Intel Charges Spark Workloads with Optane Persistent Memory

By Alex Woodie

July 30, 2019

Intel didn’t wow chip lovers earlier this year with the launch of its 2nd Generation Intel Xeon Scalable processors “Cascade Lake” processors, which are based on the same 14nm process as the first generation processors. But the launch also included the delivery of Optane Data Center Persistent Memory Module (DCPMM), which is poised to deliver big benefits for SQL and machine learning workloads on Apache Spark and other frameworks.

Optane is Intel‘s latest storage innovation that blends the characteristics of fast but volatile RAM and slower but persistent NAND storage technology. Originally based on the 3D Xpoint technology that it started co-developing with Micron years ago, the storage-class memory technology was designed to provide a major boost in the ability of users to work with large data sets by providing the speed of DRAM but the capacity and persistence of NAND.

Intel already shipped an Optane product in the form of NVMe drive, and now it’s coming to market in the guise of Optane DCPMMs. Delivered as standard DIMMs, Optane DCPMMs plug right into the PCIe bus on industry-standard X86 servers. Those systems will, however, need to be running Cascade Lake processors, while the NVMe format was more flexible in system configurations. However, what the DCPMM lacks in flexibility it should make up in capability.

Intel is shipping DCPMMs in three sizes: 128GB, 256GB, and 512GB. Each DCPMM requires its own memory channel, and customers can load up to six DCPMM DIMMs in single socket. Users can co-locate DCPMMs next to DRAM, but they cannot use multiple sizes of DCPMMs.

This gives customers with a two-socket server the capability to have up to 6TB of memory per server, according Intel engineer Piotr Balcer, who spoke at Databricks’ Spark + AI Summit 2019 recently. “Quite a lot of space for your whole data,” he said.

With multiple servers, DCPMM enables customers to store up to 1PB of data in 1U of a rack, Intel said.

Speeding Data with Optane

There are two modes supported with Optane DCPMM: App Direct mode and Memory Mode (there’s also Storage Over App Direct Mode).

Users who want to take advantage of Optane’s data persistence capabilities will need to choose App Direct mode, since the data is wiped clean during power shutdowns in Memory Mode, which is how traditional DRAM works. (But because DCPMMs are still cheaper than traditional DRAM DIMMs, Optane retains an advantage.)

Balcer and his Intel colleague Cheng Xu demonstrated how Spark users can get a performance boost during their Spark + AI Summit session, titled “Accelerate Your Apache Spark with Intel Optane DC Persistent Memory.”

“Persistent memory is exposed to the application through the file system,” Balcer said. “It uses the same normal interface as storage.” Currently DCPMM supports XFS, EXT4, and NTFS file systems, using those file systems’ block storage system calls to read and write data.

“It behaves like DRAM for access, so you can use normal load semantics, which means we don’t have to go through the kernel,” he said. “We don’t have to have that control point.”

To enable applications to directly access data and use normal load storage instructions, Intel developed something called DAX, which stands for direct access, Balcer said.

“Which means it allows the application to mount the persistent memory into the other space of the application, and bypass the page cache, because the page cache is what you traditionally will use when you use memory mounts,” he said. “Because we now have very, very fast memory, we don’t really need the page cache to amortize the block storage.”

Using the DAX layer, DCPMM enables users to mount persistent memory into the address space of the application and then use the load store instructions of the CPU, which is the fastest data path the application can take, Balcer said.

“What this ultimately means,” he continued, “is that the application can now store data persistently on storage yielding the load store instructions of the CPU, and that was never possible before. So there’s nothing in between the application and the storage. There’s no software. There’s no firmware. Well, there is firmware, but there’s nothing in the kernel space that interferes with the application performance.”

Spark on Optane

The performance benefits of DCPMM are directly applicable to Spark SQL and machine learning workloads that are either memory-bound or are burdened by large amounts of I/O, the Intel engineers told the Spark + AI audience.

In App Direct Mode, DCPMM has the potential to move data at multiple tens of gigabytes per second with nanosecond latencies, compared to single-digit GB/s on throughput with microsecond latencies with fast NAND-based solid state disks, according to Lenovo’s handbook on DCPMM.

However, achieving those rates requires users to specially configure their DCPMM setup, Lenovo states. “If an application hasn’t been modified to support App Direct Mode, it can utilize DCPMM in Storage over App Direct Mode operation, which is a more conventional setup using a supported DAX model in the operating system,” the vendor writes.

Intel has addressed this requirement by developing special software that allows Spark users to take full advantage of the DCPMM capabilities, without modifying their Spark machine learning or SQL applications.

Intel’s Spark on DCPMM stack consists of several layers, including a DAX file system interface discussed above, Intel’s native DCPMM library dubbed VMEMCACHE, and OAP, or the Open Analytics Packager.

The Scala-based OAP contains several elements that make it easy for Spark users to take advantage of DCPMM with their SQL and machine learning workloads, According to Xu.

“Today Spark is running very fast and very easy for the user to use. But sometimes a customer may be facing a memory issue,” Xu said. “We hear a lot of customer complaining about memory usage, so that sometimes they try to config the memory for specific workload, but when they try to run another workload, they run into other issues.”

Optimizing Spark’s usage of memory is one of the goals of OAP, which is a free and open source piece of software that users can obtain at Github. OAP levaerges DCPMM to bring three key capabilities to Spark users, including a front-end I/O cache, a cache-aware scheduler, and self-management of off-heap memory.

The I/O cache will be especially useful for Spark SQL and machine learning users who are pulling data from slower data stores, including on-premise hard disk drives and also from remote BLOB stores, such as Azure ALDS or Amazon S3, Xu said.

“For example, you have a table ABC, but for your workload, you just access the first column A,” Xu said. “In our implementation, we just cache column A because column A is hotter data compared to the rest of the columns.”

The I/O cache will also help machine learning use cases on Spark, Xu said, particularly for algorithms with an interactive nature, such as Kmeans. “Now we have a very large capacity of memory, so you can put the entire data set into the Optane persistent memory, so you can achieve even better performance than the previous tiered storage design,” he said.

OAP’s cache-aware scheduler will also boost performance for Spark users by optimizing workloads according to data locality, Xu said. The cache-aware scheduler is based on Apache Spark version 2.0 APIs, he added. Lastly, better management of off-heap memory will also boost Spark application, Xu said.

You can access the Intel employees’ recorded Spark + AI Summit session here.

This article originally appeared at sister publication Datanami.

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!

Simulating Car Crashes with Supercomputers – and Lego

October 18, 2019

It’s an experiment many of us have carried out at home: crashing two Lego creations into each other, bricks flying everywhere. But for the researchers at the General German Automobile Club (ADAC) – which is comparabl Read more…

By Oliver Peckham

NASA Uses Deep Learning to Monitor Solar Weather

October 17, 2019

Solar flares may be best-known as sci-fi MacGuffins, but those flares – and other space weather – can have serious impacts on not only spacecraft and satellites, but also on Earth-based systems such as radio communic Read more…

By Oliver Peckham

Federated Learning Applied to Cancer Research

October 17, 2019

The ability to share and analyze data while protecting patient privacy is giving medical researchers a new tool in their efforts to use what one vendor calls “federated learning” to train models based on diverse data Read more…

By George Leopold

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

NSB 2020 S&E Indicators Dig into Workforce and Education

October 16, 2019

Every two years the National Science Board is required by Congress to issue a report on the state of science and engineering in the U.S. This year, in a departure from past practice, the NSB has divided the 2020 S&E Read more…

By John Russell

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

HPE Extreme Performance Solutions

Intel FPGAs: More Than Just an Accelerator Card

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

How Do We Power the New Industrial Revolution?

[Attend the IBM LSF, HPC & AI User Group Meeting at SC19 in Denver on November 19!]

Almost everyone is talking about artificial intelligence (AI). Read more…

What’s New in HPC Research: Rabies, Smog, Robots & More

October 14, 2019

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

NSB 2020 S&E Indicators Dig into Workforce and Education

October 16, 2019

Every two years the National Science Board is required by Congress to issue a report on the state of science and engineering in the U.S. This year, in a departu Read more…

By John Russell

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Summit Simulates Braking – on Mars

October 14, 2019

NASA is planning to send humans to Mars by the 2030s – and landing on the surface will be considerably trickier than landing a rover like Curiosity. To solve Read more…

By Staff report

Trovares Drives Memory-Driven, Property Graph Analytics Strategy with HPE

October 10, 2019

Trovares, a high performance property graph analytics company, has partnered with HPE and its Superdome Flex memory-driven servers on a cybersecurity capability the companies say “routinely” runs near-time workloads on 24TB-capacity systems... Read more…

By Doug Black

Intel, Lenovo Join Forces on HPC Cluster for Flatiron

October 9, 2019

An HPC cluster with deep learning techniques will be used to process petabytes of scientific data as part of workload-intensive projects spanning astrophysics to genomics. AI partners Intel and Lenovo said they are providing... Read more…

By George Leopold

Optimizing Offshore Wind Farms with Supercomputer Simulations

October 9, 2019

Offshore wind farms offer a number of benefits; many of the areas with the strongest winds are located offshore, and siting wind farms offshore ameliorates many of the land use concerns associated with onshore wind farms. Some estimates say that, if leveraged, offshore wind power... Read more…

By Oliver Peckham

Harvard Deploys Cannon, New Lenovo Water-Cooled HPC Cluster

October 9, 2019

Harvard's Faculty of Arts & Sciences Research Computing (FASRC) center announced a refresh of their primary HPC resource. The new cluster, called Cannon after the pioneering American astronomer Annie Jump Cannon, is supplied by Lenovo... Read more…

By Tiffany Trader

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Quantum Bits: Neven’s Law (Who Asked for That), D-Wave’s Steady Push, IBM’s Li-O2- Simulation

July 3, 2019

Quantum computing’s (QC) many-faceted R&D train keeps slogging ahead and recently Japan is taking a leading role. Yesterday D-Wave Systems announced it ha Read more…

By John Russell

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

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