Researchers Squeeze Record I/O from Hopper

By Alex Woodie

June 5, 2013

Researchers with the Lawrence Berkeley National Laboratory and Cray squeezed more I/O from the NERSC Cray XE6 “Hopper” supercomputer than ever before in a plasma physics simulation involving more than a trillion particles. The work paved the way for even bigger, exascale HDF5 workloads in the future, and yielded a scientific discovery as a bonus.

Researchers ran 10 separate trillion-particle datasets, each ranging from 30 to 42 TB in size, through Hopper, an Opteron-based system that is currently 19th on the Top 500 list. The files were written as HDF5 files on the scratch system, achieving a sustained I/O rate of 27 gigabytes per second.

The simulation–which used about 80 percent of Hopper’s computing resources, 90 percent of the available memory on each node, and 50 percent of the Lustre scratch file system–was the largest ever for a NERSC application, researchers say.

“It is quite a feat when you consider that even the smallest bottleneck in a production I/O stack can degrade performance at scale,” says Prabhat, a researcher in Berkeley Lab’s Scientific Visualization Group and the leader of the ExaHDF5 group, which is working to stretch the I/O capabilities of HDF5.

Prabhat (who goes by one name) says the simulation validates the work of the ExaHDF5 group, which is funded by the Department of Energy’s Office of Advanced Scientific Research.

“If we had attempted a run like this three years ago, I would have been unsure about the level of performance that we could get from HDF5,” Prabhat says in a NERSC story. “But thanks to substantial progress made over the course of the ExaHDF5 project, we are now able to demonstrate that HDF5 can scale to petascale platforms like Hopper and achieve near peak I/O rates.” 

Surendra Byna, a research scientist at the Berkeley Lab and lead author of the award-winning paper about the particle simulation job, says the project will lead to better parallel I/O auto-tuning tools and help HDF5 continue to scale. “Our goal with this project was to identify parameters that would make apps of this scale successful for a broad base of science users,” Byna says in the NERSC story.

Hopper ran VPIC, a large-scale plasma physics application that describes how particles behave in magnetic reconnection, which is the physical mechanism involved in the aurora borealis, solar flares, and how gaps develop in Earth’s magnetic field. Thanks to the work, physicists at University of California, San Diego and Los Alamos National Lab were able to discover a power-law distribution in the particles’ energy spectrum. The power-law was expected to exist, but hadn’t yet been validated.

 

Related Articles

Hopper Lights Up the Cosmos

NERSC Managers Shed Light on ‘Edison’

Computing the Physics of Bubbles

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!

Live and in Color, Meet the European Student Cluster Teams

November 21, 2017

The SC17 Student Cluster Competition welcomed two teams from Europe, the German team of FAU/TUC and Team Poland, the pride of Warsaw. Let's get to know them better through the miracle of video..... Team FAU/TUC is a c Read more…

By Dan Olds

SC17 Student Cluster Kick Off – Guts, Glory, Grep

November 21, 2017

The SC17 Student Cluster Competition started with a well-orchestrated kick-off emceed by Stephen Harrell, the competition chair. It began with a welcome from SC17 chair Bernd Mohr, where he lauded the competition for Read more…

By Dan Olds

Activist Investor Starboard Buys 10.7% Stake in Mellanox; Sale Possible?

November 20, 2017

Starboard Value has reportedly taken a 10.7 percent stake in interconnect specialist Mellanox Technologies, and according to the Wall Street Journal, has urged the company “to improve its margins and stock and explore Read more…

By John Russell

HPE Extreme Performance Solutions

Harness Scalable Petabyte Storage with HPE Apollo 4510 and HPE StoreEver

As a growing number of connected devices challenges IT departments to rapidly collect, manage, and store troves of data, organizations must adopt a new generation of IT to help them operate quickly and intelligently. Read more…

Installation of Sierra Supercomputer Steams Along at LLNL

November 20, 2017

Sierra, the 125 petaflops (peak) machine based on IBM’s Power9 chip being built at Lawrence Livermore National Laboratory, sometimes takes a back seat to Summit, the ~200 petaflops system being built at Oak Ridge Natio Read more…

By John Russell

Live and in Color, Meet the European Student Cluster Teams

November 21, 2017

The SC17 Student Cluster Competition welcomed two teams from Europe, the German team of FAU/TUC and Team Poland, the pride of Warsaw. Let's get to know them bet Read more…

By Dan Olds

SC17 Student Cluster Kick Off – Guts, Glory, Grep

November 21, 2017

The SC17 Student Cluster Competition started with a well-orchestrated kick-off emceed by Stephen Harrell, the competition chair. It began with a welcome from Read more…

By Dan Olds

SC Bids Farewell to Denver, Heads to Dallas for 30th

November 17, 2017

After a jam-packed four-day expo and intensive six-day technical program, SC17 has wrapped up another successful event that brought together nearly 13,000 visit Read more…

By Tiffany Trader

SC17 Keynote – HPC Powers SKA Efforts to Peer Deep into the Cosmos

November 17, 2017

This week’s SC17 keynote – Life, the Universe and Computing: The Story of the SKA Telescope – was a powerful pitch for the potential of Big Science projects that also showcased the foundational role of high performance computing in modern science. It was also visually stunning. Read more…

By John Russell

How Cities Use HPC at the Edge to Get Smarter

November 17, 2017

Cities are sensoring up, collecting vast troves of data that they’re running through predictive models and using the insights to solve problems that, in some Read more…

By Doug Black

Student Cluster LINPACK Record Shattered! More LINs Packed Than Ever before!

November 16, 2017

Nanyang Technological University, the pride of Singapore, utterly destroyed the Student Cluster Competition LINPACK record by posting a score of 51.77 TFlop/s a Read more…

By Dan Olds

Hyperion Market Update: ‘Decent’ Growth Led by HPE; AI Transparency a Risk Issue

November 15, 2017

The HPC market update from Hyperion Research (formerly IDC) at the annual SC conference is a business and social “must,” and this year’s presentation at S Read more…

By Doug Black

Nvidia Focuses Its Cloud Containers on HPC Applications

November 14, 2017

Having migrated its top-of-the-line datacenter GPU to the largest cloud vendors, Nvidia is touting its Volta architecture for a range of scientific computing ta Read more…

By George Leopold

US Coalesces Plans for First Exascale Supercomputer: Aurora in 2021

September 27, 2017

At the Advanced Scientific Computing Advisory Committee (ASCAC) meeting, in Arlington, Va., yesterday (Sept. 26), it was revealed that the "Aurora" supercompute Read more…

By Tiffany Trader

NERSC Scales Scientific Deep Learning to 15 Petaflops

August 28, 2017

A collaborative effort between Intel, NERSC and Stanford has delivered the first 15-petaflops deep learning software running on HPC platforms and is, according Read more…

By Rob Farber

Oracle Layoffs Reportedly Hit SPARC and Solaris Hard

September 7, 2017

Oracle’s latest layoffs have many wondering if this is the end of the line for the SPARC processor and Solaris OS development. As reported by multiple sources Read more…

By John Russell

AMD Showcases Growing Portfolio of EPYC and Radeon-based Systems at SC17

November 13, 2017

AMD’s charge back into HPC and the datacenter is on full display at SC17. Having launched the EPYC processor line in June along with its MI25 GPU the focus he Read more…

By John Russell

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

Google Releases Deeplearn.js to Further Democratize Machine Learning

August 17, 2017

Spreading the use of machine learning tools is one of the goals of Google’s PAIR (People + AI Research) initiative, which was introduced in early July. Last w Read more…

By John Russell

GlobalFoundries Puts Wind in AMD’s Sails with 12nm FinFET

September 24, 2017

From its annual tech conference last week (Sept. 20), where GlobalFoundries welcomed more than 600 semiconductor professionals (reaching the Santa Clara venue Read more…

By Tiffany Trader

Amazon Debuts New AMD-based GPU Instances for Graphics Acceleration

September 12, 2017

Last week Amazon Web Services (AWS) streaming service, AppStream 2.0, introduced a new GPU instance called Graphics Design intended to accelerate graphics. The Read more…

By John Russell

Leading Solution Providers

EU Funds 20 Million Euro ARM+FPGA Exascale Project

September 7, 2017

At the Barcelona Supercomputer Centre on Wednesday (Sept. 6), 16 partners gathered to launch the EuroEXA project, which invests €20 million over three-and-a-half years into exascale-focused research and development. Led by the Horizon 2020 program, EuroEXA picks up the banner of a triad of partner projects — ExaNeSt, EcoScale and ExaNoDe — building on their work... Read more…

By Tiffany Trader

Delays, Smoke, Records & Markets – A Candid Conversation with Cray CEO Peter Ungaro

October 5, 2017

Earlier this month, Tom Tabor, publisher of HPCwire and I had a very personal conversation with Cray CEO Peter Ungaro. Cray has been on something of a Cinderell Read more…

By Tiffany Trader & Tom Tabor

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

Cray Moves to Acquire the Seagate ClusterStor Line

July 28, 2017

This week Cray announced that it is picking up Seagate's ClusterStor HPC storage array business for an undisclosed sum. "In short we're effectively transitioning the bulk of the ClusterStor product line to Cray," said CEO Peter Ungaro. Read more…

By Tiffany Trader

Intel Launches Software Tools to Ease FPGA Programming

September 5, 2017

Field Programmable Gate Arrays (FPGAs) have a reputation for being difficult to program, requiring expertise in specialty languages, like Verilog or VHDL. Easin Read more…

By Tiffany Trader

HPC Chips – A Veritable Smorgasbord?

October 10, 2017

For the first time since AMD's ill-fated launch of Bulldozer the answer to the question, 'Which CPU will be in my next HPC system?' doesn't have to be 'Whichever variety of Intel Xeon E5 they are selling when we procure'. Read more…

By Dairsie Latimer

Flipping the Flops and Reading the Top500 Tea Leaves

November 13, 2017

The 50th edition of the Top500 list, the biannual publication of the world’s fastest supercomputers based on public Linpack benchmarking results, was released Read more…

By Tiffany Trader

IBM Advances Web-based Quantum Programming

September 5, 2017

IBM Research is pairing its Jupyter-based Data Science Experience notebook environment with its cloud-based quantum computer, IBM Q, in hopes of encouraging a new class of entrepreneurial user to solve intractable problems that even exceed the capabilities of the best AI systems. Read more…

By Alex Woodie

Share This