SDSC Puts Data at Center Stage

By Michael Feldman

September 7, 2010

The naming of Michael Norman as director of the San Diego Supercomputer Center (SDSC) last week was long overdue. SDSC has been without an official director for more than 14 months, with Norman filling the spot as the interim head since last July. The appointment could mark something of a comeback for the center, which has not only gone director-less during this time, but has been operating without a high-end supercomputer as well.

DataStar, an aged 15-teraflop IBM P690 system was retired in October of 2008 and the center’s relatively small Blue Gene/L machine was mothballed in June 2009. But Trestles, a new 100-teraflop supercomputer funded by the NSF, is scheduled to be up and running before the end of the year. And with the addition of Gordon, a 245-teraflop supercomputer slated for deployment in mid-2011, SDSC will again be a relatively FLOPS-happy place.

You might say that our FLOPS profile looked like the Dow Jones,” laughed Norman. “It really swooned in 2008 and 2009. With the Trestles system coming at the end of 2010, we’ll be back on the board.”

A Little History

Norman, a computational astrophysicist, got his start at Lawrence Livermore in the 1970s, where he was able to combine his love of astronomy (his major at Caltech) with his interest in all things computational. “And then basically, I was a gypsy, going after supercomputer cycles where ever I could find them,” said Norman.

After his stint at Livermore, Norman did a four-year tour (1980 – 1984) at the Max Planck institute for Astrophysics, owners of the first Cray 1 system in Western Europe. It was during his time at Max Planck when he collaborated heavily with Larry Smarr, currently UC San Diego’s director of Calit2.

“I have worked closely with Mike for over 30 years, since he was a grad student at Livermore,” said Smarr. “He brings a wealth of experience from working at multiple national and international supercomputer centers, as well as being a hands-on pioneer in computational astrophysics and cosmology.”

It was also during this period at Max Planck that he and Smarr conceived of the idea of the National Center for Supercomputing Applications (NCSA). Two years after Norman had left the the institute, NCSA was born. But in the interim Norman went to Los Alamos to work as a staff scientist, before rejoining Smarr at NCSA in 1986. He stayed there for 14 years, before coming to San Diego.

There, he got involved with SDSC, first as a researcher from the UC San Diego physics department, then as a member of the center’s Executive Committee. Toward the end of 2007, Norman jumped into the NSF funding fray to help SDSC win one of agency’s Track 2 supercomputer procurements. The first attempt was not successful, but the second one was, resulting in the award for the Gordon system, with Norman as the principle investigator. In the summer of 2009 Norman became the interim director of the center after Fran Berman relinquished her directorship, moving to Rensselaer Polytechnic Institute as the VP of Research.

Data-Centric Supercomputing

Norman’s ascendance at SDSC ratifies the center’s new focus on data-intensive supercomputing. He, more than anyone, wanted to make San Diego a place for HPC and HPD (high-performance data), a term that he coined to draw attention to the data-centric model. The idea is to support the whole scientific enterprise, and that requires a more highly integrated storage infrastructure supporting the supercomputers.

“There are these two cultures: the HPC culture and the culture of data-intensive science, or fourth paradigm, whatever you want to call it,” explained Norman. “They seem to be living in different worlds. I’m hoping to bring them together at SDSC.”

Part of that goal will be served by the upcoming Gordon supercomputer, which will feature a quarter of a petabyte of flash memory and virtual shared memory software. At 245 teraflops, the machine delivers only moderate performance by today’s elite supercomputing standards. But a lot of today’s applications are I/O bound, rather than compute bound, and would really prefer to have their big datasets sitting in main memory. Since RAM is rather expensive, flash is turning out to be the next best thing. Because of its unique memory architecture, Gordon is expected to do exceeding well at dealing with terascale-sized databases.

The driver for all this is the so-called “data deluge,” which is flowing across multiple disciplines — in traditional technical computing areas such as physics, astronomy engineering, bioinformatics, and medicine, as well as in less traditional realms, such as social sciences, arts, and economics.

Terabyte streams coming from ocean observing sensors, astronomical CCD cameras, and genome sequencers are just a few examples of how data is outrunning the computing infrastructure. Some of these, like the astronomical data streams, can require their own dedicated supercomputer.

The problem is even more acute for genome sequencers. Genome biologists are accustomed to doing their work on a workstations, because that used to be perfectly adequate. But the throughput on these machines has increased so rapidly that sequencers have gone from generating gigabytes to terabytes in just a couple of years. Even bigger improvements on the horizon. “They’re really at sea right now,” said Norman, “and they’re realizing they can’t do this work in their labs anymore.”

The centerpiece of the data-intensive remodel at the SDSC will be something called Data Oasis, a very large scalable file store designed to serve multiple HPC clusters as well as data-intensive machines. Basically it’s an extensible disk farm that will have high connectivity through a very large 10 gigabit switch. From Norman’s perspective, this basically turns the datacenter inside out, with the compute machinery and data generators at the periphery and the data storage in the center.

Industry Partner Program Reboot

Once the new infrastructure gets in place, Norman hopes to revive the center’s industry partnership program. Since retiring their capacity supercomputers over the last couple of years, SDSC hasn’t been able to attract a lot of commercial collaborators. After DataStar was switched off, the center used internal funds to buy Triton, a 20-teraflop Appro cluster. According to Norman, they garnered a few industrial partners with that system, but it really doesn’t have the capacity to support a large program.

The Trestles supercomputer, true to its name, will act as bridge system, until the larger Gordon machine is installed next year. (Trestles, by the way, is also a the name of a famous surf break in San Diego.) Shell Oil is very interested in the Gordon architecture, said Norman. Currently, the oil company is employing Dash, a smaller flash memory-accelerated prototype of Gordon, for an undisclosed project, and they are hoping to grow that work once its more capable successor comes online.

According to Norman, they’re also active cultivating the biomedical informatics business, starting with work at the local USCD medical center. They intend to tap faculty working at the university’s School of Medicine to help build up some of this expertise, with the hope that this work could spill into commercial relationships.

Boutique Funding

With it’s data-centric focus, SDSC has chosen not to be part of the latest petaflop-to-exaflop race. While that gives the center an interesting niche, it’s generally at odds with the funding model the NSF uses to fund supercomputing nowadays. Tighter budgets have convinced the agency to spread the money in a more piecemeal way. So you might get money for a supercomputer, but not for the data store or the network infrastructure that’s needed by the whole facility. “In the old days when we had true supercomputer center funding, there was enough money to create an integrated environment,” explained Norman.

In that sense, the centers are no longer funded as such. They’re funded as places where the agency can plop down a resource. From Norman’s perspective, that’s not a workable long-term strategy for supercomputing centers. “It’s possible we’ll get back to a more sustainable model,” he said. “I certainly hope so.”

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!

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understanding on January 10. The MOU represents the continuation of a 1 Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Tennessee), Satoshi Matsuoka (Tokyo Institute of Technology), Read more…

By John Russell

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown and Spectre security updates on the performance of popular H Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE and NREL Take Steps to Create a Sustainable, Energy-Efficient Data Center with an H2 Fuel Cell

As enterprises attempt to manage rising volumes of data, unplanned data center outages are becoming more common and more expensive. As the cost of downtime rises, enterprises lose out on productivity and valuable competitive advantage without access to their critical data. Read more…

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension around the potential changes that could affect or disrupt Lustre Read more…

By Carlos Aoki Thomaz

UCSD, AIST Forge Tighter Alliance with AI-Focused MOU

January 18, 2018

The rich history of collaboration between UC San Diego and AIST in Japan is getting richer. The organizations entered into a five-year memorandum of understandi Read more…

By Tiffany Trader

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Fostering Lustre Advancement Through Development and Contributions

January 17, 2018

Six months after organizational changes at Intel's High Performance Data (HPDD) division, most in the Lustre community have shed any initial apprehension aroun Read more…

By Carlos Aoki Thomaz

When the Chips Are Down

January 11, 2018

In the last article, "The High Stakes Semiconductor Game that Drives HPC Diversity," I alluded to the challenges facing the semiconductor industry and how that may impact the evolution of HPC systems over the next few years. I thought I’d lift the covers a little and look at some of the commercial challenges that impact the component technology we use in HPC. Read more…

By Dairsie Latimer

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

ANL’s Rick Stevens on CANDLE, ARM, Quantum, and More

January 8, 2018

Late last year HPCwire caught up with Rick Stevens, associate laboratory director for computing, environment and life Sciences at Argonne National Laboratory, f Read more…

By John Russell

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

Japan Unveils Quantum Neural Network

November 22, 2017

The U.S. and China are leading the race toward productive quantum computing, but it's early enough that ultimate leadership is still something of an open questi Read more…

By Tiffany Trader

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

IBM Begins Power9 Rollout with Backing from DOE, Google

December 6, 2017

After over a year of buildup, IBM is unveiling its first Power9 system based on the same architecture as the Department of Energy CORAL supercomputers, Summit a Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Leading Solution Providers

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Perspective: What Really Happened at SC17?

November 22, 2017

SC is over. Now comes the myriad of follow-ups. Inboxes are filled with templated emails from vendors and other exhibitors hoping to win a place in the post-SC thinking of booth visitors. Attendees of tutorials, workshops and other technical sessions will be inundated with requests for feedback. Read more…

By Andrew Jones

Tensors Come of Age: Why the AI Revolution Will Help HPC

November 13, 2017

Thirty years ago, parallel computing was coming of age. A bitter battle began between stalwart vector computing supporters and advocates of various approaches to parallel computing. IBM skeptic Alan Karp, reacting to announcements of nCUBE’s 1024-microprocessor system and Thinking Machines’ 65,536-element array, made a public $100 wager that no one could get a parallel speedup of over 200 on real HPC workloads. Read more…

By John Gustafson & Lenore Mullin

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

GlobalFoundries, Ayar Labs Team Up to Commercialize Optical I/O

December 4, 2017

GlobalFoundries (GF) and Ayar Labs, a startup focused on using light, instead of electricity, to transfer data between chips, today announced they've entered in Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

  • arrow
  • Click Here for More Headlines
  • arrow
Share This