HPC.

Platform HPC Enterprise Edition brings together several pieces of Platform’s HPC toolkit into one offering that will help customers manage their cluster from deployment and management to monitoring and job submission. It includes Cluster Manager, LSF, Platform MPI (recall that Platform bought MPI stacks from both HP and Scali), Application Center, RTM monitoring dashboard, and ISF Adaptive Cluster into a single, web-based interface for the entire system lifecycle.

Enterprise Edition is the evolution of what Platform used to call Platform HPC Workgroup Manager — now called HPC Workgroup Edition — but without the 32-node limitation of that solution. Although it could theoretically be used to manage systems of arbitrary size, it really is designed for smaller clusters and COTS applications.

Platform hopes that it can ease the cluster integration and training worries of the IT admin group by providing its pre-integrated tools for installation, management, and monitoring. HPC EE will probably run on your favorite x86-64 Linux, with support for popular distros such as Red Hat, SUSE, CentOS, and Scientific Linux. If you are a mixed Windows/Linux shop then Adaptive Cluster, which integrates with LSF to reconfigure a pool of nodes for either Linux- or Windows-based jobs on the fly, will also address the real requirement that companies not have to reinvent their application infrastructure to move to HPC.

Getting users over the hurdle

But it is the inclusion of Platform Application Center and the pre-integrated COTS applications templates that will help get the users of these systems over some of their entry hurdles. Launched during SC09, Application Center is a shrink-wrapped role-based portal framework. Users or system managers can create templates for various applications and types of jobs (using XML) that allow users to launch applications and manage files from within a web portal. HPC Enterprise Edition comes with seven templates that integrate applications popular with Platform customers: Abaqus, Ansys, Blast, Eclipse, Fluent, LS-Dyna, and Nastran. Visualization is not supported out of the box with HPC Enterprise Edition, but users can upgrade their installation to enable vis in the portal.

The pre-integration of those seven application templates is part of what William Lu, Platform’s director of HPC marketing, emphasized when I spoke with him as the shrink-wrapped advantage. “HPC Enterprise Edition groups our existing commercial-grade technologies together into a single solution,” Lu says. “It is not just a collection of open source technologies.” Whether this line of marketing continues to hold up over time is entirely up to the open source community.

If you’re going to have an HPC hardware vendor as your launch partner…

When asked about pricing Lu said that HPC Enterprise Edition will run customers “a few hundred dollars per node,” and that Platform expects the majority of licenses will ship out through hardware partners, although they will also sell to users directly through their existing sales channels (you can’t buy this online at the website — not yet, anyway). HPC Enterprise Edition is already available, and Platform is launching with a significant HPC hardware partner: Cray. Cray is rebranding the software with its own Cray Cluster Manager nameplate and shipping it to CX1 and CX1000 customers. Although Lu wasn’t ready to talk about other partners yet, he did mention that they are in discussions with Dell and HP.

Interestingly, Cray’s Ian Miller (senior vice president of the productivity solutions group and marketing) told me that Cray Cluster Manager is now the default clusterware on both the CX1 and the CX1000. The Cray CX1-iWS sold by Dell won’t ship with CCM, which makes sense since it is entirely a Windows platform. “However, some customers have their own preferred cluster management software,” says Miller, “and some of our resellers are also aligned with other partners in this space, giving us the flexibility to be able to handle these situations too.”

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Using HPC to understand (and beat) Alzheimer’s disease

John West — Thu, 22 Apr 2010 15:36:26 +0000

Alzheimer’s is a progressive and fatal disease that is the number one cause of dementia in the United States, accounting for between 50 and 80% of dementia cases. In 2006 26.6 million people had the disease worldwide, and today it is the 7th leading cause of death in the United States.

There is no cure for Alzheimer’s, and even the causes and mechanisms of disease have yet to be worked out. But scientists are making progress. One of the researchers working on Alzheimer’s is using supercomputers at the Ohio Supercomputing Center to understand what role misfolded proteins may play in the disease process.

In the nucleus of nearly every human cell, long strands of DNA are packed tightly together to form chromosomes, which contain all the instructions a cell needs to function. To deliver these instructions to various other cellular structures, the chromosomes dispatch very small protein fibers – called oligomers – that fold into three- dimensional shapes. Misfolded proteins – called amyloid fibrils – cannot function properly and tend to accumulate into tangles and clumps of waxy plaque, robbing brain cells of their ability to operate and communicate with each other, according to NIH.

…“The exact mechanism of amyloid formation and the origin of its toxicity are not fully understood, primarily due to a lack of sufficient atomic-level structural information from traditional experimental approaches, such as X-ray diffraction, cryoelectron microscopy and solid-state NMR data,” [Jie Zheng, Ph.D.]. explained. “Molecular simulations, in contrast, allow one to study the three-dimensional structure and its kinetic pathway of amyloid oligomers at full atomic resolution.”

Zheng’s research group is developing a multiscale modeling and simulation platform that integrates structural prediction, computational biology and bioinformatics to establish a direct correlation between the formation of oligomers and their biological activity in cell membranes. This research is important for understanding the build-up of protein plaque, how it contributes to the breakdown of cells and how the process might be prevented.

Zheng’s research project recently won an NSF CAREER award, one of the most prestigious the NSF bestows. You can read more about Zheng’s research here.

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NASA launches earth portal on its most power supercomputer [UPDATED]

John West — Tue, 20 Apr 2010 15:34:16 +0000

Yesterday NASA launched its earth science portal, the NASA Earth Exchange, on the 640 TFLOPS Pleiades system, the SGI Altix ICE that currently holds the number 6 slot on the Top500. According to coverage at InformationWeek, NEX follows in a long line of friendly front ends to complicated supercomputing workflows and applications (though few have been fielded on resources in the top 10 of the list)

The application — NEX for short — will allow even unsavvy users to take advantage of NASA supercomputing power via the NEX Collaborative Portal, a Web-based portal through which members of the Earth science community will be able to model and analyze the information in their own virtual environments. The portal will also include collaboration features like social networking that will allow scientists to share research results with one another or work together on projects.

The launch is timed to coincide with Earth Week, so feel the green. According to a description on the NEX web page

The NASA Earth Exchange (NEX) represents a new collaboration platform for the Earth science community that provides a mechanism for scientific collaboration and knowledge sharing. NEX combines state-of-the-art supercomputing, Earth system modeling, workflow management, NASA remote sensing data feeds, and a social networking platform to deliver a complete work environment in which users can explore and analyze large datasets, run modeling codes, collaborate on new or existing projects, and quickly share results among the Earth science communities.

The work environment provides NEX members with community supported modeling, analysis and visualization software in conjunction with datasets that are common to the Earth systems science domain. By providing data, software, and large-scale computing power together in a flexible framework, NEX reduces the need for duplicated efforts in downloading data, developing pre-processing software tools, and expanding local compute infrastructures—while accelerating fundamental research, development of new applications, and reducing project costs.

NASA has been working with computational portal provider Parabon Computation, with announcements about that collaboration going back as far as January of last year (see here, and here). That collaboration was expanded into a $600,000, two-year effort in February of this year; here is a portion of that press release

Built upon Parabon’s Frontier Grid Platform, which manages some of the largest computational grids, the new Modeling and Simulation as a Service (M&SaaS) solution will provide web-based Platform as a Service tools. These tools – such as a browser-based source code editor, online collaboration utilities, and virtualized build and runtime environment management interfaces – will allow developers to more efficiently create and modify a wide variety of high-performance computing (HPC) applications. In addition, the web-centric nature of the project will allow researchers around the world to work together seamlessly, removing barriers that have heretofore hampered scientific collaboration, dramatically increasing productivity for NASA and other organizations.

If I was a betting man I’d say that NEX is probably built on Frontier Grid Platform, but I’m not, so I’ll just send a few emails instead. Let you know what I find out.

According to the NEX wiki, the portal will be available to researchers beginning in May.

[UPDATE: I got in touch with the fine folks at Parabon today, and they let me know that NEX is not built on their technology. Good thing I'm not a betting man.]

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The quest for graphene-based electronics

John West — Fri, 16 Apr 2010 12:42:43 +0000

Engineers at Ohio State University have made progress on research that may enable them to mass produce graphene, a form of carbon that has lots of interesting properties, courtesy of their friendly neighborhood supercomputer

Experts believe that graphene — the sheet-like form of carbon found in graphite pencils — holds the key to smaller, faster electronics. It might also deliver quantum mechanical effects that could enable new kinds of electronics.

…“Graphene has huge potential — it’s been dubbed ‘the new silicon,’” said Padture, who is also director of Ohio State’s Center for Emergent Materials. “But there hasn’t been a good process for high-throughput manufacturing it into chips. The industry has several decades of chip-making technology that we can tap into, if only we could create millions of these graphene structures in precise patterns on predetermined locations, repeatedly. This result is a proof-of-concept that we should be able to do just that.”

Daydreams of potential uses include chemical sensors, and in future computer chips

Researchers have shown that a single sheet, or even a few sheets, of graphene can exhibit special properties. One such property is very high mobility, in which electrons can pass through it very quickly — a good characteristic for fast electronics. Another is magnetism: magnetic fields could be used to control the spin of graphene electrons, which would enable spin-based electronics, also called spintronics.

What’s the computing angle?

In computer simulations, they found that each material [tested as a potential substrate] interacts differently with the graphene. So success might rely on finding just the right combination of substrate materials to coax the graphene to break off in one or two layers. This would also tailor the properties of the graphene.

Those simulations were run at the Ohio Supercomputer Center using the Vienna Ab-initio Simulation Package. From OSC’s web site

“The calculations are computationally very demanding for the systems under consideration due to their size and complexity, and they couldn’t have been done without our allotment at the Ohio Supercomputer Center,” Windl explained. “Based on our initial success with these computer simulations, we currently model adhesion on different substrates along with the resulting electrical transport through the graphene to optimize the stamping process and the resulting devices.”

More in the article at the link above, along with a pointer to a detailed paper in the journal Advanced Materials.

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Supercomputing and the fight against H1N1

John West — Thu, 15 Apr 2010 16:56:00 +0000

OSC sent us news this week about a researcher at The Ohio State University who has been using OSC’s supers to develop a new application to track and analyze the genetic codes of swine flu virus as it travels the world, moving from host to host and mutating to resist antiviral drugs.

In a journal article published in the April 2010 online issue of Cladistics, Daniel Janies, Ph.D., explains how Supramap (http://supramap.osu.edu) was created to track the avian influenza virus (H5N1) and, more recently, to monitor the H1N1 virus. Cladistics refers to the scientific classification of living organisms, based on common ancestry, into evolutionary trees. Evolutionary trees are used by many researchers studying infectious diseases to understand the geographic and host origins of pathogens and how the pathogens change over time. Supramap puts phylogenies in a geographic context as well.

“The integration of our core phylogenetic reconstruction codes with Supramap has allowed an entirely new way to view linked evolutionary and geographic information,” said Ward Wheeler, a coauthor of the article and curator-in-charge of scientific computing at the American Museum of Natural History (AMNH). “The Supramap tool set has broad utility not only in tracking human disease in time and space, but historical patters of biodiversity and global biotic changes.”

This is one of those applications that just screams for someone to think hard about how to make it available to non-HPC specialists.

Janies and his colleagues used a small cluster computer at OSU to beta-test the Supramap application, which has been developed through a grant from the Defense Advanced Research Projects Agency (DARPA).

The research team also adapted the Supramap code to function smoothly on the OSC’s flagship IBM Cluster 1350 “Glenn” system, which features 9,500 cores and 24 terabytes of memory. They now are working with the Center’s staff to finish development of a Web interface to provide easy Internet access to the application by scientists and public health officials.

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