Summit Puts Spotlight on High-Performance Grid Computing

By By Charles Coleman, Ph.D., and Cheryl Doninger, SAS Institute Inc.

October 22, 2007

HPC and grid computing — and the promises and challenges for biomedical applications — were the focus of the first annual Biomedical High Performance Computing Leadership Summit on Oct. 1-2, which was hosted by Harvard Medical School in the Medical School’s Rotunda in Boston.

The content was presented by a broad cross-section of researchers and computing experts from both public and private entities. Their presentations touched on several recurring themes and conclusions:

  • Distributed and parallel file systems are a critical component to successful HPC architecture and applications.
  • Interest and research into usage of virtualization technology and “in silico” simulations are accelerating at breakneck speed: Need to define appropriate usage scenarios as well as how to support and manage.
  • ·Data, data and more data: IDC estimates that by 2010 the amount of digital data worldwide will be doubling every 11 hours — get ready for yottabytes.
  • Trends: There is a movement from 1U compute resources to blades.
  • Sophisticated data management and analytics tools will be in increasing demand.
  • Accessibility versus security and the role of institutional research governance remains an issue.
  • The users/customers of the HPC infrastructure rule.
  • The roles of open architecture, open standards and open source are still open questions.
  • Storage, vast storage, persistent storage and on-demand archival retrieval remain vast and persistent requirements.
  • Still the $64,000 question: Establishing costs and ROI for HPC and grid environments. The “big payback”?
  • Individual researchers, especially, need to get over their Gollum-like obsessive hoarding of their (“My Precious”) data (“It’s mine!”).

Approximately 150 participants from a wide variety of public and private entities attended, with more than 18 presenters and three keynotes. This event was a great success, as evidenced by more than half of the attendees rating this summit a 100 percent “valuable-use-of-their-time” in the post-conference survey, while more than two-thirds claimed the learning experience would “definitely be useful in their future work.”

The opening address, by Dr. Philip Papadopoulos (program director of grid and cluster computing, San Diego Supercomputing Center), focused the audience on “OS Virtualization and its Impact on Science and Cyber Environments,” followed by Dr. Phil Andrews’ (University of Tennessee/Oak Ridge National Laboratory) lively discussion regarding “TeraGrid Technologies and Applications” and the rapidly growing role of simulation and managing massive data sets. Dr. Wolfgang Gentzsch (coordinator, D-Grid, Germany) covered the expanding European grid collaborations and reported on “Lessons Learned” regarding “Building and Maintaining Large-Scale Grid Infrastructures.” Despite them being cumbersome, costly and politically charged, Gentzsch’s report was positive and optimistic — the EU is making significant strides in developing and establishing grid computing at the university and research levels.
Dr. Brian Athey’s candid reflections on the reality of federating and growing high-performance computing and data environments to support research at the University of Michigan Medical School were greeted with a mix of sobriety and introspection. His graphic analysis of the amount of time, energy and money required to actually achieve a fully integrated, federated HPC environment for medical research was immensely helpful in citing the “gotchas” in rolling out highly complex and visible clinical and research computing networks.

Four speakers from the private sector — Dr. John Hurley (Boeing), Dr. Mark Linesch (HP), Chris Dagdigian (Bioteam Inc.) and Cheryl Doninger (SAS Institute) — presented surprisingly varying views of how HPC and grid were being embraced and deployed in their corporations for either internal use or for product development. Despite the obvious differences between these industries, there were actually several common goals for leveraging and implementing an HPC solution, including the needs to manage information and data, share infrastructure across multiple users and applications, and collaborate with suppliers and partners to solve common problems.

Dagdigian, a brains-for-hire HPC/grid consultant, enacted a spirited real-world revival of Michael Caine’s “A Bridge Too Far” gap-analysis of vision versus reality in implementing grid infrastructure, notably on the hardware and storage fronts. He also stressed the impact on the environment via the cost of cooling large grid and HPC implementations.
Juxtaposed against Dagdigian’s true-grit “Trends from the Trenches” was Scott Collins’ (manager of scientific computing and software engineering, Janelia Farm Research Campus, Howard Hughes Medical Institute (HHMI)) portrayal of The Janelia Farm Information Infrastructure for HPC at HHMI. Here, and elsewhere in the conference, presenters momentarily waxed poetic in their depictions of a “Field of Dreams” approach (“build it and then we’ll solve it”) to harnessing HPC and grid infrastructure to solve world-class computing problems. Collins’ rendering of Janelia Farm was as bucolic as it was inspirational, and the Farm is in an enviable position to prove what can be done with HPC and grid environments in medical science.

A surprise visit and animated presentation by Dr. Zak Kohane quickly surfaced the subliminal notion of translational medicine and CTSA by focusing in on the role of HPC and grid computing to help dramatically close the gap in bench-to-clinician-to-patient information and communication. Here, the use of HPC computational infrastructure to really impact the quality of health care through the availability of evidence gleaned and reported in real time can and does save lives. Kohane’s one slide on Rofecoxib (Vioxx, Ceoxx, Ceeoxx) told the whole story of how clinical metrics, measurement and reporting across multiple clinical datasets are invaluable in improving quality of care, and how industrial-strength computing environments, if managed well, can dramatically improve clinical care with the right data mining, clinical performance “intelligence” and data management tools.

An evening keynote by Dr. John Halamka (CIO, Harvard Medical School and Beth Israel Deaconess Medical Center; chair, Health Information Technology Standards Panel) helped to transpose the summit’s content into a real-time bioinformatics and health care perspective in his presentation entitled “Emergence and Convergence: National Health Information Standards, Personal Genomes and Shared High Performance Computing.”

Themes and best practices for managing shared computing infrastructure for creating flexible clusters and grids specifically for the sciences were traversed by Dr. Jay Boisseau (Texas Advanced Computing Center), Dr. Mark Ellisman (National Center for Microscopy and Imaging Research; founder, BIRN), Dr. Rick Stevens (Argonne National Laboratory and the University of Chicago), and Mary Kratz (University of Michigan).

Some specific HPC and grid-ready applications were demonstrated as well, including a joint presentation on clinical trials simulation by Dr. Peter Westfall (Texas Tech University) and SAS’s Doninger. This application leverages an HPC environment to process large data sets and complex algorithms for clinical trials simulation to achieve time savings while reducing the cost of a clinical trial by millions of dollars.

Administrative and technical staff from North Carolina State University table-topped a singularly cutting-edge virtual high-performance computing platform supporting its campus-wide Virtual Computing Environment. The environment allows students and faculty to, using any browser, dynamically spawn a remote, real-time customized computing cloud over the Internet to access and “run” the numerous software applications they need — notably in science, technology, engineering and math. Twenty-four hours a day, seven days a week, 365 days a year, and at the click of a mouse, NCSU students and faculty can select applications and saved data sets from a library of proprietary and open source images and run them on Linux, Solaris and numerous Windows environments from anywhere in the world, without downloading anything to their individual laptops, desktops or laboratory workstations. Leveraging the advantages of HPC, software-as-a-service and an SOA truly have been established in higher education within a major engineering school here in the United States. Put simply, this is a grid that works every minute of every day.

Another interesting feature of this event was the ability for any of the attendees to submit polling questions that were presented to the audience for voting before each break. Following the results of the survey questions, a series of trivia questions kept the mood light and the attendees engaged. (The winner donated his cash prize to Children’s Hospital.) Marcos Athanasoulis, director of research information technology for Harvard Medical School, was the summit’s planning committee chair and host. His opening remarks were poignant and humorous: “Oh behalf of Harvard University and the Medical School, may I welcome you to the ‘Land of a Thousand CIOs.’”

The logistics were fabulous, the networking exceptional, the food organic and gourmet, and the quality of the presentations and attendees top-notch: Plan now on attending next year’s Biomedical HPC Leadership Summit. Potential 2008 presenters should contact Athanasoulis at [email protected].

About the Authors

Cheryl Doninger and Charles Coleman are employees of SAS Institute in Cary, N.C., and contribute articles and content in the fields of grid, high-performance and bio-medical computing. The opinions stated here are expressly those of the authors and do not represent the opinions of SAS Institute or Tabor Communications.


(c) Copyright Charles Coleman, PhD, and Cheryl Doninger, 2007

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Penguin Computing Brings Cascade Lake-AP to OCP Form Factor

July 7, 2020

Penguin Computing, a subsidiary of SMART Global Holdings, Inc., is announcing a new Tundra server, Tundra AP, that is the first to implement the Intel Xeon Scalable 9200 series processors (codenamed Cascade Lake-AP) in t Read more…

By Tiffany Trader

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia's Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 "Accelerator Optimized" VM A2 instance family on Google Compute Engine. The instances are powered by t Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial research. Can you discuss key developments in recent years? Read more…

By Steve Conway, Hyperion

The Barcelona Supercomputing Center Offers a Virtual Tour of Its MareNostrum Supercomputer

July 6, 2020

With the COVID-19 pandemic continuing to threaten the world and disrupt normal operations, facility tours remain a little difficult to operate, with many supercomputing centers having shuttered facility tours for visitor Read more…

By Oliver Peckham

What’s New in Computing vs. COVID-19: Fugaku, Congress, De Novo Design & More

July 2, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

AWS Solution Channel

Maxar Builds HPC on AWS to Deliver Forecasts 58% Faster Than Weather Supercomputer

When weather threatens drilling rigs, refineries, and other energy facilities, oil and gas companies want to move fast to protect personnel and equipment. And for firms that trade commodity shares in oil, precious metals, crops, and livestock, the weather can significantly impact their buy-sell decisions. Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time last year, IBM announced open sourcing its Power instructio Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia's Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 "Accelerator Optimized" VM A2 instance fam Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

HPCwire: Let's start with HLRS and work our way up to the European scale. HLRS has stood out in the HPC world for its support of both scientific and industrial Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

ISC 2020 Keynote: Hope for the Future, Praise for Fugaku and HPC’s Pandemic Response

June 24, 2020

In stark contrast to past years Thomas Sterling’s ISC20 keynote today struck a more somber note with the COVID-19 pandemic as the central character in Sterling’s annual review of worldwide trends in HPC. Better known for his engaging manner and occasional willingness to poke prickly egos, Sterling instead strode through the numbing statistics associated... Read more…

By John Russell

ISC 2020’s Student Cluster Competition Winners Announced

June 24, 2020

Normally, the Student Cluster Competition involves teams of students building real computing clusters on the show floors of major supercomputer conferences and Read more…

By Oliver Peckham

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers


Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This