Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

By Jan Rowell

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale.

That’s the conclusion drawn by the scientists and researchers of Europe’s NEXTGenIO project, an initiative funded by the European Commission’s Horizon 2020 program to explore this new technology’s potential impact for high-performance computing (HPC).

“When you put vast amounts of high-performance, byte-addressable NVRAM in the compute nodes, everything changes,” said Adrian Jackson, senior research fellow at EPCC, the supercomputing centre at the University of Edinburgh, and the software architect for a 34-node prototype platform the NEXTGenIO partner organizations co-developed to support their research. “The compute nodes become storage nodes as well as memory nodes, and you can scale your I/O bandwidth and use I/O differently. You need the right tools to access the data within the nodes, but you can use the data in different ways depending on your applications.”

The implications are exciting for HPC users like Tiago Quintino, who works with massive, fast-growing data sets at the European Center for Medium-Range Weather Forecasts (ECMWF). “We can do so much more,” he said. “We can have much more complex structures in memory. We can use the data where it is, without having to move it throughout the workflow. With the time we save, we can run more complex workflows, do more physics, increase model resolution. Extrapolating our data growth, which has been increasing three times every two years, an I/O system based on this technology will let me cope for the next 10-15 years. It is a game changer.

Exploring Non-Volatile, On-Node Memory

In addition to EPCC and ECMWF, NEXTGenIO partners include Fujitsu, Intel, Barcelona Supercomputing Center (BSC), the Technical University of Dresden, ARM, and ARCTUR. The platform they co-designed followed a requirements-driven process that also specified realistic constraints. It features a custom motherboard populated with 3 TB of Intel Optane DC persistent memory (DCPMM), dual 2nd Generation Intel Xeon Scalable processors, and 192 GB of DRAM. The Intel Optane DC memory is hosted as standard DIMMS that reside on the memory bus and can be controlled by the CPU’s integrated memory controllers. Nodes also connect to two Intel Omni-Path high-performance networks, making it possible for MPI traffic to travel over one network and storage communications across the other.

Software developed for the system includes a multi-node, local and distributed NVRAM file system that allows legacy applications to transparently benefit from the new memory/storage layer without application changes. The distributed file system uses application object stores to provide data locality and reduce reliance on parallel file systems such as Lustre. Other system software includes performance profiling and debugging tools, as well as extensions to the SLURM scheduler and workload manager for managing data locality and incorporating a job’s energy consumption into job placement decisions.

Fujitsu built the system and motherboard at its facility in Augsburg, Germany, and the system was installed at EPCC in late March 2019. It will be available to NEXTGenIO collaborators and select I/O researchers for the next three years, giving Europe a major resource to advance the understanding and use of a significant new memory technology.

Project members have begun sharing initial results that demonstrate the technology’s impact for varied HPC use cases.[1] Here are three examples.

ECMWF’s Integrated Forecasting System: Intense I/O in a Time-Critical Workflow

Based in the UK, ECMWF produces weather forecasts five to fifteen days out, multiple times per day, for its customers around the world. Its Integrated Forecasting System (IFS) writes its result—about 25 TB per hour—into ECMWF’s distributed Fields Database (FDB). The subsequent workflow involves several hundred postprocessing steps, many conducted in parallel and needing rapid access to the data output. If the central parallel file system is slowed by other workloads, forecasters have to throttle the forecast and slow the model.

Using the NEXTGenIO platform, ECMWF demonstrated the ability to output the data to the new class of memory and significantly increase performance. For IFS writing into ECMWF’s Fields Database, 16 NEXTGenIO nodes delivered 60 GiB/s read bandwidth and 72 GiB/s write bandwidth compared to sustained read throughput of 22.4 GiB/s and write throughput of 20 GiB/s on a system with 288 Lustre Object Store Service (OST) nodes with 10 disks per node. It produced an end-to-end improvement in the workflow of more than an order of magnitude. ECMWF expects to see further improvements upon optimizing the FDB code.

CASTEP: Massive Memory Requirements, Minimal I/O

CASTEP is shared source software that uses density functional theory to calculate material properties from first principles. It is used for a range of materials and substances, including DNA as well as new and exotic elements.

Many CASTEP simulations require large amounts of memory per MPI process, exceeding the memory capacity of typical HPC systems. This often forces users to reduce the number of MPI processes per node, underpopulating the CPUs and running the simulation over many nodes in order to fit the simulation into DRAM.

EPCC used CASTEP to run a memory-hungry DNA simulation on the NEXTGenIO platform, enabling a single DNA simulation that requires 20 nodes when using DRAM-only to run on just a single node, albeit much more slowly. On four nodes (Table 1), using five times fewer, the DCPMM implementation was just over three times slower than an all-DRAM execution on the NEXTGenIO system.

Table 1. CASTEP Benchmark Results

The practical implications are immense, providing HPC sites with an economical and power-efficient if somewhat slower alternative to deploying a full-DRAM platform for workloads where memory requirements outstrip compute needs. The freed nodes can be used for other jobs, optimizing overall throughput and adding to the cost benefits.

OpenFOAM: Heavy I/O with Numerous Small Files

OpenFOAM is an open source 3D computational fluid dynamics package that is effectively a collection of applications used in a complex workflow of tasks from mesh creation through postprocessing.

Here the challenge is not only the overall quantity of data, but also the large number of small files written for each time step. To explore the problem, EPCC simulated the air flow around a small electric aircraft. In 1,000 time steps, OpenFOAM was configured to write its results every five time steps. Running on 16 nodes with 448 processes, the interim results reached 806,400 files and 1.2 TB of data. Performance analysis showed that in a traditional implementation, I/O consumed 50 percent of the execution time, severely limiting scalability.

EPCC used the system software to effectively mount a node-local file system on the compute nodes’ Intel Optane DC memory. Interim results were written to the local node, using the DCPMM as storage and having the system software move the data on and off the nodes as needed. This reduced the overall runtime by as much as 50 percent, and the advantage increased with scale. These runtime savings provide opportunities to do more compute and explore more solution alternatives.

Insights from Early Adopters

NEXTGenIO collaborators offered the following suggestions for HPC users and technology innovators.

  • Think differently. “Don’t judge this technology the way you judge a parallel file system like Lustre,” said Quintino. “Lustre is like a truck—it moves a lot of data slowly. Given a lot of trucks, you can move a lot of data and have a lot of throughput. This is a Formula One race car, the pinnacle of an I/O system. It can be the first layer in a layered system, it can be a burst buffer, but we should think beyond that. It opens workflows we’ve never thought of before.”
  • Be curious. Think about what use cases are pertinent to your workload and data center challenges. “At ECMWF, DCPMM is part of the storage hierarchy,” said Jackson. “Other apps can use it as a file store, or as a multi-node file system that uses the memory to do normal parallel I/O. Some are using it to create a larger memory space so they can put a problem in a single node instead of 20 or 30 nodes. Exploiting DCPMM requires careful thought and design for applications, but the benefits can be large.”
  • Be willing to do some work. Quintino compares Intel Optane DC persistent memory to GPUs, which required some code modifications to fully benefit from. While DCPMM can be used without code modifications, many applications will benefit from explicit control of the memory. Intel offers tools and libraries to facilitate using the memory’s full feature set.

A Way to Do More Science                 

The NEXTGenIO platform will be available to HPC users whose research goals are compatible with those of the NEXTGenIO project. Fujitsu is offering the new class of memory for select PRIMERGY and PRIMEQUEST models, and its technical teams are applying their NEXTGenIO learnings as they consult with customers.

Intel Optane DC persistent memory and the innovation added by the NEXTGenIO partners mark a welcome change in the HPC landscape, according to Michèle Weiland, a senior research fellow at EPCC and project manager for NEXTGenIO. “DCPMM represents a change in the landscape in how memory, I/O, and storage systems will evolve over next few years,” she said. “It can potentially show that there’s a way out of the problems we’re currently seeing. For people who are struggling with current traditional HPC systems, who don’t have enough memory or fast enough storage, or who are limited by the amount of data they can write, this approach may give them a way to improve this, and do more science.”

To learn more about the NEXTGenIO project, visit http://nextgenio.eu

For information about gaining access to the platform, contact Professor Mark Parsons, [email protected], or Dr Michèle Weiland, [email protected]

About the Author 

Jan Rowell covers technology trends and innovations in HPC, artificial intelligence, and other areas.

[1] A paper describing some of these results will appear as “An Early Evaluation of Intel’s Optane DC Persistent Memory Module and its Impact on High Performance Scientific Applications” by Michèle Weiland and others, in SC ’19 Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis. Quintino and others from ECMWF describe the object-store file system in “A High-Performance Distributed Object-Store for Exascale Numerical Weather Prediction and Climate,” in PASC ’19: Proceedings of the Platform for Advanced Scientific Computing Conference, https://dl.acm.org/citation.cfm?id=3324989.3325726

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!

U.S. CTO Michael Kratsios Adds DoD Research & Engineering Title

July 13, 2020

Michael Kratsios, the U.S. Chief Technology Officer, has been appointed acting Undersecretary of Defense for research and engineering. He replaces Mike Griffin, who along with his deputy Lis Porter, stepped down last wee Read more…

By John Russell

Supercomputer Research Reveals Star Cluster Born Outside Our Galaxy

July 11, 2020

The Milky Way is our galactic home, containing our solar system and continuing into a giant band of densely packed stars that stretches across clear night skies around the world – but, it turns out, not all of those st Read more…

By Oliver Peckham

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprised of Intel Xeon processors and Nvidia A100 GPUs, and featuri Read more…

By Tiffany Trader

Xilinx Announces First Adaptive Computing Challenge

July 9, 2020

A new contest is challenging the computing world. Xilinx has announced the first Xilinx Adaptive Computing Challenge, a competition that will task developers and startups with finding creative workload acceleration solutions. Xilinx is running the Adaptive Computing Challenge in partnership with Hackster.io, a developing community... Read more…

By Staff report

Reviving Moore’s Law? LBNL Researchers See Promise in Heterostructure Oxides

July 9, 2020

The reality of Moore’s law’s decline is no longer doubted for good empirical reasons. That said, never say never. Recent work by Lawrence Berkeley National Laboratory researchers suggests heterostructure oxides may b Read more…

By John Russell

AWS Solution Channel

Best Practices for Running Computational Fluid Dynamics (CFD) Workloads on AWS

The scalable nature and variable demand of CFD workloads makes them well-suited for a cloud computing environment. Many of the AWS instance types, such as the compute family instance types, are designed to include support for this type of workload.  Read more…

Intel® HPC + AI Pavilion

Supercomputing the Pandemic: Scientific Community Tackles COVID-19 from Multiple Perspectives

Since their inception, supercomputers have taken on the biggest, most complex, and most data-intensive computing challenges—from confirming Einstein’s theories about gravitational waves to predicting the impacts of climate change. Read more…

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: 1) Industries of the Future (IotF), chaired be Dario Gil (d Read more…

By John Russell

Max Planck Society Begins Installation of Liquid-Cooled Supercomputer from Lenovo

July 9, 2020

Lenovo announced today that it is supplying a new high performance computer to the Max Planck Society, one of Germany's premier research organizations. Comprise Read more…

By Tiffany Trader

President’s Council Targets AI, Quantum, STEM; Recommends Spending Growth

July 9, 2020

Last week the President Council of Advisors on Science and Technology (PCAST) met (webinar) to review policy recommendations around three sub-committee reports: Read more…

By John Russell

Google Cloud Debuts 16-GPU Ampere A100 Instances

July 7, 2020

On the heels of the Nvidia’s Ampere A100 GPU launch in May, Google Cloud is announcing alpha availability of the A100 “Accelerator Optimized” VM A2 instance family on Google Compute Engine. The instances are powered by the HGX A100 16-GPU platform, which combines two HGX A100 8-GPU baseboards using... Read more…

By Tiffany Trader

Q&A: HLRS’s Bastian Koller Tackles HPC and Industry in Germany and Europe

July 6, 2020

In this exclusive interview for HPCwire – sadly not face to face – Steve Conway, senior advisor for Hyperion Research, talks with Dr.-Ing Bastian Koller about the state of HPC and its collaboration with Industry in Europe. Koller is a familiar figure in HPC. He is the managing director at High Performance Computing Center Stuttgart (HLRS) and also serves... Read more…

By Steve Conway, Hyperion

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

Supercomputer Modeling Tests How COVID-19 Spreads in Grocery Stores

April 8, 2020

In the COVID-19 era, many people are treating simple activities like getting gas or groceries with caution as they try to heed social distancing mandates and protect their own health. Still, significant uncertainty surrounds the relative risk of different activities, and conflicting information is prevalent. A team of Finnish researchers set out to address some of these uncertainties by... Read more…

By Oliver Peckham

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Supercomputer Simulations Reveal the Fate of the Neanderthals

May 25, 2020

For hundreds of thousands of years, neanderthals roamed the planet, eventually (almost 50,000 years ago) giving way to homo sapiens, which quickly became the do Read more…

By Oliver Peckham

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Neocortex Will Be First-of-Its-Kind 800,000-Core AI Supercomputer

June 9, 2020

Pittsburgh Supercomputing Center (PSC - a joint research organization of Carnegie Mellon University and the University of Pittsburgh) has won a $5 million award Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

By Doug Black

Leading Solution Providers

Contributors

Nvidia’s Ampere A100 GPU: Up to 2.5X the HPC, 20X the AI

May 14, 2020

Nvidia's first Ampere-based graphics card, the A100 GPU, packs a whopping 54 billion transistors on 826mm2 of silicon, making it the world's largest seven-nanom Read more…

By Tiffany Trader

‘Billion Molecules Against COVID-19’ Challenge to Launch with Massive Supercomputing Support

April 22, 2020

Around the world, supercomputing centers have spun up and opened their doors for COVID-19 research in what may be the most unified supercomputing effort in hist Read more…

By Oliver Peckham

Australian Researchers Break All-Time Internet Speed Record

May 26, 2020

If you’ve been stuck at home for the last few months, you’ve probably become more attuned to the quality (or lack thereof) of your internet connection. Even Read more…

By Oliver Peckham

15 Slides on Programming Aurora and Exascale Systems

May 7, 2020

Sometime in 2021, Aurora, the first planned U.S. exascale system, is scheduled to be fired up at Argonne National Laboratory. Cray (now HPE) and Intel are the k Read more…

By John Russell

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

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

$100B Plan Submitted for Massive Remake and Expansion of NSF

May 27, 2020

Legislation to reshape, expand - and rename - the National Science Foundation has been submitted in both the U.S. House and Senate. The proposal, which seems to Read more…

By John Russell

John Martinis Reportedly Leaves Google Quantum Effort

April 21, 2020

John Martinis, who led Google’s quantum computing effort since establishing its quantum hardware group in 2014, has left Google after being moved into an advi 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