Adventures with HPC Accelerators: GPUs and Intel MIC Coprocessors

By Aaron Dubrow

August 15, 2011

Researchers from Mellanox Technologies and the Texas Advanced Computing Center share early experiences at TeraGrid ‘11

For the past few years, the buzz around hardware accelerators, particularly graphics processing units (GPUs), has been growing.  Designed with a massive number of floating point units and very high memory bandwidth so as to accelerate certain computing processes, GPUs and other emerging accelerates are being embraced by the scientific computing world as a way to speed up simulation, modeling, visualization, and data analysis.

At the TeraGrid 2011 conference in Salt Lake City, Utah, Pak Liu, a software engineer from Mellanox Technologies, and Lars Koesterke, a computational researcher at the Texas Advanced Computing Center (TACC), shared results from their experiences using emerging accelerator and coprocessor technology.

Lui’s talk focused on GPUDirect, a new transfer protocol that reduces latency and increases performance for end-to-end data transfers between GPUs. The problem, Lui explained, is that current GPU communication is redundant, requiring data to be copied between “pinned” memories during an operation, and often needs to steal cycles from the CPU to schedule and initiate jobs.

“There are many things you can do with the GPU capability and the good floating point arithmetic it provides,” Lui said. “But to scale out and use many machines together, you need Infiniband to get the communication across.”

Developed collaboratively by Mellanox, NVIDIA, and researchers at several HPC center, GPUDirect allows for faster GPU to GPU communication. Lui showed benchmarks of the protocol for two well-known molecular dynamics codes, AMBER and LAMMPS. GPUDirect reduced latency in the codes by 30 percent and improved overall performance by 20-40 percent. Lui stressed that performance gains depend on the specific application, the dataset size, and communication required.

In order to achieve these gains, the researchers had to modify the Linux kernel, the NVIDIA drivers, and the Mellanox drivers to eliminate memory copies and CPU involvement in the GPU data transfer.

“Eventually, scientific applications must scale to many GPU nodes and we needed to find an efficient way to communicate,” Lui said.

First released in June 2010, GPUDirect v1.0 is supported by InfiniBand solutions from Mellanox and QLogic, and other vendors are adding support for the technology in their hardware and software products.

Whereas GPUs have been used in the high-performance computing world for several years, Intel’s many integrated core (or MIC, pronounced “Mike”) architecture is yet to hit the market. Intel has granted several dozen institutions, including TACC, early access to MIC cards and trained these partners in how to use the technology. TACC’s role has been to test various computing codes on the MICs and provide Intel with feedback regarding the programming support, optimization, and needs of the HPC community.

“The most important question is how will we exploit this new technology? How difficult will it be to code?” Koesterke said.

MIC is Intel’s answer to NVIDIA and AMD’s GPU challenge. Both GPUs and Intel’s MIC coprocessors allow far greater processing speeds by enabling many more threads to occur simultaneously. Both connect to the CPU through a PCI bus. The key difference between the two technologies, according to Koesterke, is that Intel’s MICs take advantage of the x86 architecture that has dominated the high-performance (and consumer) computing world for decades, whereas GPUs have a stream processing architecture quite different from traditional cores.

Also, MICs are coded using C, C++, Fortran and OpenMP — languages familiar to the open science community. GPUs are coded with CUDA and OpenCL, newer languages that many in the community have not yet mastered. According to Koesterke, the community’s familiarity with the x86 architecture means researchers should have an easier time taking advantage of the capabilities of the new technology with less recoding and a faster ramp up time.

Though promising, MICs are not without risks. “MIC is not yet a product,” Koesterke said. “The programming models are all there, but sustained performance is yet to be proven.”

Koesterke could not provide the details from initial benchmarking efforts at TACC (under non-disclosure); however, he said the evidence suggests that MICs will be an attractive option to computational scientists when they are released in late 2012 or early 2013.

Other sessions at the conference highlighted the development of MATLAB for GPUs and tuning GPUs for matrix multiplication. In addition, many of the finalists in the scientific visualization contest  were created using GPU cluster systems.

Several of the nation’s advanced computing systems that are part of the newly announced Extreme Digital Environment for Science and Engineering (XSEDE), formerly the TeraGrid, currently run on GPUs. The Forge cluster at the National Center for Supercomputing Applications, Nautilus at the National Institute for Computational Sciences, TeraDRE at Purdue University, the Longhorn and Spur systems at the Texas Advanced Computing Center, and the Keeneland Project, developed under a partnership that includes the Georgia Institute of Technology, the University of Tennessee at Knoxville, and Oak Ridge National Laboratory all employ GPUs.

Hardware accelerators are changing the way computational scientists think about their problems, allowing even greater parallelism and processing power. Much work is still needed for the community to take full advantage of these technologies, but based on the early adoption patterns in the TeraGrid community, it appears these new processors will be part of the performance equation for a long time to come.

Subscribe to HPCwire's Weekly Update!

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

Quantum Market, Though Small, will Grow 22% and Hit $1.5B in 2026

December 7, 2023

Few markets as small as the quantum information sciences market generate as much lively discussion. Hyperion Research pegged the worldwide quantum market at $848 million for 2023 and expects it to reach ~$1.5 billion in Read more…

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed its new Instinct MI300X GPU is the fastest AI chip in the worl Read more…

Finding Opportunity in the High-Growth “AI Market” 

December 6, 2023

 “What’s the size of the AI market?” It’s a totally normal question for anyone to ask me. After all, I’m an analyst, and my company, Intersect360 Research, specializes in scalable, high-performance datacenter Read more…

Imagine a Beowulf Cluster of SuperNODEs …
(They did)

December 6, 2023

Clustering resources for faster performance is not new. In the early days of clustering, the Beowulf project demonstrated that high performance was achievable from commodity hardware. These days, the "Beowulf cluster mem Read more…

The IBM-Meta AI Alliance Promotes Safe and Open AI Progress

December 5, 2023

IBM and Meta have co-launched a massive industry-academic-government alliance to shepherd AI development. The new group has united under the AI Alliance banner to promote responsible innovation in AI. Historically, techn Read more…

AWS Solution Channel

Shutterstock 2030529413

Reezocar Rethinks Car Buying Using Computer Vision and ML on AWS

Overview

Every car that finds its way to a landfill marks another dent in the fight for a sustainable future. Reezocar, an online hub for buying and selling used cars, has a mission to change this. Read more…

QCT Solution Channel

QCT and Intel Codeveloped QCT DevCloud Program to Jumpstart HPC and AI Development

Organizations and developers face a variety of issues in developing and testing HPC and AI applications. Challenges they face can range from simply having access to a wide variety of hardware, frameworks, and toolkits to time spent on installation, development, testing, and troubleshooting which can lead to increases in cost. Read more…

ChatGPT Friendly Programming Languages
(hello-world.llm)

December 4, 2023

 Using OpenAI's ChatGPT to write code is an alluring goal. Describing "what to" solve, but not "how to solve" would be a huge breakthrough in computer programming. Alas, we are nowhere near this capability. In particula Read more…

Quantum Market, Though Small, will Grow 22% and Hit $1.5B in 2026

December 7, 2023

Few markets as small as the quantum information sciences market generate as much lively discussion. Hyperion Research pegged the worldwide quantum market at $84 Read more…

Shutterstock 1285747942

AMD’s Horsepower-packed MI300X GPU Beats Nvidia’s Upcoming H200

December 7, 2023

AMD and Nvidia are locked in an AI performance battle – much like the gaming GPU performance clash the companies have waged for decades. AMD has claimed it Read more…

Finding Opportunity in the High-Growth “AI Market” 

December 6, 2023

 “What’s the size of the AI market?” It’s a totally normal question for anyone to ask me. After all, I’m an analyst, and my company, Intersect360 Res Read more…

Imagine a Beowulf Cluster of SuperNODEs …
(They did)

December 6, 2023

Clustering resources for faster performance is not new. In the early days of clustering, the Beowulf project demonstrated that high performance was achievable f Read more…

The IBM-Meta AI Alliance Promotes Safe and Open AI Progress

December 5, 2023

IBM and Meta have co-launched a massive industry-academic-government alliance to shepherd AI development. The new group has united under the AI Alliance banner Read more…

Shutterstock 1336284338

ChatGPT Friendly Programming Languages
(hello-world.llm)

December 4, 2023

 Using OpenAI's ChatGPT to write code is an alluring goal. Describing "what to" solve, but not "how to solve" would be a huge breakthrough in computer programm Read more…

IBM Quantum Summit: Two New QPUs, Upgraded Qiskit, 10-year Roadmap and More

December 4, 2023

IBM kicks off its annual Quantum Summit today and will announce a broad range of advances including its much-anticipated 1121-qubit Condor QPU, a smaller 133-qu Read more…

The Annual SCinet Mandala

November 30, 2023

Perhaps you have seen images of Tibetan Buddhists creating beautiful and intricate images with colored sand. These sand mandalas can take weeks to create, only Read more…

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

Leading Solution Providers

Contributors

SC23 Booth Videos

Achronix @ SC23
AMD @ SC23
AWS @ SC23
Altair @ SC23
CoolIT @ SC23
Cornelis Networks @ SC23
CoreHive @ SC23
DDC @ SC23
HPE @ SC23 with Justin Hotard
HPE @ SC23 with Trish Damkroger
Intel @ SC23
Intelligent Light @ SC23
Lenovo @ SC23
Penguin Solutions @ SC23
QCT Intel @ SC23
Tyan AMD @ SC23
Tyan Intel @ SC23
HPCwire LIVE from SC23 Playlist

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire