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Indiana University Dedicates Big Red II Supercomputer

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Today Indiana University unveiled the Big Red II supercomputer, a hybrid petascale Cray system.

There are other universities that hold legal title to computers as fast or faster than Big Red II, but IU is the first in the world to have its own one petaFLOPS supercomputer as a dedicated university resource,” said Craig Stewart, IU Pervasive Technology Institute executive director and associate dean of research technologies. “Big Red II will be used by IU, for IU to support IU’s activities in the arts,humanities and sciences, and to support the economic development of Indiana, without any constraints from an outside funding agency.”

The new system is a next-generation Cray XK supercomputer, specifically crafted for IU’s needs. Housed in the university’s state-of-the-art Data Center, Big Red II has more than 21,000 computer processor cores (compared to Big Red’s 4,100). Big Red II will support big data applications in computational research. To further advance Big Data research, IU is also implementing a new disk storage system called the Data Capacitor II (DCII), a five petabyte, high speed/high bandwidth storage system.

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HPC Advisory Council European Workshop Coming to Leipzig June 16

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The HPC Advisory Council will hold their 2013 European Conference on June 16th, 2013, in conjunction with the ISC’13 conference in Leipzig, Germany. The workshop will focus on HPC productivity and futures, and will bring together system managers, researchers, developers, computational scientists and industry affiliates to discuss recent developments and future advancements in supercomputing.

The Call for Speakers and initial agenda are now posted. See you in Leipzig!

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Student Programming Competition Coming to XSEDE13 this Summer

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Students from high school to grad school levels are invited to participate in a programming contest at XSEDE13 high performance computing conference, which takes place in San Diego on July 22-25.

Created as an opportunity to showcase student expertise in a friendly yet spirited competition, the XSEDE13 Student Programming Competition aims to introduce the next generation of students to the high-performance computing community. Over the last couple of years, the competition has drawn teams from around the world, including China, South America, Canada, Africa and Europe. With access to parallel computing resources, teams consisting of up to five students (high school, undergraduate, and/or graduate students) will receive a variety of interesting computational science problems to address at the conference. Awards will recognize creativity, quality of solutions, and good coding practices of the teams who solve the most problems during the daylong competition.

Contest registration will open April 30, 2013 and close May 30, 2013.

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insideHPC Video Archive

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insideHPC Video Archive

We try to keep this page up to date, but you can always find our latest works on our RichReport YouTube Channel.

2013 Event Coverage:

SC12 Videos (Alphabetical by Vendor Name):

Adaptive Computing

Adaptive Computing SC12 Booth Theater

Aeon

Allinea

Altair

AMD

Asetek

Bull

CAPS-Enterprise

Colfax International

Cycle Computing

DDN

  • DDN Powers Genomics at the Virginia Bioinformatics Institute. Dr. Harold (Skip) Garner from the Virginia Bioinformatics Institute describes how Big Data I/O is required to crunch Genomics data in the fight against cancer.
  • DDN Ramps Up for Exascale at SC12. Jeff Denworth from Data Direct Networks describes the company’s high performance storage solutions for HPC. Used by 60 percent of the TOP100 supercomputers in the works, DDN recently announced a $100 Million dollar investment in Exascale technologies.
  • Steve Simms on the Data Capacitor II at Indiana University. Steve Simms from Indiana University describes a recent upgrade to the Data Capacitor project, a high-speed, high-capacity storage facility for very large data sets. With 5 PB of storage, Data Capacitor II will support big data applications used in computational research. IU partnered with DDN to develop Data Capacitor II, which is scheduled to be installed in the IU Data Center in spring 2013.

Dell

Gnodal

HPC Advisory Council

  • HPC Advisory Council Announces Student Cluster Teams for ISC’12. Gilad Shainer, Tong Liu, and Pak Lui from the HPC Advisory Council revue the organization’s outreach efforts for the past year and look forward to 2013. The council is an active sponsor of international Student Cluster Competitions that encourage young people to learn parallel programming skills.

IBM

IDC

  • IDC HPC Market Update from SC12. Did you know that 3Q2012 was the biggest quarter of revenue in the history of HPC? In this video from SC12, Earl Joseph from IDC presents the latest on the supercomputing market.

Inktank

  • Inktank Boosts Open Source Ceph File System. Neil Levine from Inktank describes the company’s efforts to commercialize and support the Ceph open source file system. With high reliability and nearly unlimited scalability, Ceph has great potential for Big Data applications as well as an enabling technology for Exascale computing.

Intel

Intersect360 Research

NAG

Nirvana

Numascale

Nvidia

Mellanox

  • Mellanox Breaks Performance Records, Dominates TOP500 at SC12. Todd Wilde from Mellanox describes the company’s recent advancements in high speed InfiniBand interconnects. Infiniband recently InfiniBand has become the leading interconnect on the TOP500 with 224 clusters and the Connect-IB dual-port 56Gb/s FDR InfiniBand adapter recently achieved the industry’s highest throughput of more than 100Gb/s utilizing PCI Express 3.0 x16 and over 135 million messages per second, 4.5X higher than previous or competing solutions.

OpenSFS & EOFS

Panasas

  • Panasas Showcases ActiveStor 14 at SC12. By accelerating small file and metadata performance with Solid State Drive (SSD) technology, ActiveStor 14 delivers extreme performance, for the technical computing and big data workloads commonly found in HPC environments.
  • Panasas Chief Scientist on Where HPC Meets Big Data and Hadoop. Panasas ActiveStor not only accelerates product design and scientific discovery applications, but will perform seamless Hadoop analyses, ensuring that customers can extract maximum value from their existing big data infrastructure.

Penguin Computing

Rogue Wave Software

Samplify

SC12 Committee

  • SC12 Press Conference with Jeff Hollingsworth. In this video, SC12 General Chair Jeff Hollingsworth opens the show press conference in Salt Lake City. This year there were a record number of exhibitors have booths at the show. Recorded Nov. 12, 2012.

Scalable Informatics

Seneca

SGI

  • Interview: SGI Teams with Altair on the Road to Exascale. Paul Kinyon from SGI’s product management team describes how the company is working with partners like Altair to solve customer’s toughest computational challenges. The company is looking at a range of technologies that could enbable Exascale computing capabilities at a practical level of power consumption.
  • Intel Xeon Phi Adds Smarts to SGI UV. SGI’s Chief Marketing Office Franz Aman describes the company’s full range of solutions featuring the new Intel Xeon Phi coprocessor for HPC.

Solarflare

Spectra Logic

Supermicro

Sugon

Texas Instruments

The Portland Group

  • PGI’s Michael Wolfe on OpenACC Directives for GPUs. Michael Wolfe from The Portland Group discusses the origins of the OpenACC standard for programming directives in GPUs. He also weighs in on the recent OpenMP 4.0 technical report, which proposed to incorporate OpenACC directives into OpenMP 4.0 sometime in 2013.

VMware

  • Interview: Josh Simons on HPC Cloud Trends at SC12. Josh Simons from the VMware CTO office describes recent trends in Cloud Computing for HPC. The company is looking at how virtualization technologies could benefit supercomputing on the road to Exascale.

Xyratex


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George Michael Fellowship Helps HPC Community Thrive

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For doctoral candidates in supercomputing, the George Michael Memorial HPC Fellowship offers a rapid plug-in to the global network of leading high performance computing organizations, from research institutions to industry.

Past recipients report that the fellowship ticket to the annual supercomputing conference (SC) can be a career affirming and life changing experience.

Coupled with the opportunity to display my research at a well-attended conference, the Fellowship has had a tremendous impact on my work future,” said Ryan Gabrys, a 2012 fellow. “The George Michael Fellowship has provided me with more freedom to pursue the areas of research I find the most exciting.”

A doctoral student at UCLA, Gabrys’ HPC specialty is coding for HPC storage systems.

Fellowship candidates are exceptional PhD students whose research focus is on high-performance computing (HPC) applications, networking, storage, or large-scale data analysis using the most powerful computers currently available.
Recipients of the George Michael Memorial HPC Fellowship receive a $5,000 honorarium, travel and registration for SC13, and recognition at the SC13 Awards Ceremony. Past recipients report that the fellowship ticket to the supercomputing conference (SC) can be a career affirming and life changing experience.

The deadline of May 1 to apply for the 2013 fellowship is rapidly approaching. To apply or for more information, see the SC13 website.

Xinyu Que, a 2011 fellow, notes that the fellowship helps students make the most of what can be an “overwhelming” experience at SC. “It provides opportunities to meet other George Michael fellows and make new connections. The profound technical talks helped me better understand research topics and trends.

Not only did I have a chance to present and demonstrate my doctoral research to well-known, senior researchers, but I also learned about future challenges and opportunities in my research areas. It was very stimulating,” said Que, who at the time was a doctoral candidate in Parallel Architecture and System Laboratory in the Department of Computer Science & Software Engineering at Auburn University.
Abhinav Bhatele, a 2009 fellow from the University of Illinois Urbana-Champaign, found the fellowship an effective vehicle for spreading the word about his research. “The fellowship award has been instrumental in disseminating my research and dissertation work on ‘topology aware task mapping’ within the field of HPC,” said Bhatele, who is now a researcher in the Computation Department at Lawrence Livermore National Laboratory. “It also has helped me to connect with others in the field and I have become good friends with other George Michael fellows.”

For Ignacio Laguna Peralta, another 2011 fellow, the fellowship offered the opportunity to get feedback from experts in his field – failure diagnosis and localization in HPC applications.

I received constructive criticism of my work, which I used to improve it. Also, I was able to interact with other students and researchers in my field and to gain valuable professional connections,” said Laguna Peralta, who received his PhD. from Purdue in 2012. “Other benefits of the fellowship include the opportunity to visit and present research to a variety of organizations. This helps in finding collaborators in labs or companies outside your University and in making connections for a future job.”

The fellowship introduced Mark Hoemmen to the Supercomputing Conference (SC) and opened his eyes to the breadth and vitality of the HPC community. Hoemmen, a specialist in architecture-aware iterative linear solvers, currently works at Sandia National Laboratories in New Mexico.

Had I not received the Fellowship, I might not have attended the conference until later in my career, and I might have missed out on seeing how grand and dynamic the field of HPC is,” said Hoemmen, a 2008 fellow from UC Berkeley. “It struck me how much interest industry has in the conference, not just as vendors of HPC technology, but also as consumers. This helped me better understand industry’s interest in HPC, which has served me well in my current responsibility as a central developer of a popular open-source scientific software product.”

Sponsored by the ACM and the IEEE-CS, the George Michael fellowship seeks to address the critical issue of training the next generation of high performance computing scientists and engineers.

The late George Michael, a computational physicist at Lawrence Livermore, was a founder of the annual supercomputing conference (SC), which is now in its 25th year. Michael, who died in 2008, is remembered for his ability to bring together diverse talent from academia, industry and national labs to advance HPC.

To qualify, applicants must be enrolled in a full-time PhD program at an accredited college or university and are expected to have completed at least one year of study in their doctoral program. Women, minorities, and all who contribute to workforce diversity are encouraged to apply.

For more information or to apply, visit the SC13 site. Submissions opened in early March and will close on May 1.

Please send any questions to: hpc-fellowship-questions@info.supercomputin[email protected]

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Predicting Twisters with HPC

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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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Allinea DDT Goes to 4.0, Brings HPC Software Development Closer to Home

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The new Allinea DDT 4.0 release is designed to make it easier for scientists to debug and optimize HPC code even when they’re on the road.

We’ve got a lot of academics, lab people, and industry people who are on the road a lot for conferences and meetings. It’s important for them to be able to work remotely,” says David Bernholdt, a senior computational scientist in R&D at ORNL. “Instead of having to put statements in the code, recompile, reset, and go through this whole long cycle, they’ll be able to pop up their clients on their laptops and figure out what’s going on right away.”

The release of Allinea DDT 4.0 includes native remote clients for Linux, Windows and Mac. These clients allow debugging of HPC applications, wherever they are hosted – on nationwide HPC resources or out in the rapidly growing HPC Cloud.

The new native client approach is paying dividends for users. “The advantage of a true native client is in the response times,” adds Chris January, VP Engineering at Allinea, “when you’re debugging code on a cluster you don’t want a slow connection to make you step twice or accidentally delete breakpoints. Only a native client can respond quickly enough to keep users in complete control.”

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Sign Up for the Argonne Training Program on Extreme-Scale Computing, July 28-August 9

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Computational scientists are invited to register for the upcoming Argonne Training Program on Extreme-Scale Computing (ATPESC). The event will take place in the greater Chicago area from July 28-August 9, 2013.

The program provides intensive hands-on training on the key skills, approaches, and tools to design, implement, and execute computational science and engineering applications on current high-end computing systems and the leadership-class computing systems of the future. As a bridge to that future, this two-week program to be held in suburban Chicago fills the gap that exists in the training computational scientists typically receive through formal education or other shorter courses.

Applications are currently being accepted for the program. The deadline for applying is May 22, 2013. Read the Full Story.

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INCITE-ful Proposals Now Being Accepted

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Proposals are now being accepted for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. INCITE will allocate more than five billion core-hours on leadership-class supercomputers in 2014.

INCITE enables transformational advances in science and technology for computationally intensive, large-scale research projects through large allocations of computer time and supporting resources at the Argonne and Oak Ridge Leadership Computing Facility (LCF) centres, operated by the US Department of Energy (DOE) Office of Science.

INCITE seeks research enterprises for capability computing: production simulations – including ensembles – that use a large fraction of the LCF systems or require the unique LCF architectural infrastructure for high-impact projects that cannot be performed anywhere else to address some of the toughest challenges in science and engineering.

INCITE is currently soliciting proposals of research for awards of time on the 27-petaflop Cray XK7 ‘Titan’ and the 10-petaflop IBM Blue Gene/Q ‘Mira’ beginning Calendar Year (CY) 2014. Average awards per project for CY 2014 are expected to be on the order of tens to hundreds of millions of core-hours. Proposals may be for up to three years. The INCITE programme is open to US- and non-US-based researchers and research organisations needing large allocations of computer time, supporting resources and data storage. Applications undergo a two-phase review process to identify projects with the greatest potential for impact and a demonstrable need for leadership-class systems to deliver solutions to grand challenges.

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

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Roadmap Update Published for HPC Research in Europe

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The good folks at the PlanetHPC project have published an update to their report: “A Strategy for Research and Innovation through High Performance Computing.” The report makes the case for investment in HPC at the European level, and suggests a strategy for HPC research, development, and innovation.

High Performance Computing (in common with the computing domain in general) is at a cross roads; technological challenges threaten to disrupt three decades of continuous exponential growth in the computational power of HPC systems. Europe must act to counter this threat. HPC is a proven technology for delivering economic and societal benefits, and many developed and emerging economies outside the European Union are investing heavily in it. Many countries have recognised that to out-compute is to out-compete.

Download the Report (PDF).

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DDN to Build World’s Fastest Storage System for Titan Supercomputer

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Today DDN announced that Oak Ridge National Laboratory has selected the company to build the “world’s fastest storage system” to power the #1 Titan supercomputer.

Using DDN’s SFA12K-40 storage systems as the backbone for Spider II, this new file storage system is designed with 40 petabytes of raw capacity and is capable of ingesting, storing, processing and distributing research data at unprecedented speed. This amount of storage capacity is equivalent to more than 227,000 miles of stacked books – or the distance from ORNL’s facility in Oak Ridge, TN to the moon – and enables ORNL to dramatically increase Titan’s computational efficiency and deliver vastly more accurate predictive models than ever before.

The DDN storage system will deliver over 1 Terabyte/sec in throughput to drive radical advances in science and Big Data analysis essential to DOE and Office of Science Missions.

When building the world’s fastest system for data intensive computing, we carefully considered all aspects of high-throughput I/O infrastructure and how efficient storage platforms can complement our supercomputer’s efficiency. The ORNL and DDN teams have worked together to architect a file system designed to enhance the performance of our Titan supercomputer and enable our users to achieve unprecedented simulations and big data insights through massively scalable computing.”

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Jeff Layton on the Cloud’s Changing Role in HPC

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Over at Admin HPC, Dell’s Jeff Layton writes that a pair of recent use cases have helped changed his mind about the validity of using the Cloud for HPC.

At first, it was fairly easy to dismiss cloud computing for traditional HPC workloads. The “HP,” after all, stands for “high performance,” and doing anything to reduce performance is counterproductive. You are paying more and getting less. However, new workloads are being added to HPC all of the time that might be very different from the classic MPI applications in HPC and have different characteristics. The amount of computation in these new workloads is increasing at an alarming rate – so much so, that I think HPC is giving way to RC (research computing).

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Should CFD be an Exact Science?

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Over at the IMAGINiT CFD Blog, Ryan Stamm writes that while Computational Fluid Dynamics is not an exact science, it is good engineering.

I’ve been asked to carry out results data to 3 or 4 decimal places! Really? Do results showing 4.015 psi drive product development in a different direction than 4 psi? If so, you don’t need CFD simulation, you need a professor and enough capital to embark on a 6 month research project. Don’t get me wrong, CFD analysis can be exact! However it requires a high degree of scrutiny and more time to capture every minuscule detail. I come across many engineers who feel the need to include every detail is required to derive any value from simulation. This cannot be further from the truth. CFD can be exact but CFD does not have to be exact to drive product development decisions.

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Poland Gives Green Light to Blue Gene Project

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IBM Blue Gene/Q, the most powerful single architecture supercomputer in Poland, has been chosen by The Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw (ICM) of Poland to support the country’s largest biomedical and biotechnological research initiative, the Centre for Pre-clinical Research and Technology (CePT).

More than 500 life sciences and biomedical researchers, physicians and students, from a consortium led by The Medical University of Warsaw (WUM) and consisting of three universities and seven research centres of the Polish Academy of Sciences, will use the supercomputer and its supporting e-infrastructure to gain further insight into chronic diseases.

CePT, a EUR 100 million project, aims to support Poland’s transition towards more preventive and patient-centric healthcare,’ said Dr Robert Sot, director of CePT, Warsaw University. The project will allow the medical community to provide a more holistic approach and open collaboration for the development of innovative treatments and drugs that will improve patients’ quality of life over the long term.”

Estimations show that more than a quarter of Poland’s ageing population has developed at least one or, very often, more chronic diseases such as: cancer, diabetes, heart disease, respiratory conditions, stroke, and neurological disorders. Early detection and timely diagnosis of these diseases translate into well-targeted and optimised healthcare, as well as improved quality of a patient’s life.

Similar demands could stimulate the need to carry out clinical and pre-clinical tests covering three to five million Polish citizens, and generate massive volumes of valuable health data which can, in turn, be used by laboratories.

ICM’s new BlueGene/Q, code named Nostromo, will help scientists process up to 16 terabytes of Big Data per sequence by running compute-intensive simulations at the speed of 209.7 trillion operations per second. The supercomputer will use algorithms moving beyond the ‘routine’ sequencing of human or animal genomes, to tackle more complex processes that will reveal the rare variants in human genetics, (i.e. those that cause predispositions to Alzheimers, cancer, diabetes, downs syndrome, etc.).

By understanding what prevents protein molecules, which build and maintain human bodies, from folding up properly and triggering a disease, scientists will be able to develop a new drug or treatment.

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

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PSC Patents Zest, a Fresh Approach to Saving Data

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Scientists at Pittsburgh Supercomputing Center (PSC) have patented Zest, software that takes a rapid “snapshot” of a supercomputer’s calculations as it works.

Zest is aimed at speeding up the ability to store complex calculations as a hedge against a system failure, saving precious supercomputing time and slowing calculations down far less than current methods.

PSC co-inventors of Zest included Paul Nowoczynski, Jason Sommerfield, Nathan Stone, and Jared Yanovich.

In the same way regular computer users save their work as they go, scientists carrying out vast computations such as those required for detailed weather predictions or earthquake science need to periodically store — or ‘checkpoint’ — the machine’s computational state. In the case of a system malfunction, this allows them to avoid having to start from the beginning after hours or days of work.

The problem, according to J. Ray Scott, director of systems and operations at PSC, is that retrieving and storing these data takes time away from calculation, which is carefully rationed to researchers using highly in-demand supercomputers. In fact, he added, over the last seven years the memory available in the largest machines has increased about 25-fold, while the capacity for retrieving that memory has increased only about four-fold.

If you have a large job, checkpointing the run often means writing out tens of terabytes of data,’ Scott explained. ‘This takes a nontrivial amount of time. The whole time you’re doing the checkpoint, you’re not using the computer.”

The Zest software works by tightly managing the supercomputer’s disk drives, continuously routing checkpoint storage to disks that aren’t being used for computation.

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

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