Samplify Puts the Squeeze on Compression

By Nicole Hemsoth

June 27, 2013

Last week at ISC, Silicon Valley-based, Samplify Systems announced its APAX HDF Storage Library for HPC, which they say can push disk throughput by 3-8x and reduce storage needs for those tapping the HDF5 file format. 

This could find wide appeal in a number of HPC application areas, including those related to CFD, climate modeling and multiphysics simulations–in short, the areas where HDF5 (and memory, disk and network bottlenecks) are common.

However, when you start talking compression to researchers, the first questions that come to mind are around data quality–followed closely by concerns about performance. Many scientists, especially in the data-intensive field of climate studies, look to GRIB2-based encoding methods, which while lossy, have served the community well. The problem, however, is that this still introduces some data quality and processing overhead–and for these users, neither are optimal sacrifices.

When it comes to compression, scientists are stuck between choosing lossless compression, which maintain fidelity but can be cumbersome and slow or lossy compression, which produces its own host of worries when it comes to archiving and validating scientific data. 

But compression, even if it has the risk-laden name of “lossy”, doesn’t mean a pinch in quality–at least not if users are granted fine-tuned control over the compression features. According to Samplify Systems’ CEO, Allan Evans, the sacrifices on the lossy compression front are minimal–at least for those who are looking into their own APAX technology and their profiler technology which lets users set the accuracy to encoding levels. 

Further, he explains, that another fear is that such compression would require dramatic code tweaking. He says that with their technology, this provides a transparent layer which actually opens access to the data. 

According to Evans, lossy compression isn’t the risky business one might suspect–and it can lead to better performance when done properly. While this type of technology has wide play in other, non-HPC markets, a presentation from the company’s CTO at ISC ’13 last week spelled out just how viable extreme compression can be for a wide set of HPC applications, especially those with a large number of variables that can be run as standalone simulations against existing datasets.

In that presentation it was argued that “the most easily obtained benefit from lossy compression of climate datasets is a significant reduction in disk file size and a corresponding increase in disk bandwidth.” In terms of throughput, the CTO noted that their single-pass algorithm led to better cache usage and that overall, compared to the aforementioned compression methods, this offered a 1.6x improvement in compression and “better encoding for most climate variables due to its superior compression or data quality.”

To put this in better context, take a climate simulation, which can have close to 100 different state variables (pressure, temperature, etc), each of which is multi-dimensional (for example, different latitudes, altitudes, etc.). To add complexity, this simulation runs for a period of time, say between now and 2050. The simulation will provide interval-based snapshots while on the backend, the commonly-used HDF5 file format will containerize each of those variables for each snapshot–saving metadata so the information can be read back over quickly. The goal is to have a simulation where a user can pinpoint a particular place and date to understand exactly what the weather will be like. 

Samplify has uncovered a way to use lossy compression to reduce these HDF5 files without changing the solver application (as long as it’s already using HDF5, of course). The data compression is then applied in real-time first as the data is being saved or read back from the file–then the size is reduced via their plug-in to HDF5. The operator can then decide how much compression to apply in the face of what will be lost–in essence, to see how they can go–before the fidelity is at unacceptable levels. 

This means it’s possible for the scientist (versus a developer) to profile different variables–applying variable by variable compression that’s optimized for each variable type.

Outside of the compression angle, there is also the issue of performance. The APAX technology is Samplify’s numerical encoder that targets any integer or floating point data type and weighs in at 3:1 to 8:1 on the encoding rate scale. The key here is that it does so without having any direct impact on the actual application. Their APAX libraries can be snapped into an application’s core to let it work on data in memory, on disk or streaming across networks. It’s primed for Intel CPUs–Evans says the throughput is around 200 MB/sec per core.

While there appears no way to “try before you buy” directly, Samplify hopes this will be a valuable enough proposition for climatology and other researchers to plunk down an estimated $50,000 for a petabyte storage array. He notes that when priced against other solutions that take aim at the bottenecks in large-scale storage environments, this is on par, if not better. 

As it stands, the company has lined up some impressive use cases, including one of note at Lawrence Livermore National Laboratory that’s worth taking a look at.

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!

RSC Reports 500Tflops, Hot Water Cooled System Deployed at JINR

April 18, 2018

RSC, developer of supercomputers and advanced HPC systems based in Russia, today reported deployment of “the world's first 100% ‘hot water’ liquid cooled supercomputer” at Joint Institute for Nuclear Research (JI Read more…

By Staff

New Device Spots Quantum Particle ‘Fingerprint’

April 18, 2018

Majorana particles have been observed by university researchers employing a device consisting of layers of magnetic insulators on a superconducting material. The advance opens the door to controlling the elusive particle Read more…

By George Leopold

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’s introduction of an ARM-based system (XC-50) last November. Read more…

By John Russell

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…

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 Symposium on Computer Architecture (ISCA) in Los Angeles. The Read more…

By Staff

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’ Read more…

By John Russell

IBM: Software Ecosystem for OpenPOWER is Ready for Prime Time

April 16, 2018

With key pieces of the IBM/OpenPOWER versus Intel/x86 gambit settling into place – e.g., the arrival of Power9 chips and Power9-based systems, hyperscaler sup Read more…

By John Russell

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

Cloud-Readiness and Looking Beyond Application Scaling

April 11, 2018

There are two aspects to consider when determining if an application is suitable for running in the cloud. The first, which we will discuss here under the title Read more…

By Chris Downing

Transitioning from Big Data to Discovery: Data Management as a Keystone Analytics Strategy

April 9, 2018

The past 10-15 years has seen a stark rise in the density, size, and diversity of scientific data being generated in every scientific discipline in the world. Key among the sciences has been the explosion of laboratory technologies that generate large amounts of data in life-sciences and healthcare research. Large amounts of data are now being stored in very large storage name spaces, with little to no organization and a general unease about how to approach analyzing it. Read more…

By Ari Berman, BioTeam, Inc.

IBM Expands Quantum Computing Network

April 5, 2018

IBM is positioning itself as a first mover in establishing the era of commercial quantum computing. The company believes in order for quantum to work, taming qu Read more…

By Tiffany Trader

FY18 Budget & CORAL-2 – Exascale USA Continues to Move Ahead

April 2, 2018

It was not pretty. However, despite some twists and turns, the federal government’s Fiscal Year 2018 (FY18) budget is complete and ended with some very positi Read more…

By Alex R. Larzelere

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

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

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

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

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

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

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

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

Leading Solution Providers

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

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

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

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

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

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

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

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

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