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!

UT Dallas Grows HPC Storage Footprint for Animation and Game Development

October 28, 2020

Computer-generated animation and video game development are extraordinarily computationally intensive fields, with studios often requiring large server farms with hundreds of terabytes – or even petabytes – of storag Read more…

By Staff report

Frame by Frame, Supercomputing Reveals the Forms of the Coronavirus

October 27, 2020

From the start of the pandemic, supercomputing research has been targeting one particular protein of the coronavirus: the notorious “S” or “spike” protein, which allows the virus to pry its way into human cells a Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. The acquisition helps AMD keep pace during a time of consolida Read more…

By John Russell

Nvidia-Arm Deal a Boon for RISC-V?

October 26, 2020

The $40 billion blockbuster acquisition deal that will bring chip maker Arm into the Nvidia corporate family could provide a boost for the competing RISC-V architecture. As regulators in the U.S., China and the Europe Read more…

By George Leopold

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a reference collection of open-source HPC software components and bes Read more…

By John Russell

AWS Solution Channel

Rapid Chip Design in the Cloud

Time-to-market and engineering efficiency are the most critical and expensive metrics for a chip design company. With this in mind, the team at Annapurna Labs selected Altair AcceleratorRead more…

Intel® HPC + AI Pavilion

Berlin Institute of Health: Putting HPC to Work for the World

Researchers from the Center for Digital Health at the Berlin Institute of Health (BIH) are using science to understand the pathophysiology of COVID-19, which can help to inform the development of targeted treatments. Read more…

NASA Uses Supercomputing to Measure Carbon in the World’s Trees

October 22, 2020

Trees constitute one of the world’s most important carbon sinks, pulling enormous amounts of carbon dioxide from the atmosphere and storing the carbon in their trunks and the surrounding soil. Measuring this carbon sto Read more…

By Oliver Peckham

AMD Reports Record Revenue and $35B Deal to Buy Xilinx

October 27, 2020

AMD this morning reported record quarterly revenue of $2.8 billion and a finalized deal to buy FPGA-maker Xilinx for $35 billion in an all-stock transaction. Th Read more…

By John Russell

OpenHPC Progress Report – v2.0, More Recipes, Cloud and Arm Support, Says Schulz

October 26, 2020

Launched in late 2015 and transitioned to a Linux Foundation Project in 2016, OpenHPC has marched quietly but steadily forward. Its goal “to provide a referen Read more…

By John Russell

Nvidia Dominates (Again) Latest MLPerf Inference Results

October 22, 2020

The two-year-old AI benchmarking group MLPerf.org released its second set of inferencing results yesterday and again, as in the most recent MLPerf training resu Read more…

By John Russell

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

HPE to Build Australia’s Most Powerful Supercomputer for Pawsey

October 20, 2020

The Pawsey Supercomputing Centre in Perth, Western Australia, has had a busy year. Pawsey typically spends much of its time looking to the stars, working with a Read more…

By Oliver Peckham

DDN-Tintri Showcases Technology Integration with Two New Products

October 20, 2020

DDN, a long-time leader in HPC storage, announced two new products today and provided more detail around its strategy for integrating DDN HPC technologies with Read more…

By John Russell

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I 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

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

Google Hires Longtime Intel Exec Bill Magro to Lead HPC Strategy

September 18, 2020

In a sign of the times, another prominent HPCer has made a move to a hyperscaler. Longtime Intel executive Bill Magro joined Google as chief technologist for hi Read more…

By Tiffany Trader

HPE Keeps Cray Brand Promise, Reveals HPE Cray Supercomputing Line

August 4, 2020

The HPC community, ever-affectionate toward Cray and its eponymous founder, can breathe a (virtual) sigh of relief. The Cray brand will live on, encompassing th 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

Aurora’s Troubles Move Frontier into Pole Exascale Position

October 1, 2020

Intel’s 7nm node delay has raised questions about the status of the Aurora supercomputer that was scheduled to be stood up at Argonne National Laboratory next year. Aurora was in the running to be the United States’ first exascale supercomputer although it was on a contemporaneous timeline with... Read more…

By Tiffany Trader

Is the Nvidia A100 GPU Performance Worth a Hardware Upgrade?

October 16, 2020

Over the last decade, accelerators have seen an increasing rate of adoption in high-performance computing (HPC) platforms, and in the June 2020 Top500 list, eig Read more…

By Hartwig Anzt, Ahmad Abdelfattah and Jack Dongarra

Leading Solution Providers

Contributors

European Commission Declares €8 Billion Investment in Supercomputing

September 18, 2020

Just under two years ago, the European Commission formalized the EuroHPC Joint Undertaking (JU): a concerted HPC effort (comprising 32 participating states at c Read more…

By Oliver Peckham

Nvidia and EuroHPC Team for Four Supercomputers, Including Massive ‘Leonardo’ System

October 15, 2020

The EuroHPC Joint Undertaking (JU) serves as Europe’s concerted supercomputing play, currently comprising 32 member states and billions of euros in funding. I Read more…

By Oliver Peckham

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

Microsoft Azure Adds A100 GPU Instances for ‘Supercomputer-Class AI’ in the Cloud

August 19, 2020

Microsoft Azure continues to infuse its cloud platform with HPC- and AI-directed technologies. Today the cloud services purveyor announced a new virtual machine Read more…

By Tiffany Trader

Oracle Cloud Infrastructure Powers Fugaku’s Storage, Scores IO500 Win

August 28, 2020

In June, RIKEN shook the supercomputing world with its Arm-based, Fujitsu-built juggernaut: Fugaku. The system, which weighs in at 415.5 Linpack petaflops, topp Read more…

By Oliver Peckham

HPE, AMD and EuroHPC Partner for Pre-Exascale LUMI Supercomputer

October 21, 2020

Not even a week after Nvidia announced that it would be providing hardware for the first four of the eight planned EuroHPC systems, HPE and AMD are announcing a Read more…

By Oliver Peckham

DOD Orders Two AI-Focused Supercomputers from Liqid

August 24, 2020

The U.S. Department of Defense is making a big investment in data analytics and AI computing with the procurement of two HPC systems that will provide the High Read more…

By Tiffany Trader

Oracle Cloud Deepens HPC Embrace with Launch of A100 Instances, Plans for Arm, More 

September 22, 2020

Oracle Cloud Infrastructure (OCI) continued its steady ramp-up of HPC capabilities today with a flurry of announcements. Topping the list is general availabilit 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