Flash Forward: SDSC Launches Data-Intensive Supercomputer

By Michael Feldman

December 6, 2011

Gordon, the largest flash memory-based computer on the planet, was officially launched at a ceremony that took place on Monday at the San Diego Supercomputer Center (SDSC). Two years in the making, and backed by a $20 million Track 2 grant from the National Science Foundation (NSF), Gordon represents the first really big purpose-built supercomputer for data-intensive applications.

Mark Seager, formerly of Lawrence Livermore National Laboratory and now Intel’s CTO for the HPC Ecosystems group, spoke at the event, saying that the data-intensive technologies that are being pioneered in Gordon are destined to make their way into the wider enterprise market. But, he noted, they have special relevance to the HPC community. “We see big data as a new frontier in high performance computing,” said Seager.

The intention of SDSC and the NSF is to draw in data-intensive science codes that have never had a platform this size to push the envelope. This is particularly true of in genomics, an application set that was foremost in the minds of the system engineers when the machine was being designed. Genomics is the classic “big data” science problem, and is the one most frequently cited in HPC circles as suffering from the data deluge crisis. Other application areas like graph problems, geophysics, financial market analytics, and data mining are also expected to be important domains for Gordon.

Hardware-wise, the system is a souped-up Appro HPC cluster, using the vendor’s third-generation Xtreme-X architecture and outfitted with Intel’s new 22nm “Sandy Bridge” Xeon E5 CPUs (which, by the way, are still are not generally available). Consisting of 1,024 dual-socket, nodes with 64 GB of DDR3 memory, Gordon delivers a peak performance of 280 teraflops. That’s not exactly top tier computing in the petascale age, however it was enough to earn the system 48th place on the latest TOP500 list.

But it’s the flash memory set-up that makes Gordon a data monster. The system is outfitted with over 300 TB of Intel solid state disks, spread over 64 “I/O nodes.” According to SDSC director Mike Norman, that’s enough flash capacity to store the entire Netflix movie catalog three times over. It’s also enough to hold 100,000 human genomes, which is probably bigger than that particular data set as it exists today.

More impressive is the aggregate IOPS performance of the machine. At the ceremony on Monday, Norman cranked up all 64 I/O nodes, demonstrating a peak output of 36 million IOPS. At that rate, you could download 220 movies per second.

The other unique aspect to Gordon is its use of ScaleMP’s “Versatile SMP” (vSMP) technology. It allows users to run large-memory applications on what they call a “supernode” — an aggregation of 32 Gordon servers and two I/O servers, providing access to 512 cores, 2 TB of RAM and 9.6 TB of flash. To a program running on a supernode, the hardware behaves as a big cache coherent server. As many as 32 of these supernodes can be carved from the machine at one time. According to ScaleMP founder and CEO Shai Fultheim, Gordon is the largest system in the world that is deployed with its technology.

The flash device being employed is Intel’s new iSolid-State Drive 710, which was launched in September at the Intel Developer Forum in San Francisco. The 710 uses Intel’s High Endurance Technology (HET), which is the chipmaker’s version of enterprise multi-level cell (eMLC) flash memory that other flash vendors are now offering. Like eMLC, the HET flash features the performance and resiliency of single-level cell (SLC) flash, but at a much lower cost. SDSC also developed its own flash device drivers to maximize performance of the SSD gear.

Inserting this much flash memory into a supercomputer had never been attempted before, and this aspect was probably the biggest risk for the project. When they began the Gordon effort two years ago, flash memory was just starting to make its way into enterprise storage and was an expensive and unproven technology. The $20 million in funding for a flashed-laden supercomputer was predicated on projections that the cost and density of NAND memory would make a multi-hundred terabyte SSD deployment feasible by 2011.

That more or less turned out to be the case, but the global recession and the meteoric rise of smartphones and other mobile computing devices over the last couple of years spiked the price flash memory as supplies dwindled. The recent commercialization of enterprise-capable MLC flash, as in the Intel SSDs, turned out to be something of a gift for Gordon, allowing SDSC to increase the initial flash capacity of 256 TB to more than 300 TB.

SDSC was also somewhat fortunate to have found a willing partner in Appro, a tier 2 system vendor that was prepared to build a rather unconventional HPC cluster. According to SDSC associate director Allan Snavely, they approached both IBM and Cray about taking on Gordon, but both vendors essentially said they were unwilling to tweak their product roadmaps for a single $20 million contract. Appro, of course, is hoping Gordon is not a one-off machine.

Although the system was officially launched on Monday, it is currently undergoing acceptance testing and is expected to be available for production use by XSEDE users on January 1.

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!

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than ever, the network plays a crucial role. While fast, perform Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of personalized treatments based on an individual’s genetic makeup Read more…

By Warren Froelich

WCRP’s New Strategic Plan for Climate Research Highlights the Importance of HPC

July 19, 2018

As climate modeling increasingly leverages exascale computing and researchers warn of an impending computing gap in climate research, the World Climate Research Programme (WCRP) is developing its new Strategic Plan – and high-performance computing is slated to play a critical role. Read more…

By Oliver Peckham

HPE Extreme Performance Solutions

Introducing the First Integrated System Management Software for HPC Clusters from HPE

How do you manage your complex, growing cluster environments? Answer that big challenge with the new HPC cluster management solution: HPE Performance Cluster Manager. Read more…

IBM Accelerated Insights

Are Your Software Licenses Impeding Your Productivity?

In my previous article, Improving chip yield rates with cognitive manufacturing, I highlighted the costs associated with semiconductor manufacturing, and how cognitive methods can yield benefits in both design and manufacture.  Read more…

U.S. Exascale Computing Project Releases Software Technology Progress Report

July 19, 2018

As is often noted the race to exascale computing isn’t just about hardware. This week the U.S. Exascale Computing Project (ECP) released its latest Software Technology (ST) Capability Assessment Report detailing progress so far. Read more…

By John Russell

InfiniBand Still Tops in Supercomputing

July 19, 2018

In the competitive global HPC landscape, system and processor vendors, nations and end user sites certainly get a lot of attention--deservedly so--but more than Read more…

By Tiffany Trader

HPC for Life: Genomics, Brain Research, and Beyond

July 19, 2018

During the past few decades, the life sciences have witnessed one landmark discovery after another with the aid of HPC, paving the way toward a new era of perso Read more…

By Warren Froelich

D-Wave Breaks New Ground in Quantum Simulation

July 16, 2018

Last Friday D-Wave scientists and colleagues published work in Science which they say represents the first fulfillment of Richard Feynman’s 1982 notion that Read more…

By John Russell

AI Thought Leaders on Capitol Hill

July 14, 2018

On Thursday, July 12, the House Committee on Science, Space, and Technology heard from four academic and industry leaders – representatives from Berkeley Lab, Argonne Lab, GE Global Research and Carnegie Mellon University – on the opportunities springing from the intersection of machine learning and advanced-scale computing. Read more…

By Tiffany Trader

HPC Serves as a ‘Rosetta Stone’ for the Information Age

July 12, 2018

In an age defined and transformed by its data, several large-scale scientific instruments around the globe might be viewed as a ‘mother lode’ of precious data. With names seemingly created for a ‘techno-speak’ glossary, these interferometers, cyclotrons, sequencers, solenoids, satellite altimeters, and cryo-electron microscopes are churning out data in previously unthinkable and seemingly incomprehensible quantities -- billions, trillions and quadrillions of bits and bytes of electro-magnetic code. Read more…

By Warren Froelich

Tsinghua Powers Through ISC18 Field

July 10, 2018

Tsinghua University topped all other competitors at the ISC18 Student Cluster Competition with an overall score of 88.43 out of 100. This gives Tsinghua their s Read more…

By Dan Olds

HPE, EPFL Launch Blue Brain 5 Supercomputer

July 10, 2018

HPE and the Ecole Polytechnique Federale de Lausannne (EPFL) Blue Brain Project yesterday introduced Blue Brain 5, a new supercomputer built by HPE, which displ Read more…

By John Russell

Pumping New Life into HPC Clusters, the Case for Liquid Cooling

July 10, 2018

High Performance Computing (HPC) faces some daunting challenges in the coming years as traditional, industry-standard systems push the boundaries of data center Read more…

By Scott Tease

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

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