Japanese University Boots Up 800-Teraflop GPU Supercomputer

By Michael Feldman

February 14, 2012

Japan’s newest supercomputer, an 802-teraflop GPU-accelerated Appro cluster, went into production last week at the University of Tsukuba, just north of Tokyo. The machine represents the lynchpin of the university’s HA-PACS project, a three-year effort that will attempt to push the envelope on GPU-pumped supercomputing.

HA-PACS, which stands for Highly Accelerated Parallel Advanced system for Computational Sciences, is just the latest in a series “PACS” systems at the Tsukuba. The original system, known as PACS-9, was installed in 1978 and delivered 7 kiloflops (yes kiloflops!). Every two to four years thereafter, the university’s Center for Computational Sciences upgraded to a new system. The last one, PACS-CS, was deployed in 2006 and topped out at 14.3 teraflops.

The new Appro cluster represents the 8th generation supercomputer at Tsukuba and is the first to be accelerated by GPUs. As you might suspect, the vast majority of the 802 teraflops is provided by the graphics units, in this case, based on the latest NVIDIA Tesla GPU part, the M2090. Each cluster node pairs four of them with two 8-core Xeon E5 (“Sandy Bridge”) CPUs from Intel.

In aggregate, the 268-node HA-PACS machine will house 1072 GPUs and 536 CPUs, as well as a total of 34 terabytes of memory on the CPU side and an additional 6.4 terabytes for the GPUs. External storage amounts to just over half a petabyte, based on DataDirect Network’s SFA10000 gear. As a result of the high computational density afforded by the graphics chips, the entire cluster fits into just 26-racks and draw a little over 400 KW of power.

Using the top-of-the line CPUs and GPUs makes for a dense and powerful cluster, with each node delivering just shy of 3 teraflops (peak) performance. And even though most of the flops are GPU-derived (665 gigaflops per M2090), each Xeon E5 chips in with a respectable 166 gigaflops, thanks to the addition of the new Advanced Vector Extensions (AVX) instructions.

This is Appro’s second big system deployment at Tsukuba, having delivered the 95-teraflop T2K Open Supercomputer there in 2009. That machine used AMD’s quad-core Opterons and no GPUs.

Appro, by the way is one of the few server vendors offering systems equipped with Xeon E5 CPUs these days, and already claims four such systems on the TOP500 list: “Zin” (961 teraflops) at Lawrence Livermore National Lab, “Luna” (293 teraflops) at Los Alamos National Lab, “Gordon” (262 teraflops) at the San Diego Supercomputer Center and “Chama” at Sandia National Labs. That’s a nice accomplishment, considering Intel has yet to officially release the E5 chips into the wild.

CPU’s aside, the main focus for HA-PACS is to draw the most performance from the GPU hardware. The project has a two-pronged mission in this regard: to bring more big science codes to the GPU and to develop a tightly coupled parallel computing acceleration mechanism in order to “further optimize the utility of the graphics hardware.”

On the application side, HA-PACS will be porting codes to the GPU in the areas of subatomic particles, life sciences, astrophysics, nuclear physics and environmental science. For example, astrophysics applications that deal with radiation transfer can take advantage of ray tracing methods, which modern GPUs are tailor-made for. Likewise, for elementary particle physics, GPUs can be used to great advantage to accelerate dense matrix computations.

On the computational research side, the HA-PACS team is in the process of developing custom hardware to support direct communications between the GPUs. The idea is to enable the graphics processors to quickly shuffle data between themselves without the overhead involved in going through the CPU.

This custom hardware, known as the Tightly Coupled Accelerator (TCA), will be distinct from the HA-PACS base cluster from Appro, but will eventually be integrated with it, says Taisuke Boku, deputy director of Center for Computational Sciences at University of Tsukuba. According to him, TCA will use PCIe as a communication channel between the GPUs and employ FPGA technology to facilitate this.

The FPGA will be based on an existing implementation developed at Tsukuba called PEACH, which stands for PCI Express Adaptive Communication Hub. The idea is to provide a controller that enables PCIe devices to directly communicate with one another on a peer-to-peer basis, rather than as slave devices.

To make this work for TCA, an upgraded implementation of the FPGA, known as PEACH2, will be developed. It will incorporate NVIDIA’s GPU-Direct communication protocols to facilitate data transfers between the Tesla parts. Bandwidth will also be improved from the original PEACH version, which used four ports of PCIe Gen2 x4 as the communication link. For PEACH2, four ports of PCIe Gen2 x8 will be supported, doubling throughput.

The first prototype of the TCA is under development now. The plan is to to incorporate the technology into a second cluster, which will be glued to the Appro base cluster by early 2013. The TCA cluster will add an additional 200-plus teraflops into production, bringing the integrated HA-PACS system to over a petaflop.
 
The HA-PACS work will be a precursor to future exascale systems already in the minds of Boku and his team at Tsukuba. He believes future exascale system will require some level of accelerated computing technology due to its inherent advantages in performance and energy efficiency.

“The largest issue on the accelerated computing is how to fill the gap between its powerful internal computation performance and relatively poor external communication performance,” says Boku. “In some applications, we may need a paradigm shift toward a new generation of algorithms. HA-PACS will be the testbed for developing these algorithms.”

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!

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Francisco, one would be tempted to dismiss its claims of inventing Read more…

By John Russell

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been emerging from stealth over the last year and a half, is unveili Read more…

By Tiffany Trader

Scientists Conduct First Quantum Simulation of Atomic Nucleus

May 23, 2018

OAK RIDGE, Tenn., May 23, 2018—Scientists at the Department of Energy’s Oak Ridge National Laboratory are the first to successfully simulate an atomic nucleus using a quantum computer. The results, published in Ph Read more…

By Rachel Harken, ORNL

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Mastering the Big Data Challenge in Cognitive Healthcare

Patrick Chain, genomics researcher at Los Alamos National Laboratory, posed a question in a recent blog: What if a nurse could swipe a patient’s saliva and run a quick genetic test to determine if the patient’s sore throat was caused by a cold virus or a bacterial infection? Read more…

First Xeon-FPGA Integration Launched by Intel

May 22, 2018

Ever since Intel’s acquisition of FPGA specialist Altera in 2015 for $16.7 billion, it’s been widely acknowledged that some day, Intel would release a processor that integrates its mainstream Xeon CPU server chip wit Read more…

By Doug Black

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Franci Read more…

By John Russell

Silicon Startup Raises ‘Prodigy’ for Hyperscale/AI Workloads

May 23, 2018

There's another silicon startup coming onto the HPC/hyperscale scene with some intriguing and bold claims. Silicon Valley-based Tachyum Inc., which has been eme Read more…

By Tiffany Trader

Japan Meteorological Agency Takes Delivery of Pair of Crays

May 21, 2018

Cray has supplied two identical Cray XC50 supercomputers to the Japan Meteorological Agency (JMA) in northwestern Tokyo. Boasting more than 18 petaflops combine Read more…

By Tiffany Trader

ASC18: Final Results Revealed & Wrapped Up

May 17, 2018

It was an exciting week at ASC18 in Nanyang, China. The student teams braved extreme heat, extremely difficult applications, and extreme competition in order to cross the cluster competition finish line. The gala awards ceremony took place on Wednesday. The auditorium was packed with student teams, various dignitaries, the media, and other interested parties. So what happened? Read more…

By Dan Olds

Spring Meetings Underscore Quantum Computing’s Rise

May 17, 2018

The month of April 2018 saw four very important and interesting meetings to discuss the state of quantum computing technologies, their potential impacts, and th Read more…

By Alex R. Larzelere

Quantum Network Hub Opens in Japan

May 17, 2018

Following on the launch of its Q Commercial quantum network last December with 12 industrial and academic partners, the official Japanese hub at Keio University is now open to facilitate the exploration of quantum applications important to science and business. The news comes a week after IBM announced that North Carolina State University was the first U.S. university to join its Q Network. Read more…

By Tiffany Trader

Democratizing HPC: OSC Releases Version 1.3 of OnDemand

May 16, 2018

Making HPC resources readily available and easier to use for scientists who may have less HPC expertise is an ongoing challenge. Open OnDemand is a project by t Read more…

By John Russell

PRACE 2017 Annual Report: Exascale Aspirations; Industry Collaboration; HPC Training

May 15, 2018

The Partnership for Advanced Computing in Europe (PRACE) today released its annual report showcasing 2017 activities and providing a glimpse into thinking about Read more…

By John Russell

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

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

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

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

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

CFO Steps down in Executive Shuffle at Supermicro

January 31, 2018

Supermicro yesterday announced senior management shuffling including prominent departures, the completion of an audit linked to its delayed Nasdaq filings, and Read more…

By John Russell

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

Deep Learning Portends ‘Sea Change’ for Oil and Gas Sector

February 1, 2018

The billowing compute and data demands that spurred the oil and gas industry to be the largest commercial users of high-performance computing are now propelling Read more…

By Tiffany Trader

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

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