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

By Tiffany Trader

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 HPC applications and benchmarks and are sharing their results in a paper, available on arXiv.org.

Their method was to use the application kernel module of the XD Metrics on Demand (XDMoD) tool to run tests before and after the installation of the vulnerability patches. They recorded the performance difference for the following applications and benchmarks: NWChem, NAMD, the HPC Challenge Benchmark suite (HPCC) [which includes the memory bandwidth micro-benchmark STREAM and the NASA parallel benchmarks (NPB)], IOR, MDTest and interconnect/MPI benchmarks (IMB).

Most of the application kernels were executed on one or two nodes (8 and 16 cores respectively) of a development cluster at the Center for Computational Research. Each node has two Intel L5520 CPUs (Nehalem EP) connected by QDR Mellanox InfiniBand, and can access 3 PB IBM of shared GPFS storage system. The operating system is CentOS Linux release 7.4.1708.

The worst case performance hit went as high as 54 percent for select functions (e.g., MPI random access, memory copying and file metadata operations), while real-world applications showed a 2-3 percent decrease in performance for single node jobs and a 5-11 performance decrease for parallel two-node jobs. The authors indicate there may be a way to recoup some of this loss via compiler and MPI libraries.

Also notable, Fourier transformation (FFT), matrix multiplication and matrix
transposition get slower,  6.4 percent, 2 percent and 10 percent slower (on two nodes) respectively.

The findings of the SUNY team align with those of Red Hat, which earlier this month released the results from benchmark tests it conducted specifically to measure the impact of the kernel patches. Red Hat found that CPU-intensive HPC workloads suffered only a 2-5 percent hit “because jobs run mostly in user space and are scheduled using CPU-pinning or NUMA control.” In comparison, database analytics were found to take a modest 3-7 percent hit and OLTP database workloads suffered the most (8-19 percent degradation).

The SUNY researchers have plans to conduct additional testing “with a larger number of nodes and for more application kernels” once the updates are applied to their production system.

The XD Metrics on Demand (XDMoD) tool employed for the testing was originally developed to provide independent audit capability for the XSEDE program. It was later open-sourced and is now used widely across research and commercial HPC sites. The tool includes an application kernel performance monitoring module that “allows automatic performance monitoring of HPC resources through the periodic execution of application kernels, which are based on benchmarks or real-world applications implemented with sensible input parameters.”

The paper was authored by Nikolay A. Simakov, Martins D. Innus, Matthew D. Jones, Joseph P. White, Steven M. Gallo, Robert L. DeLeon and Thomas R. Furlani. It is available on arxiv.org.

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!

Intel, Micro Up the Ante for Flash Memory

May 22, 2018

Chipmakers continue to gear designs toward AI and other demanding cloud workloads that take advantage of datacenter flash storage capacity. To that end, memory specialist Micron Technology Inc. began shipping compact sol 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 combined peak computing capacity, the new systems will extend the a 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

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…

ASC18: Tough Applications & Tough Luck

May 17, 2018

The applications at the ASC18 Student Cluster Competition were tough. Tougher than the $3.99 steak special at your local greasy spoon restaurant. The apps are so tough that even Chuck Norris backs away from them slowly. Read more…

By Dan Olds

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

US Forms AI Brain Trust

May 11, 2018

Amid calls for a U.S. strategy for promoting AI development, the Trump administration is forming a senior-level panel to help coordinate government and industry research efforts. The Select Committee on Artificial Intelligence was announced Thursday (May 10) during a White House summit organized by the Office of Science and Technology Policy (OSTP). Read more…

By George Leopold

Emerging Advanced Scale Tech Trends Focus of Annual Tabor Conference

May 9, 2018

At Tabor Communications' annual Advanced Scale Forum (ASF) held this week in Austin, the focus was on enterprise adoption of HPC-class technologies and high performance data analytics (HPDA). It’s a confab that brings together end users (CIOs, IT planners, department heads) and vendors and encourages... Read more…

By the Editorial Team

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

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

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

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

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

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

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

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