The 1000 bull genomes project aims to provide a large database of genetic variants for genomic prediction and genome wide association studies in all cattle breeds for the bovine research community.
Over at the Texas Advanced Computing Center, writes that researchers from Iowa State University are using TACC supercomputing resources to better understand bovine DNA.
Harnessing information from DNA sequences in buffalo and cattle is an important step in meeting the growing world’s demand for food. As the world’s population approaches nine billion people in 2050, the demand for food will double. Researchers are hoping new DNA variants will be identified for use in breeding programs to increase milk and meat production. Advances in DNA sequencing technologies are generating a stampede of sequence data for both the water buffalo and bovine research communities.
With help from computational experts at TACC, the researchers were able to sequence data that previously required three weeks of computing time in only 8 to 10 hours. Read the Full Story.
Adaptive Computing Enhances Moab Cloud Suite 7.2. Brady Kimball from Adaptive Computing describes enhancements to the Moab Cloud Suite, an intelligent cloud management end-to-end platform. The suite provides touchless cloud service optimization across the full cloud service life cycle including agility, cost savings and service performance.
Adaptive Computing Leverages Torque to Manage Intel Xeon Phi Resources. Nick Ihli from Adaptive Computing demonstrates how the company’s Torque resource manager works with Intel Xeon Phi. By relaying Intel Xeon Phi instrumentation such as memory availability to the company’s Moab workload manager, the system is able to schedule coprocessor resources efficiently.
Community HPC Clusters at Purdue University. Andrew Howard from Purdue discuss has the community cluster program has moved forward with the help of Moab software at the Rosen Center for Advanced Computing.
COSMOS – Fundamental Cosmology, Dark Energy, and the Cosmic Microwave Sky. The COSMOS Supercomputer Consortium, founded by Stephen Hawking and part of the Science and Technology Facilities Council DiRAC High Performance Computing facility, has chosen Moab HPC Suite 7.2 to manage its groundbreaking scientific computing workloads.
Moab/TORQUE Support for Intel Xeon Phi. The latest version of Moab was designed to recognize and work with the new Intel Xeon Phi coprocessors, including the ability to automatically detect coprocessors and determine their location and availability.
Moab HPC Suite – Remote Visualization Edition at SC12. With Moab HPC Suite — Remote Visualization Edition, you can improve the productivity, collaboration and security of the design and research process by only transferring pixels instead of data to users to do their simulations and analysis.
Demo: Allinea MAP Profiling Tool. Mark O’Connor from Allinea demonstrates the company’s new MAP performance profiler tool, a unique offering with extremely low overheard.
Altair
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.
Altair Speeds RADIOSS at SC12 Using Intel Xeon Phi. James Reinders and Paresh Pattani from Intel discuss how the new Intel Xeon Phi is already powering engineering applications like RADIOSS. Altair was able to port both the explicit and implicit versions of the RADIOSS code in short order.
AMD Powers Penguin Computing at SC12. Penguin Computing CTO Phil Pokorney describes the company’s full range of power-efficient integrated cluster solutions for HPC.
Colfax Offers Powerhouse Xeon Phi Server and Code Optimization Course at SC12. Mike Fay from Colfax International describes the company’s new CXP9000 server with up to eight Intel Xeon Phi coprocessors. After that, Vardim Karpusenko provides an overview of the company’s new training courses on optimizing code for Xeon Phi.
Cycle Computing
Cycle Computing Spins up HPC in the Cloud. Jason Stowe from Cycle Computing describes how the company helps customers maximize the utilization of existing supercomputing infrastructure and bridge the gap between traditional data centers and on-demand utility supercomputing.
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
Dell Powers Genomics Research Computing and Personalized Medicine at SC12. Glen Otero from Dell discusses his Birds of Feather session on Personalized Medicine at SC12. The company is working with researchers to enable faster, more cost-effective genome sequencing to enable better healthcare for us all.
Dell HPC Keeps Focus on Helping Researchers. Tim Carroll from Dell discusses the company’s recent Stampede supercomputer installation at the Texas Advanced Computing Center and how the company focuses on helping researchers.
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.
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.
Altair Speeds RADIOSS at SC12 Using Intel Xeon Phi. James Reinders and Paresh Pattani from Intel discuss how the new Intel Xeon Phi is already powering engineering applications like RADIOSS. Altair was able to port both the explicit and implicit versions of the RADIOSS code in short order.
Colfax Offers Powerhouse Xeon Phi Server and Code Optimization Course at SC12. Mike Fay from Colfax International describes the company’s new CXP9000 server with up to eight Intel Xeon Phi coprocessors. After that, Vardim Karpusenko provides an overview of the company’s new training courses on optimizing code for Xeon Phi.
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.
Intel Xeon Phi at the University of Tokyo. Professor Kei Hiraki from the University of Tokyo discusses the historical development of accelerator technology that has culminated in the new Intel Xeon Phi coprocessor.
Intel Parallel Studio XE Demo at SC12. Steve Lionel from Intel demonstrates the Intel Parallel Studio XE. Available for Linux and Windows, the studio suite eases application development for Xeon CPUs and Intel Xeon Phi coprocessors.
Intel Cluster Studio XE Demo at SC12. Gergana Slavova from Intel demonstrates the Intel Cluster Studio XE, an integrated tool suite for HPC development.
Demo: Intel Advisor XE 2013 Transforms Serial Code for Intel Xeon Phi at SC12. In this video from SC12, David R. Mackay from Intel demonstrates the Intel Advisor XE 2013, a design tool that helps you to transform serial code to run well on multicore hardware (such as the Intel Xeon Phi) by forecasting what might happen if the code executes in parallel.
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.
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
AMD Powers Penguin Computing at SC12.Penguin Computing CTO Phil Pokorney describes the company’s full range of AMD Opteron integrated cluster solutions for HPC.
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.
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.
Slidecast: Solarflare Processing NICs Do HPC Custom Compute. Solarflare President & CEO Russell Stern describes how the company develops network interface software and hardware to transform the way applications use networks, providing industry-leading application acceleration for the most demanding scale-out compute environments.
Spectra Logic
Spectra Logic Tape Storage Technologies Taking Off at SC12. Molly Rector from Spectra Logic describes the latest advancements in the company’s tape-based storage technologies. Along the way, she debunks the myth that Amazon’s AWS Glacier offering will be the death of tape.
Texas Instruments Offers System on a Chip for HPC. Based on its award winning KeyStone architecture, TI’s SoCs are designed to revitalize cloud computing, inject new verve and excitement into pivotal infrastructure systems and, despite their feature rich specifications and superior performance, actually reduce energy consumption.
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
Xyratex Announces OEM Deals with Dell and HPC at SC12. Mike Stoltz from Xyratex describes the company’s ClusterStor products for HPC. The company recently announced that HP and Dell will resell ClusterStor to power their advanced HPC clusters.
This week Mellanox announced that its end-to-end FDR InfiniBand technology is powering the Stampede supercomputer at the TACC. As the most powerful supercomputing system in the NSF XSEDE program, the 10 Petaflop Stampede system integrates thousands of Dell servers and Intel Xeon Phi coprocessors with Mellanox FDR 56Gb/s InfiniBand SwitchX based switches and ConnectX-3 adapter cards.
The InfiniBand network was easy to deploy and delivers incredible application performance on a consistent basis,” said Tommy Minyard , director of Advanced Computing Systems, TACC. “Utilizing Mellanox FDR 56Gb/s InfiniBand provides us with extremely scalable, high performance — a critical element as Stampede is designed to support hundreds of computationally- and data-intensive science applications from around the United States and the world.”
Stampede supports national scientific research into weather forecasting, climate modeling, drug discovery and energy exploration and production. Read the Full Story.
The book benefits software engineers, scientific researchers, and high performance and supercomputing developers in need of high-performance computing resources, by:
Providing a guide to exploiting the parallel power of the Intel Xeon Phi coprocessor for high-performance computing
Presenting best practices for portable, high-performance computing and a familiar and proven threaded, scalar-vector programming model
Including simple but informative code examples that explain the unique aspects of this new highly parallel and high performance computational product
Covering wide vectors, many cores, many threads and high bandwidth cache/memory architecture
I got my hands on a preliminary copy of the book back in November at SC12, and I can tell you that Jim and James did a great job.
The book release coincides with the formal dedication of the Stampede supercomputer at the Texas Advanced Computing Center in Austin. Stampede is currently ranked number seven on TOP500, with over 6400 Intel Xeon Phi coprocessors. Jeffers and Reinders have today committed several hundred books to support TACC’s training efforts for Stampede.
Big Data requires big computing, and the University of Illinois at Urbana-Champaign is doing its part with the launch of Blue Waters, one of the world’s fastest supercomputers.
U of I held an open house a couple of weeks ago, inviting one and all to visit its National Petascale Computing Facility and kick the tires on the $200 million machine built by Cray and funded by the National Science Foundation.
This is a petaflop machine designed to handle the challenging Big Data requirements associated with a wide range of problems – everything from unraveling complex biological systems to simulating the evolution of the cosmos.
This is where you go to get answers to questions about how the world works,’ says Bill Gropp, a computer science professor and one of four U of I researchers who oversaw the five-year development of the machine,” according to a story in Crain’s Chicago Business. The article goes on to say, “Blue Waters will keep the university in the lead on large-scale computing as researchers from around the country apply to the National Science Foundation to use the machine to crunch data for medical research, astrophysics, aerodynamics, weather forecasting, national security and other uses.”
This is not your everyday supercomputer. The Blue Waters system is a Cray XE/XK hybrid machine made up of AMD 6276 “interlagos” processors with a nominal clock speed of at least 2.3 GHz) and NIVIDIA GK110 Kepler accelerators, all connected by the Cray Gemini torus interconnect.
Blue Waters is capable of a sustained speed of over one petaflop, allowing it to perform more than one quadrillion calculations per second. The water-cooled system is housed in 276 black cabinets topped by silvery coolant pipes.
In addition to being really fast, Blue Waters has more than enough memory to handle Big Data requirements – 1.5 petabytes of total system memory and 300 petabytes of long-term storage.
In the Crain’s article, Gropp is quoted as saying, “We want people to ask, ‘What could you do if you could put massive amounts of data on a system and access it in microseconds?’”
The short answer is, “More than you can ever imagine.”
In this video from the HPC Advisory Council Switzerland Conference, Karl Schulz from the Texas Advanced Computing Center presents: Experiences from the Deployment of TACC’s Stampede System.
Stampede is one of the largest computing systems in the world for open science research. Stampede system components are connected via a fat-tree, FDR InfiniBand interconnect. One hundred and sixty compute racks house compute nodes with dual, eight-core sockets, and feature the new Intel Xeon Phi coprocessors. Additional racks house login, I/O, big-memory, and general hardware management nodes. Each compute node is provisioned with local storage. A high-speed Lustre file system is backed by 76 I/O servers.
Can scientists enlist bacteria to help save the planet? University of Texas professor Jeffrey Barrick is using TACC supercomputers to understand radical mutations and design artificial organisms.
As described in the September 2012 issue of Nature, Barrick’s research studied the rapid evolution of E. coli to trace key changes that lead to an evolutionary innovation. Using next-generation DNA sequencers and the powerful Lonestar and Ranger supercomputers at TACC, he was able to test 40 genomes from the population and trace the key changes that potentiated the mutation and showed the role of promoter capture and altered gene regulation in evolutionary innovations.
I think a lot about the engineering aspect: making bacteria do useful things,” Barrick said. “I would like bacteria to solve our energy crisis, whether that means making biofuels or something crazy like putting molecular motors in algae that push water to run a generator.”
Across the field, advanced computing is allowing researchers like Barrick to analyze genomes, develop and test synthetic organisms, and experiment with artificial populations, all of which help scientists explore evolution on a far finer-grained level.
When this E. coli experiment started, all they could measure was fitness. They had no clue why certain E. coli strains were better,” Barrick said. “Now we can understand at the molecular level what’s going on, and that’s really powerful.”
In the supercomputing world, we often think of things in tens. Over at TACC, Aaron Dubrow has posted a series of interviews with ten of the top HPC minds in Texas. With a focus what on what terascale, petascale, and exascale means to them and their field, the interviews cover a broad base of application user space.
Recently, a mouse with diminished interferon (proteins made and released by host cells in response to the presence of pathogens such as viruses, bacteria, parasites or tumor cells) was identified in our laboratory, said Bruce Beutler, Regental Professor and Director, Center for Genetics of Host Defense, UT Southwestern Medical Center. “Because we had sequenced the genomic DNA of its grandfather, we knew that the mouse likely had a mutation in a gene coding for the protein kinase TBK1. Without any mapping, we determined the exact cause of the phenotype. In former times, before it was possible to routinely sequence the genome of these mice, we would have spent months and thousands of dollars arriving at this same conclusion. This is a hint of the speed and dexterity that advanced computing can provide. It permits us to exclude obvious causes of phenotype and concentrate on what is new. Our research would be impossible without enormous computational resources.
Today OpenSFS announced that Tommy Minyard from TACC has been elected the Community Representative Director for the 2013 term. The term runs from March to March each year.
From the early days, TACC has been a major supporter of the work OpenSFS has done leading Lustre and other open source file systems development. I thank the OpenSFS board for this vote of confidence. I really look forward to contributing in this role, squarely focused on the community,” said Tommy Minyard, Director of Advanced Computing Systems at the Texas Advanced Computing Center (TACC). “Lustre has come a long way in the past two years, but we need to continue to keep the community in the forefront. The more involvement, the stronger the community gets.”
Minyard replaces Stephen Simms from Indiana University who has served as Community Representative Director for an extremely successful 2012 term. Read the Full Story.
In related news, the Lustre User Group 2013 conference will take place in San Diego April 16-18.
There is no doubt that the Sequester is putting extreme pressure on critical R&D in this country. As members of the HPC community, how can we help to ensure that we continue to fund important supercomputing research?
In this video from February 15, 2013, the House Subcommittee on Research holds a hearing on Applications for Information Technology Research & Development.
Witnesses:
Dr. Kelly Gaither, Director, Visualization Lab, Texas Advanced Computing Center, University of Texas, Austin
Dr. Ed Lazowska, Bill and Melinda Gates Chair in Computer Science and Engineering, University of Washington
The topic of this afternoon’s hearing, Applications for Information Research & Development, is important to our national security, global competitiveness and technological innovation. This hearing will provide us with examples of practical applications and the benefits of Federal investment in networking and information technology R&D. The Networking and Information Technology Research and Development program, or NITRD, was originally authorized in 1991 in the High Performance and Computing Act. It coordinates the networking and information R&D efforts of 15 Federal member agencies, including DHS, NASA, NIH, EPA and the Department of Energy. The program is the main R&D investment portfolio of member agencies in networking, computing, software, cyber security and related information technologies totaling over $3.7 billion in FY2013.
On behalf of insideHPC, I just want to say, “Great job, Kelly!” Read the Full Story.
In this RCE podcast, Brock Palen and Jeff Squyres speak with James Browne, Leonardo Fialho, and Ashay Rane about PerfExpert, an easy-to-use performance diagnosis tool for HPC applications with suggestions for bottleneck remediation.
Over at the Texas Advanced Computing Center, Paromita Pain writes that researchers at the Mount Sinai School of Medicine are using TACC supercomputers to better understand membrane proteins, which play a major role in determining whether medications are efficient and whether they have side effects.
According to Dr. Marta Filizola, understanding how opioid receptors work is an important aspect of research at the lab. Her team creates simulations that reveal the way proteins (which are never static) interact with drug molecules and other proteins. These animations help identify the factors that contribute to a molecular-level understanding of the mechanism of action of drugs at individual or oligomeric receptors. This information is used to create more efficient medications or to stop unpleasant side effects.
Side effects are an important issue,” Filizola says. “We can develop the best pain curing medication ever, but if it causes an addiction then how good is it really?”
