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 industy updates delivered to you every week!

Insights from Optimized Codes on Cineca’s Marconi

February 15, 2019

What can you do with 381,392 CPU cores? For Cineca, it means enabling computational scientists to expand a large part of the world’s body of knowledge from the nanoscale to the astronomic, from calculating quantum effe Read more…

By Ken Strandberg

What Will IBM’s AI Debater Learn from Its Loss?

February 14, 2019

The utility of IBM’s latest man-versus-machine gambit is debatable. At the very least its Project Debater got us thinking about the potential uses of artificial intelligence as a way of helping humans sift through al Read more…

By George Leopold

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst of bankruptcy proceedings. According to Dutch news site Drimb Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE Systems With Intel Omni-Path: Architected for Value and Accessible High-Performance Computing

Today’s high-performance computing (HPC) and artificial intelligence (AI) users value high performing clusters. And the higher the performance that their system can deliver, the better. Read more…

IBM Accelerated Insights

Medical Research Powered by Data

“We’re all the same, but we’re unique as well. In that uniqueness lies all of the answers….”

  • Mark Tykocinski, MD, Provost, Executive Vice President for Academic Affairs, Thomas Jefferson University

Getting the answers to what causes some people to develop diseases and not others is driving the groundbreaking medical research being conducted by the Computational Medicine Center at Thomas Jefferson University in Philadelphia. Read more…

South African Weather Service Doubles Compute and Triples Storage Capacity of Cray System

February 13, 2019

South Africa has made headlines in recent years for its commitment to HPC leadership in Africa – and now, Cray has announced another major South African HPC expansion. Cray has been awarded contracts with Eclipse Holdings Ltd. to upgrade the supercomputing system operated by the South African Weather Service (SAWS). Read more…

By Oliver Peckham

Insights from Optimized Codes on Cineca’s Marconi

February 15, 2019

What can you do with 381,392 CPU cores? For Cineca, it means enabling computational scientists to expand a large part of the world’s body of knowledge from th Read more…

By Ken Strandberg

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst o Read more…

By Tiffany Trader

UC Berkeley Paper Heralds Rise of Serverless Computing in the Cloud – Do You Agree?

February 13, 2019

Almost exactly ten years to the day from publishing of their widely-read, seminal paper on cloud computing, UC Berkeley researchers have issued another ambitious examination of cloud computing - Cloud Programming Simplified: A Berkeley View on Serverless Computing. The new work heralds the rise of ‘serverless computing’ as the next dominant phase of cloud computing. Read more…

By John Russell

Iowa ‘Grows Its Own’ to Fill the HPC Workforce Pipeline

February 13, 2019

The global workforce that supports advanced computing, scientific software and high-speed research networks is relatively small when you stop to consider the magnitude of the transformative discoveries it empowers. Technical conferences provide a forum where specialists convene to learn about the latest innovations and schedule face-time with colleagues from other institutions. Read more…

By Elizabeth Leake, STEM-Trek

Trump Signs Executive Order Launching U.S. AI Initiative

February 11, 2019

U.S. President Donald Trump issued an Executive Order (EO) today launching a U.S Artificial Intelligence Initiative. The new initiative - Maintaining American L Read more…

By John Russell

Celebrating Women in Science: Meet Four Women Leading the Way in HPC

February 11, 2019

One only needs to look around at virtually any CS/tech conference to realize that women are underrepresented, and that holds true of HPC. SC hosts over 13,000 H Read more…

By AJ Lauer

IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

For now, AI systems are mostly machine learning-based and “narrow” – powerful as they are by today's standards, they're limited to performing a few, narro Read more…

By Doug Black

Assessing Government Shutdown’s Impact on HPC

February 6, 2019

After a 35-day federal government shutdown, the longest in U.S. history, government agencies are taking stock of the damage -- and girding for a potential secon Read more…

By Tiffany Trader

Quantum Computing Will Never Work

November 27, 2018

Amid the gush of money and enthusiastic predictions being thrown at quantum computing comes a proposed cold shower in the form of an essay by physicist Mikhail Read more…

By John Russell

Cray Unveils Shasta, Lands NERSC-9 Contract

October 30, 2018

Cray revealed today the details of its next-gen supercomputing architecture, Shasta, selected to be the next flagship system at NERSC. We've known of the code-name "Shasta" since the Argonne slice of the CORAL project was announced in 2015 and although the details of that plan have changed considerably, Cray didn't slow down its timeline for Shasta. Read more…

By Tiffany Trader

The Case Against ‘The Case Against Quantum Computing’

January 9, 2019

It’s not easy to be a physicist. Richard Feynman (basically the Jimi Hendrix of physicists) once said: “The first principle is that you must not fool yourse Read more…

By Ben Criger

AMD Sets Up for Epyc Epoch

November 16, 2018

It’s been a good two weeks, AMD’s Gary Silcott and Andy Parma told me on the last day of SC18 in Dallas at the restaurant where we met to discuss their show news and recent successes. Heck, it’s been a good year. Read more…

By Tiffany Trader

Intel Reportedly in $6B Bid for Mellanox

January 30, 2019

The latest rumors and reports around an acquisition of Mellanox focus on Intel, which has reportedly offered a $6 billion bid for the high performance interconn Read more…

By Doug Black

US Leads Supercomputing with #1, #2 Systems & Petascale Arm

November 12, 2018

The 31st Supercomputing Conference (SC) - commemorating 30 years since the first Supercomputing in 1988 - kicked off in Dallas yesterday, taking over the Kay Ba Read more…

By Tiffany Trader

Looking for Light Reading? NSF-backed ‘Comic Books’ Tackle Quantum Computing

January 28, 2019

Still baffled by quantum computing? How about turning to comic books (graphic novels for the well-read among you) for some clarity and a little humor on QC. The Read more…

By John Russell

Contract Signed for New Finnish Supercomputer

December 13, 2018

After the official contract signing yesterday, configuration details were made public for the new BullSequana system that the Finnish IT Center for Science (CSC Read more…

By Tiffany Trader

Leading Solution Providers

SC 18 Virtual Booth Video Tour

Advania @ SC18 AMD @ SC18
ASRock Rack @ SC18
DDN Storage @ SC18
HPE @ SC18
IBM @ SC18
Lenovo @ SC18 Mellanox Technologies @ SC18
NVIDIA @ SC18
One Stop Systems @ SC18
Oracle @ SC18 Panasas @ SC18
Supermicro @ SC18 SUSE @ SC18 TYAN @ SC18
Verne Global @ SC18

Deep500: ETH Researchers Introduce New Deep Learning Benchmark for HPC

February 5, 2019

ETH researchers have developed a new deep learning benchmarking environment – Deep500 – they say is “the first distributed and reproducible benchmarking s Read more…

By John Russell

ClusterVision in Bankruptcy, Fate Uncertain

February 13, 2019

ClusterVision, European HPC specialists that have built and installed over 20 Top500-ranked systems in their nearly 17-year history, appear to be in the midst o Read more…

By Tiffany Trader

IBM Quantum Update: Q System One Launch, New Collaborators, and QC Center Plans

January 10, 2019

IBM made three significant quantum computing announcements at CES this week. One was introduction of IBM Q System One; it’s really the integration of IBM’s Read more…

By John Russell

Nvidia’s Jensen Huang Delivers Vision for the New HPC

November 14, 2018

For nearly two hours on Monday at SC18, Jensen Huang, CEO of Nvidia, presented his expansive view of the future of HPC (and computing in general) as only he can do. Animated. Backstopped by a stream of data charts, product photos, and even a beautiful image of supernovae... Read more…

By John Russell

HPC Reflections and (Mostly Hopeful) Predictions

December 19, 2018

So much ‘spaghetti’ gets tossed on walls by the technology community (vendors and researchers) to see what sticks that it is often difficult to peer through Read more…

By John Russell

IBM Bets $2B Seeking 1000X AI Hardware Performance Boost

February 7, 2019

For now, AI systems are mostly machine learning-based and “narrow” – powerful as they are by today's standards, they're limited to performing a few, narro Read more…

By Doug Black

The Deep500 – Researchers Tackle an HPC Benchmark for Deep Learning

January 7, 2019

How do you know if an HPC system, particularly a larger-scale system, is well-suited for deep learning workloads? Today, that’s not an easy question to answer Read more…

By John Russell

Intel Confirms 48-Core Cascade Lake-AP for 2019

November 4, 2018

As part of the run-up to SC18, taking place in Dallas next week (Nov. 11-16), Intel is doling out info on its next-gen Cascade Lake family of Xeon processors, specifically the “Advanced Processor” version (Cascade Lake-AP), architected for high-performance computing, artificial intelligence and infrastructure-as-a-service workloads. Read more…

By Tiffany Trader

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