Rethinking HPC Platforms for ‘Second Gen’ Applications

By John Russell

February 22, 2017

Just what constitutes HPC and how best to support it is a keen topic currently. A new paper posted last week on arXiv.org – Rethinking HPC Platforms: Challenges, Opportunities and Recommendations – by researchers from the University of Edinburgh and University of St. Andrews suggests the emergence of “second generation” HPC applications (and users) requires a new approach to supporting infrastructure that draws on container-like technology and services.

(Lead author Ole Weidner spoke with HPCwire after this article was first published and discussed further how it relates to other HPC container efforts. Please see the addendum at the end of the article for his additional comments.)

In the paper they describe a set of services, which they call ‘cHPC’ (container HPC), to accommodate these emerging HPC application requirements and indicate they plan to benchmark key applications as a next step. “Many of the emerging second generation HPC applications move beyond tightly-coupled, compute-centric methods and algorithms and embrace more heterogeneous, multi-component workflows, dynamic and ad-hoc computation and data-centric methodologies,” write authors Ole Weidner, Rosa Filgueira Vicente, Malcolm Atkinson, and Adam Barker.

“While diverging from the traditional HPC application profile, many of these applications still rely on the large number of tightly coupled cores, cutting-edge hardware and advanced interconnect topologies provided only by HPC clusters. Consequently, HPC platform providers often find themselves faced with requirements and requests that are so diverse and dynamic that they become increasingly difficult to fulfill efficiently within the current operational policies and platform models.”

It’s best to read the paper in full which examines in some detail the challenges and potential solutions. The authors single out three applications areas and report that as a group they have deep experience working with them:

  • Data Intensive Applications. Data-intensive applications require large volumes of data and devote a large fraction of their execution time to I/O and manipulation of data. Careful attention to data handling is necessary to achieve acceptable performance or completion. “They are frequently sensitive to local storage for intermediate results and reference data. It is also sensitive to the data-intensive frameworks and workflow systems available on the platform and to the proximity of data it uses.” Examples of large-scale, data-intensive HPC applications are seismic noise cross-correlation and misfit calculation as encountered, e.g. in the VERCE project.
  • Dynamic Applications. These fall into two broad categories: “applications for which we do not have full understanding of the runtime behavior and resource requirements prior to execution and (ii) applications which can change their runtime behavior and resource requirements during execution.” Two examples cited are: (a) applications that use ensemble Kalman-Filters for data assimilation in forecasting, (b) simulations that use adaptive mesh refinement (AMR) to refine the accuracy of their solutions.
  • Federated applications. “Based on the idea that federation fosters collaboration and allows scalability beyond a single platform, policies and funding schemes explicitly supporting the development of concepts and technology for HPC federations have been put into place. Larger federations of HPC platforms are XSEDE in the US, and the PRACE in the EU. Both platforms provide access to several TOP-500 ranked HPC clusters and an array of smaller and experimental platforms.”

“To explore the implementation options for our new platform model, we have developed cHPC, a set of operating-system level services and APIs that can run alongside and integrate with existing job via Linux containers (LXC) to pro- vide isolated, user-deployed application environment containers, application introspection and resource throttling via the cgroups kernel extension. The LXC runtime and software-defined networking are provided by Docker and run as OS services on the compute nodes,” say the authors. (see figure 2 from the papers shown here)

The authors note prominently in their discussion that many traditional HPC applications are still best served by traditional HPC environments for which they have been carefully coupled.

“It would be false to claim that current production HPC platforms fail to meet the requirements of their application communities. It would be equally wrong to claim that the existing platform model is a pervasive problem that generally stalls the innovation and productivity of HPC applications…[There are] significant classes of applications, often from the monolithic, tightly-coupled parallel realm, [that] have few concerns regarding the issues out-lined in this paper…They are the original tenants and drivers of HPC and have an effective social and technical symbiosis with their platform environments.

“However, it is equally important to understand that other classes of applications (that we call second generation applications) and their respective user communities share a less rosy perspective. These second generation applications are typically non-monolithic, dynamic in terms of their runtime behavior and resource requirements, or based on higher-level tools and frameworks that manage compute, data and communication. Some of them actively explore new compute and data handling paradigms, and operate in a larger, federated context that spans multiple, distributed HPC clusters.”

To qualify and quantify their assumptions, the authors report they are in the process of designing a survey that will be sent out to platform providers and application groups to verify current issues on a broader and larger scale. They write, “The main focus of our work will be on the further evaluation of our prototype system. We are working on a ‘bare metal’ deployment on HPC cluster hardware at EPCC. This will allow us to carry out detailed measurements and benchmarks to analyze the overhead and scalability of our approach. We will also engage with computational science groups working on second generation applications to explore their real-life application in the context of cHPC.”

Link to paper (Rethinking HPC Platforms: Challenges, Opportunities and Recommendations): https://arxiv.org/pdf/1702.05513.pdf

Addendum (3/1/17):

The authors are well aware of the many ongoing efforts to leverage container technology for HPC. Lead author Weidner told HPCwire, “I am familiar with the work on Singularity that Gregory Kurtzer and his peers at LBNL are doing. It is a prominent project with quite significant real-world uptake and definitely needs to be, along with a few others, added to the related work section in the next iteration of our paper.

“We can definitely observe that over the past year, operating-system level virtualization and containers have become more and more common place in HPC application and middleware stacks, especially in projects that rely on, or support what we call “second gen.” applications. Take Cornell’s BioHPC Lab (https://cbsu.tc.cornell.edu/lab/lab.aspx) for example, or NERSC’s Shifter (http://www.nersc.gov/users/software/using-shifter-and-docker/using-shifter-at-nersc/). I think with Singularity leading the way, the objective of most of these projects is to address what we refer to as the “centralized (software) deployment monopolies” and “application mobility” in our paper.

The scope for cHPC tries to be a bit broader, says Weidner. “First of all, unlike Singularity, cHPC is not production-grade software. It is a research prototype. Having said that, the vision of cHPC and the conceptual work we are doing around it is not just to encapsulate (end-)user applications but to incorporate more low-level HPC system components. Our aim is to develop blueprints for more “data-driven” HPC environments in which application adaptivity, elastic scalability and resilience strategies are supported explicitly by the platform.

“We believe that a data-driven HPC software stack is one of the critical, but still missing components to address the upcoming exascale application challenges in which real-time predictive operational analytics will play an important role to support resilience and efficiency at extreme scales. Containers are an excellent vehicle to research these new data-data driven system and application architectures without having to implement an entire HPC system from scratch. That’s why we have developed cHPC.”

Weidner and his colleagues are working on a paper in which we lay out a comprehensive framework for operational data management in HPC systems (“Data-Driven HPC”).

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!

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the increasingly important goals of data best practices and work Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated, analysts said the acquisition would cement Nvidia’s stat Read more…

By George Leopold

Summer Reading: Here’s a Quantum Advantage You Can Bet On!

August 3, 2020

While quantum computing researchers today vigorously chase a demonstration of a quantum advantage – an application which when run on a quantum computer provides sufficient advantage to warrant switching from a classica Read more…

By John Russell

What’s New in HPC Research: the LHC, Nuclear Reactors, Legion & More

August 1, 2020

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

HPC Career Notes: August 2020 Edition

August 1, 2020

In this monthly feature, we’ll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it’s a promotion, new company hire, or even an accolade, we’ Read more…

By Mariana Iriarte

AWS Solution Channel

AWS announces the release of AWS ParallelCluster 2.8.0

AWS ParallelCluster is a fully supported and maintained open source cluster management tool that makes it easy for scientists, researchers, and IT administrators to deploy and manage High Performance Computing (HPC) clusters in the AWS cloud. 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…

Heterogeneous Computing Gets a Code Similarity Tool

July 31, 2020

A machine programming framework for heterogeneous computing championed by Intel Corp. and university partners is built around an automated engine that analyzes code for similarities. The approach could eventually allow n Read more…

By George Leopold

Machines, Connections, Data, and Especially People: OAC Acting Director Amy Friedlander Charts Office’s Blueprint for Innovation

August 3, 2020

The path to innovation in cyberinfrastructure (CI) will require continued focus on building HPC systems and secure connections between them, in addition to the Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Nvidia Said to Be Close on Arm Deal

August 3, 2020

GPU leader Nvidia Corp. is in talks to buy U.K. chip designer Arm from parent company Softbank, according to several reports over the weekend. If consummated Read more…

By George Leopold

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

PEARC20 Plenary Introduces Five Upcoming NSF-Funded HPC Systems

July 30, 2020

Five new HPC systems—three National Science Foundation-funded “Capacity” systems and two “Innovative Prototype/Testbed” systems—will be coming onlin Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

Nvidia Dominates Latest MLPerf Training Benchmark Results

July 29, 2020

MLPerf.org released its third round of training benchmark (v0.7) results today and Nvidia again dominated, claiming 16 new records. Meanwhile, Google provided e Read more…

By John Russell

$39 Billion Worldwide HPC Market Faces 3.7% COVID-related Drop in 2020

July 29, 2020

Global HPC market revenue reached $39 billion in 2019, growing a healthy 8.2 percent over 2018, according to the latest analysis from Intersect360 Research. A 3 Read more…

By Tiffany Trader

Agenting Change: PEARC20 Keynote Encourages Cultural Change to Make Tech Better, More Diverse

July 29, 2020

The tech world will need to become more diverse if it is to thrive and survive, said Cherri Pancake, director of the Northwest Alliance for Computational Resear Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

In Big Win for COVID-19 Research, Neocortix Brings Arm Support to [email protected], [email protected]

July 28, 2020

Normally, Neocortix offers distributed cloud computing for its clients by way of PhonePaycheck, an app that pays users in exchange for the idle processing time Read more…

By Oliver Peckham

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

Supercomputer-Powered Research Uncovers Signs of ‘Bradykinin Storm’ That May Explain COVID-19 Symptoms

July 28, 2020

Doctors and medical researchers have struggled to pinpoint – let alone explain – the deluge of symptoms induced by COVID-19 infections in patients, and what 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

Intel’s 7nm Slip Raises Questions About Ponte Vecchio GPU, Aurora Supercomputer

July 30, 2020

During its second-quarter earnings call, Intel announced a one-year delay of its 7nm process technology, which it says it will create an approximate six-month shift for its CPU product timing relative to prior expectations. The primary issue is a defect mode in the 7nm process that resulted in yield degradation... Read more…

By Tiffany Trader

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

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

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

Leading Solution Providers

Contributors

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

‘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

Joliot-Curie Supercomputer Used to Build First Full, High-Fidelity Aircraft Engine Simulation

July 14, 2020

When industrial designers plan the design of a new element of a vehicle’s propulsion or exterior, they typically use fluid dynamics to optimize airflow and in Read more…

By Oliver Peckham

$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

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

[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

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