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!

At SC18: Humanitarianism Amid Boom Times for HPC

November 14, 2018

At SC18 in Dallas, the feeling on the ground is one of forward-looking buoyancy. Like boom times that cycle through the Texas oil fields, the HPC industry is enjoying a prosperity seen only every few decades, one driven Read more…

By Doug Black

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, produ Read more…

By John Russell

New Panasas High Performance Storage Straddles Commercial-Traditional HPC

November 13, 2018

High performance storage vendor Panasas has launched a new version of its ActiveStor product line this morning featuring what the company said is the industry’s first plug-and-play, portable parallel file system that d Read more…

By Doug Black

HPE Extreme Performance Solutions

AI Can Be Scary. But Choosing the Wrong Partners Can Be Mortifying!

As you continue to dive deeper into AI, you will discover it is more than just deep learning. AI is an extremely complex set of machine learning, deep learning, reinforcement, and analytics algorithms with varying compute, storage, memory, and communications needs. Read more…

IBM Accelerated Insights

New Data Management Techniques for Intelligent Simulations

The trend in high performance supercomputer design has evolved – from providing maximum compute capability for complex scalable science applications, to capacity computing utilizing efficient, cost-effective computing power for solving a small number of large problems or a large number of small problems. Read more…

SC18 Student Cluster Competition – Revealing the Field

November 13, 2018

It’s November again and we’re almost ready for the kick-off of one of the greatest computer sports events in the world – the SC Student Cluster Competition. This is the twelfth time that teams of university undergr Read more…

By Dan Olds

At SC18: Humanitarianism Amid Boom Times for HPC

November 14, 2018

At SC18 in Dallas, the feeling on the ground is one of forward-looking buoyancy. Like boom times that cycle through the Texas oil fields, the HPC industry is en Read more…

By Doug Black

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 Read more…

By John Russell

New Panasas High Performance Storage Straddles Commercial-Traditional HPC

November 13, 2018

High performance storage vendor Panasas has launched a new version of its ActiveStor product line this morning featuring what the company said is the industry Read more…

By Doug Black

SC18 Student Cluster Competition – Revealing the Field

November 13, 2018

It’s November again and we’re almost ready for the kick-off of one of the greatest computer sports events in the world – the SC Student Cluster Competitio Read more…

By Dan Olds

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

OpenACC Talks Up Summit and Community Momentum at SC18

November 12, 2018

OpenACC – the directives-based parallel programing model for optimizing applications on heterogeneous architectures – is showcasing user traction and HPC im Read more…

By John Russell

How ASCI Revolutionized the World of High-Performance Computing and Advanced Modeling and Simulation

November 9, 2018

The 1993 Supercomputing Conference was held in Portland, Oregon. That conference and it’s show floor provided a good snapshot of the uncertainty that U.S. supercomputing was facing in the early 1990s. Many of the companies exhibiting that year would soon be gone, either bankrupt or acquired by somebody else. Read more…

By Alex R. Larzelere

At SC18: GM, Boeing, Deere, BP Talk Enterprise HPC Strategies

November 9, 2018

SC18 in Dallas (Nov.11-16) will feature an impressive series of sessions focused on the enterprise HPC deployments at some of the largest industrial companies: Read more…

By Doug Black

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

TACC Wins Next NSF-funded Major Supercomputer

July 30, 2018

The Texas Advanced Computing Center (TACC) has won the next NSF-funded big supercomputer beating out rivals including the National Center for Supercomputing Ap Read more…

By John Russell

IBM at Hot Chips: What’s Next for Power

August 23, 2018

With processor, memory and networking technologies all racing to fill in for an ailing Moore’s law, the era of the heterogeneous datacenter is well underway, Read more…

By Tiffany Trader

Requiem for a Phi: Knights Landing Discontinued

July 25, 2018

On Monday, Intel made public its end of life strategy for the Knights Landing "KNL" Phi product set. The announcement makes official what has already been wide Read more…

By Tiffany Trader

House Passes $1.275B National Quantum Initiative

September 17, 2018

Last Thursday the U.S. House of Representatives passed the National Quantum Initiative Act (NQIA) intended to accelerate quantum computing research and developm Read more…

By John Russell

CERN Project Sees Orders-of-Magnitude Speedup with AI Approach

August 14, 2018

An award-winning effort at CERN has demonstrated potential to significantly change how the physics based modeling and simulation communities view machine learni Read more…

By Rob Farber

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

New Deep Learning Algorithm Solves Rubik’s Cube

July 25, 2018

Solving (and attempting to solve) Rubik’s Cube has delighted millions of puzzle lovers since 1974 when the cube was invented by Hungarian sculptor and archite Read more…

By John Russell

Leading Solution Providers

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

TACC’s ‘Frontera’ Supercomputer Expands Horizon for Extreme-Scale Science

August 29, 2018

The National Science Foundation and the Texas Advanced Computing Center announced today that a new system, called Frontera, will overtake Stampede 2 as the fast Read more…

By Tiffany Trader

HPE No. 1, IBM Surges, in ‘Bucking Bronco’ High Performance Server Market

September 27, 2018

Riding healthy U.S. and global economies, strong demand for AI-capable hardware and other tailwind trends, the high performance computing server market jumped 28 percent in the second quarter 2018 to $3.7 billion, up from $2.9 billion for the same period last year, according to industry analyst firm Hyperion Research. Read more…

By Doug Black

Intel Announces Cooper Lake, Advances AI Strategy

August 9, 2018

Intel's chief datacenter exec Navin Shenoy kicked off the company's Data-Centric Innovation Summit Wednesday, the day-long program devoted to Intel's datacenter Read more…

By Tiffany Trader

Germany Celebrates Launch of Two Fastest Supercomputers

September 26, 2018

The new high-performance computer SuperMUC-NG at the Leibniz Supercomputing Center (LRZ) in Garching is the fastest computer in Germany and one of the fastest i Read more…

By Tiffany Trader

Houston to Field Massive, ‘Geophysically Configured’ Cloud Supercomputer

October 11, 2018

Based on some news stories out today, one might get the impression that the next system to crack number one on the Top500 would be an industrial oil and gas mon Read more…

By Tiffany Trader

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

Google Releases Machine Learning “What-If” Analysis Tool

September 12, 2018

Training machine learning models has long been time-consuming process. Yesterday, Google released a “What-If Tool” for probing how data point changes affect a model’s prediction. The new tool is being launched as a new feature of the open source TensorBoard web application... Read more…

By John Russell

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