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High Performance Computing

High Performance Computing
A discussion venue for all things high performance computing (HPC), supercomputing, and the technologies that enables scientific research and discovery.
  • Higher Value in High Performance Computing (HPC) Advances Manufacturing

    My colleague Kirsten Billhardt blogged about this week's invitation-only Digital Manufacturing Revolution hosted by the National Center for Manufacturing Sciences (NCMS). She notes that along with the launch of the Michigan Grid Cell™ Innovation Center at GE’s Advanced Manufacturing and Software Technology Center (AMSTC) in Van Buren, Michigan, the event also focuses on the "missing middle" - those smaller companies that haven't yet adopted high-performance computing (HPC) technology.

    In her brief corresponding video she outlines three significant reasons that those organizations are quickly becoming no longer among the missing:

    1. The cost of computing power is decreasing rapidly. What used to be the exclusive purview of large, big-name manufacturers is now affordable to much smaller organizations.

    2. Correspondingly, the value and cost efficacy of HPC is more clearly understood. Allowing for hundreds and even thousands of virtual simulations saves money by freeing companies from the need to build multiple prototypes.

    3. The technological advancements allowing millions of bits of data to be run in a simulation rather than thousands of pieces of data simply allow organizations to do more in less time.

    HPC is increasingly becoming a vital part of any manufacturer's research and design capabilities - regardless of size. You can read more about the event in Kirsten's blog here.

  • Finding the Way Forward in Genomic Research

    By Kristina Kermanshahche, Chief Architect, Health & Life Sciences, Intel Corporation. Posted by Christine Fronczak

    A few weeks ago I was at an industry conference and heard a colleague engaged in cancer research talk about personalized medicine and clinical analytics, and how these two important aspects of healthcare need to come together to benefit patient care. “We have the will to do this,” he said. “But do we have the way?”

    After seeing Intel work closely with several life sciences customers and technology leaders recently, I believe we do have the way. Here are a few examples:

    • Using high performance computing, Intel and Dell are working together on the next generation of DNA analytics platforms that is breaking down barriers to data and information.
    • Working with the open source community to optimize leading genomics codes, introducing new ideas and efficiencies to the process.  Recent examples include Bowtie2 from Johns Hopkins, GATK from The Broad Institute, and ABySS from Canada’s Michael Smith Genome Sciences Centre.
    • Intel has been shoulder-to-shoulder with life science thought leaders, such as the Translational Genomics Research Institute (TGen), to accelerate scientific discoveries into actionable implementation. Close collaboration is helping everyone understand the challenges of personalized medicine and genomic sequencing, and see how technology and software optimization can help standardize and streamline the genomics pipeline.


    A key takeaway from Intel’s work with the life sciences industry is watching the dramatic decrease in the amount of time needed to gather results.

    Intel’s collaboration with TGen and Dell has focused on this aspect of genomic research. We optimized the analytics pipeline to the point where a sequencing test that used to take seven days to evaluate now can be done in four hours. This is hugely important because clinicians now have the ability to sequence multiple times during the course of a patient’s treatment, closely monitoring how that patient responds to the personalized protocols such as developing *** resistance, and perform any necessary treatment interventions within a clinically meaningful timeframe. For a cancer patient, this time savings could mean the difference between life and death. That is the way forward.

    At the end of the day, there is little doubt that genomics research is positively impacting clinical treatments. Analyzing genomic information and incorporating the data into practice is happening now. Not five or 10 years from now, but today. This translates into actionable clinical care and leads to efficient treatment plans.

    That is the way forward.

    What questions do you have about genomics, personalized medicine and clinical analytics?

    For additional information:  http://www.dellhpcsolutions.com/dellhpcsolutions/static/genomics.html

    About Kristina Kermanshahche

     Kristina Kermanshahche is Chief Architect of Healthcare/Life Sciences at Intel Corporation.  Her focus area is Big Data/Analytics in Healthcare/Life Sciences, helping to drive transformation at the intersect of Next-Gen Sequencing (NGS), high performance computing (HPC), and healthcare informatics.  She works closely with customers and ecosystem partners to optimize high throughput sequencing and analytics, overcome systemic challenges faced by the industry, and deliver solutions which accelerate adoption of precision medicine worldwide.  Her twenty-five year career in software development spans nearly every industry, with an emphasis on complex distributed systems, parallelism, high availability, networking, and data analytics.
  • High Performance Computing and Extreme Science to be discussed at XSEDE13

    Hold on to your seats - the Extreme Science and Engineering Discovery Environment (XSEDE) is almost here. The XSEDE13 event will be held in San Diego this year, July 22-25. I'm especially excited to see one of Dell's high performance computing (HPC) & life sciences experts Glen Otero participating in one of the panel discussions. Here is yet another great example of how supercomputing tools have become essential to extreme science discovery.

    XSEDE has a Biosciences Day on July 24 with the theme of focus on scientific gateways. Glen's panel is titled: Transforming Biosciences through Advancements in Computing and Data Analytics. The panel will be led by Kevin Patrick, a professor specializing in family and preventive medicine at University of California-San Diego, and also director at Center for Wireless and Population Health Systems at CalIT2.

    In addition to Glen, other panel members include:

    • Mark Adams is scientific director for the J. Craig Venter Institute
    • Alex Dickinson is senior vice president, Cloud Genomics, at Illumina, Inc.
    • Donald Jones serves as vice president of Global Strategy and Market Development for Qualcomm Life, a wholly owned subsidiary of Qualcomm Incorporated
    • Darryl León, Ph.D., is an associate director with Product Management in the Ion Torrent division of Life Technologies
    • Nicholas Schork is director of Bioinformatics and Biostatistics at the Scripps Translational Science Institute and professor, Department of Molecular and Experimental Medicine, at The Scripps Research Institute
    • Kevin Patrick is professor of Family and Preventive Medicine at the University of California, San Diego, editor-in-chief of the American Journal of Preventive Medicine and director of the Center for Wireless and Population Health Systems at the California Institute for Telecommunications and Information Technology (Calit2), San Diego Division


    It's sure to be a great event - and the panel if you are in San Diego, is not to be missed.


  • Congratulations to Students at the South Africa Centre for High Performance Computing

    Team South Africa Wins! No I’m not talking about the World Cup or some sailing competition, but the Student Cluster Competition, the world’s most prestigious high performance computing contest involving higher education students.

    STUDENT CLUSTER COMPETITION JUNE 2013 WINNING TEAM FROM SOUTH AFRICA

    Education and high performance computing (HPC) naturally go together. The two are so entwined because a lot of important scientific research takes place at institutions of higher education. It’s always exciting to watch the Student Cluster Challenge events, now held twice a year at the International Supercomputing Conference (ISC) in Germany in June, and the Supercomputing (SC) event held in the United States each November. The competition makes university-based teams compete and demonstrate the incredible capabilities of state-of-the-art HPC systems and applications on the event show-floor.

    The latest winner at ISC’13 is the CHPC team from South Africa, and here are some interesting facts from this June’s winning team:

    • Only one of two teams that completed each competition phase
    • The youngest team in the competion, consisting of all under-graduates
    • Cluster Computing System Stats: Dell PowerEdge R320/R720 servers, Dual Xeon E5-2660 processors, 512 GH member, Mellanox FDR IB, NVIDIA K20 cards

    The Student Cluster Challenge is one of my favorite programs that Dell supports – and has turned out to be a fun and unexpected program to be involved with! Under a theme of Inspiring the next generation HPC professional, Dell has sponsored multiple teams in the Student Cluster Challenge for several years. We’re thrilled another team Dell has sponsored has come out on top.  Just six months ago, the University of Texas, aslo supported by Dell, won the Student Cluster Challenge at SC12 in Salt Lake City. The reality is, this program is providing a venue for students to get involved and learn about what an exciting industry and career path the world of HPC presents. So congratulations to all of the teams who competed this year, and we’ll be watching for the next friendly yet spirited competition at SC13 in Denver.

    Read more about this win from insideHPC

  • South African HPC Student Team Wins Competition, Gains Knowledge

    At Dell, we pride ourselves in our support of the high performance computing (HPC) industry. As an example, the last few years, we have been avid supporters of the Student Cluster Competitions at the SC Conference events. The theme of supporting students has extended well beyond the SC events, and recently we had the pleasure of a special visit to the Global Engineering Lab by the winners of the South African HPC student challenge.

    South African Team during their visit to Austin, during the week of Jan. 28, 2013. *

    As a sponsor of the HPC and Data Applications for Increased Impact on Research program held in December 2012 in Durban South Africa http://www.chpcconf.co.za/, Dell agreed to provide an award for the winners of the student challenge. As part of the reward for winning, the team was flown to Austin to spend a week with Dell. Eight students and CSIR Representative David Neil Macleod spent the week of Jan. 28th in Austin. During their visit, the student team was hosted in the Dell Global Solutions Engineering (GSE) lab to get a better understanding of how Dell creates and engineers solutions. Here, they interacted with engineers not only on our HPC Solutions team but also with Converged Infrastructure Solutions, Database and Business Intelligence Solutions, Custom Solutions, Solutions Performance Analysis teams as well. Part of their trip also included a visit to Texas Advanced Computing Center (TACC). TACC recently published a great write up about the visit in its newsletter that you can read here.

    South African Team during their visit to Austin, during the week of Jan. 28, 2013. *

    Finally, this winning team will represent South Africa at the Student Cluster Competition in Germany at the annual International Supercomputing Conference (ISC) in June 2013. The students were also able to receive feedback from the Dell HPC Engineering Team about some of their design ideas for the ISC competition.

    In the end, we were honored and thrilled to host these great students at Dell, in the spirit of helping inspire and develop the next generation HPC professionals. We are also honored to be a part of Dr. Happy Sithole’s (Director of CSIR – CHPC) great vision of making South Africa the center of gravity for HPC in the African continent and we will continue to support this vision.

    Congratulations - and best of luck to the team at ISC this June!

    * Names of the students:
    Eugene Botma
    Nobantu  Evelyn Maria Khoboka
    Abednigo Setabele Masilo
    Katlego Kgobalala Moukangwe
    Muhammad Atif
    Kerren Mark Ortlepp
    Jan-Willem Walter Steeb
    Ryan David Strange
     
    CSIR Representative: David Neil Macleod
     
    Partner Representative (Eclipse Holdings): Hellen Nyatsambo
     
    Dell SA Rep who accompanied the team: Vernon Nicholls

  • Congratulations to the 2013 People to Watch in HPC

    Each year there are numerous industry awards & recognition programs that we pay attention to - some more than others. I look forward to one such program in particular, HPCWire's People to Watch 2013!

    I suppose I especially enjoy this program due to the fact that we're recognizing the people behind the HPC programs that are changing the world.

    Congratulations to everyone on the list - clearly you're making a difference in our community, and making waves that will last well beyond 2013!

    People to Watch 2013 List Details: http://www.hpcwire.com/specialfeatures/people_to_watch_2013

    Podcast Discussion of People to Watch 2013:
    http://media2.hpcwire.com/audio/130125_Episode203.mp3

  • HPC Helps Scientists at Queensland Institute of Medical Research in Fight Against AIDS

    "This is why I love my job," was the subject line of an email I received from one of our colleagues for Dell Australia, Brendan Bouffler. In exciting news, a team of scientists from Queensland Institute of Medical Research have made big progress in the fight against AIDS. According to this story from ABC News, the research team has identified a potential way turn HIV against itself! Amazing as it sounds, this is what is causing a lot of excitement from our friends Down Under.

      

    I have to agree with Brendan with how great it is to be working within this world of High Performance Computing (HPC). Time and time again we've proven that when we provide powerful HPC tools to the world's top scientists, great things happen that change our world. While still an early discovery against the fight against this terrible disease, it's very exciting to consider the possibilities.
     
    View the news broadcast and related story here: http://www.abc.net.au/news/2013-01-16/scientists-hail-potential-cure-for-aids/4466766
     
    Congratulations and good luck to Queensland Institute of Medical Research & the team of scientists working on the project. We'll be following your progress.

  • Dell HPC systems power TGen’s fight against pediatric cancer

     Editor's Note: Below is a guest blog post from James Lowey, the Translational Genomics Research Institute (TGen) Director of High-Performance Biocomputing. You can read James' full bio here, and here's his guest post.


    What a huge difference a year makes.

    Exactly a year ago this week, the Translational Genomics Research Institute, where I work as TGen’s Director of High-Performance Biocomputing, announced a partnership with Dell and the Neuroblastoma and Medulloblastoma Translational Research Consortium (NMTRC) to make a significant leap in the ability of doctors to treat children with cancer.

     As part of this partnership, Dell announced a major commitment of funding, employee engagement  and cloud computing technology to support pediatric cancer research programs globally, including the world’s first personalized medicine trial for pediatric cancer conducted by NMTRC.

    Dell’s High Performance Computing (HPC) is supporting TGen’s work on the NMTRC personalized medicine clinical trial, enabling ever-faster diagnosis and treatment for some of the most aggressive types of cancer in children for whom time is extremely precious.

    Neuroblastoma strikes one in 100,000 children annually, usually before the age of 5, and despite it being so rare, it is so deadly that it is responsible for one in seven pediatric cancer deaths.  It attacks the sympathetic nervous system, which controls heart rate, blood pressure and digestion, with aggressive tumors that are unique to each child.

    Using Intel and Dell technology, we’ve been able to make a real difference in the time it takes to analyze Next Generation Sequencing samples, significantly minimizing the time it takes to discover the genetic flaws in the 3-billion-letter DNA code of these patients.

    We need to get this information into the hands of physicians in a timely way, enabling them to improve the outcomes for children with cancer. Armed with this information, an oncologist can prescribe the best possible drugs to knock down and, perhaps some day, cure these types of cancers.

     With the Dell team, we at TGen have worked together to push the performance envelope.

    I will deliver details of these advances at Supercomputing 12, or SC12, the International Conference for High Performance Computing, Networking, Storage and Analysis. My presentation is set for 12:15 p.m. Tuesday, Nov. 13, at The Salt Palace convention center in Salt Lake City.

    This “Birds of a Feather” session — Genomics Research Computing: The Engine that Drives Personalized Medicine Forward — will include information based upon practical experience on how to optimize bioinformatics, algorithms and HPC architectures for use in genomics analysis.

    Specifically, I will elaborate on what the Dell/TGen teams have done to reduce critical analysis times in these clinical trial studies from as many as 7 days to just 1.

    For example, it used to take up to 2 days just to copy data to HPC resources, and as many as 5 days to align that data using the resources that were available to TGen. By leveraging Dell technologies and expertise, that work can be done in just 1 day.

    That is a substantial time savings when young lives are on the line.

  • HPC Community Event in Dublin Addresses Memory Performance, Serial vs. Parallel Processing, and OS Upgrade Needs

    Despite all of the technology that allows us to virtually connect with others today,  face-to-face is still one of the most powerful ways to come together and address important issues facing our community. A recent gathering of High Performance Computing (HPC) higher education professionals at the Dunsink Observatory, and Dublin Institute for Advanced Studies (DIAS) proved an old school get-together is still tops.  

    Enterprise Marketing Manager for Dell in Ireland Peter Trevaskis recently attended, and provided a great summary of the event as well as some of the topics discussed that were addressed. Held Oct. 18, 2012 and hosted by Dell, the event attracted representatives from some of the top institutions in the region, including Trinity Collge, UCD, DCU, Limerick University, the Tyndall Institute, and the Irish Centre for High End Computing (ICHEC).

    Some of the issues addressed included:

    • Challenges with memory performance
    • Serial processing vs. parallel processing
    • Need for an operating system to be able to handle massive parallel processing

    Peter's blog makes me think of how important the upcoming SC12 event will be in November in Salt Lake City. I'm personally looking forward to more face-to-face meetings with the colleagues and leading HPC professionals we all work with throughout the year.

    To read Peter's full blog, click here: High Performance Computing Inaugural Event

  • Worldwide Collaboration Enabled for Great Scientific Adventures

    Congratulations to the ATLAS Outreachers at CERN for beating out more than 500 other projects, and winning the "Best Online Event" from the Digital Communication Awards for excellence in online communication. The award was presented for an amazing program called ATLAS Virtual Visits.  But winning the award isn't the big deal here - the big deal is what this Virtual Visits program enables.

    From the ATLAS Virtual Visits site:
        "Using web-based video conferencing tools, participants talk with an ATLAS physicist, receive a tour of the control room, and get answers to their questions."

    Providing public access to this amazing resource ATLAS Experiment is appropriately dubbed one of the world's greatest scientific adventures.

    You can learn more about the Virtual Visits program by visiting the ATLAS Experiment website.