Kubernetes, Containers and HPC

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

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.

Recently, high performance computing (HPC) is moving closer to the enterprise and can therefore benefit from an HPC container and Kubernetes ecosystem, with new requirements to quickly allocate and deallocate computational resources to HPC workloads. Compute capacity, be it for enterprise or HPC workloads, can no longer be planned years in advance.

Getting on-demand resources from a shared compute resource pool has never been easier as cloud service providers and software vendors are continuously investing and improving their services. In enterprise computing, packaging software in container images and running containers is meanwhile standard. Kubernetes has become the most widely used container and resource orchestrator in the Fortune 500 companies. The HPC community, led by efforts in the AI community, is picking up the concept and applying it to batch jobs and interactive applications.

Containers and HPC: Why Should We Care?

HPC leaders have a hard time. There are lots of changes and new ways of thinking in software technology and IT operations. Containerization have become ubiquitous; container orchestration with Kubernetes is the new standard. Deep learning workloads are continuously increasing their footprint, and Site Reliability Engineering (SRE) has been adopted on many sites. It is very hard for each of the new technologies to judge their usefulness for HPC type of workloads.

Introduction to Kubernetes

If your engineers or operators are running a single container on their laptop, they probably use Docker for doing that. But when having multiples of containers potentially on dozens or hundreds of machines, it becomes difficult to get them maintained. Kubernetes simplifies container orchestration by providing scheduling, container life-cycle management, networking functionalities and more in a scalable and extensible platform.

Major components of Kubernetes are the Kubernetes master which contains an API server, scheduler, and a controller manager. Controllers are a main concept: they watch out for the current state of resources and compare them with the expected state. If they differ, they take actions to move to an expected state. On the execution side we have the kubelet which is in contact with the master as well as a network proxy. The kubelet manages containers by using the container runtime interface (CRI) for interacting with runtimes like Docker, containerd, or CRI-O.

Running Kubernetes or HPC Schedulers?

Kubernetes is doing workload and resource management. Sounds familiar? Yes, in many ways it shares lots of functionalities with traditional HPC workload managers. The main differences are the workload types they focus on. While HPC workload managers are focused on running distributed memory jobs and support high-throughput scenarios, Kubernetes is primarily built for orchestrating containerized microservice applications.

HPC workload managers like Univa Grid Engine added a huge number of features in the last decades. Some notable functionalities are:

–  Support for shared and distributed memory (like MPI based) jobs

–  Advance reservations for allocating and blocking resources in advance

–  Fair-share to customize resource usage patterns across users, projects, and departments

–  Resource reservation for collecting resources for large jobs

–  Preemption for stopping low prior jobs in favor for running high prior jobs

–  NUMA aware scheduling for automatically allocating cores and sockets

–  Adhere to standards for job submission and management (like DRMAA and DRMAAv2)

HPC workload managers are tuned for speed, throughput, and scalability, being capable of running millions of batch jobs a day and supporting the infrastructure of the largest supercomputers in the world. What traditional HPC workload managers lack are means for supporting microservice architectures, deeply integrated container management capabilities, network management, and application life-cycle management. They are primarily built for running batch jobs in different scenarios like high-throughput, MPI jobs spanning across potentially hundreds or thousands of nodes, jobs running weeks, or jobs using special resource types (GPUs, FPGAs, licenses, etc.).

Kubernetes on the other hand is built for containerized microservice applications from the bottom- up. Some notable features are:

–  Management of sets of pods. Pods consist of one or more co-located containers.

–  Networking functionalities through a pluggable overlay network

–  Self-healing through controller concept comparing expected with current state

–  Declarative style configuration

–  Load balancing functionalities

–  Rolling updates of different versions of workloads

–  Integrations in many monitoring and logging solutions

–  Hooks to integrate external persistent storage in pods

–  Service discovery and routing

What Kubernetes lacks at this time is a proper high-throughput batch job queueing system with a sophisticated rule system for managing resource allocations. But one of the main drawbacks we see is that traditional HPC engineering applications are not yet built to interact with Kubernetes. But this will change in the future. New kinds of AI workloads on the other hand are supporting Kubernetes already very well – in fact many of these packages are targeted to Kubernetes.

Can HPC Workload Be Managed by Kubernetes?

We should combine both Kubernetes and HPC workload-management systems to fully meet the HPC requirements. Kubernetes will be used for managing HPC containers along with all the required services. Inside the containers, not just the engineering application can be run, but also the capability to either plug into an existing HPC cluster or run an entire HPC resource manager installation (like SLURM or Univa Grid Engine) needs to be provided. In that way, we can provide compatibility to the engineering applications and can exploit the extended batch scheduling capabilities. At the same time our whole deployment can be operated in all Kubernetes enabled environments with the advantages of standardized container orchestration.

Ease of Administration

HPC environments consist of a potentially large set of containers. The higher abstraction of container orchestration compared to self-managing container single runtime engines provides the necessary flexibility we need to fulfill different customer requirements. Management operations like scaling the deployment are much simpler to implement and execute.

The Run-Time for Hybrid and Multi-Cloud Offers True Portability

Portability is a key value of containers. Kubernetes provides us this portability for fleets of containers. We can have the same experience on-premises as well as on different cloud infrastructures. Engineers can seamlessly switch the infrastructure without any changes for the engineers. In that way we can choose the infrastructure by criteria like price, performance, and capabilities. When running on premises we can start offering true hybrid-cloud experience by providing a consistent infrastructure with the same operational and HPC application experience and seamlessly use on-demand cloud resources when required.

What’s Next?

Embracing Kubernetes for the specific requirements of HPC and engineering workload is not straight forward. But due to the success of Kubernetes and its open and extensible architecture the ecosystem is opening up for HPC applications primarily driven by the demand of new AI workloads and HPC containers.

About the Authors

Daniel Gruber, Burak Yenier, and Wolfgang Gentzsch are with UberCloud, a company that started in 2013 with developing HPC container technology and containerized engineering applications, to facilitate access and use of engineering HPC workload in a shared on-premise or on-demand cloud environment. This article is based on a white paper they wrote detailing their experience using UberCloud HPC containers and Kubernetes.

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!

On the Spack Track @SC19

December 5, 2019

At the annual supercomputing conference, SC19 in Denver, Colorado, there were Spack events each day of the conference. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three U.S. national Department of Energy (DOE) laboratories and Sylabs... Read more…

By Elizabeth Leake

Intel’s New Hyderabad Design Center Targets Exascale Era Technologies

December 3, 2019

Intel's Raja Koduri was in India this week to help launch a new 300,000 square foot design and engineering center in Hyderabad, which will focus on advanced computing technologies for the AI and exascale era. "Over th Read more…

By Tiffany Trader

AWS Debuts 7nm 2nd-Gen Graviton Arm Processor

December 3, 2019

The “x86 Big Bang,” in which market dominance of the venerable Intel CPU has exploded into fragments of processor options suited to varying workloads, has now encompassed CPUs offered by the leading public cloud serv Read more…

By Doug Black

Medical Imaging Gets an AI Boost

December 3, 2019

AI technologies incorporated into diagnostic imaging tools have proven useful in eliminating confirmation bias, often outperforming human clinicians who may bring their own prejudices. Another issue slowing progress is t Read more…

By George Leopold

Ride on the Wild Side – Squyres SC19 Mars Rovers Keynote

December 2, 2019

Reminding us of the deep and enabling connection between HPC and modern science is an important part of the SC Conference mission. And yes, HPC is a science itself. At SC19, Steve Squyres’ opening keynote recounting th 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…

IBM Accelerated Insights

AI Needs Intelligent HPC infrastructure

Artificial Intelligence (AI) has revolutionized entire industries and enables humanity to solve some of the most daunting challenges. To accomplish this, it requires massive amounts of data from heterogeneous sources that is processed it new ways that differs significantly from HPC applications. Read more…

NSCI Update – Adapting to a Changing Landscape

December 2, 2019

It was November of 2017 when we last visited the topic of the National Strategic Computing Initiative (NSCI). As you will recall, the NSCI was started with an Executive Order (E.O. No. 13702), that was issued by President Obama in July of 2015 and was followed by a Strategic Plan that was released in July of 2016. The question for November of 2017... Read more…

By Alex R. Larzelere

On the Spack Track @SC19

December 5, 2019

At the annual supercomputing conference, SC19 in Denver, Colorado, there were Spack events each day of the conference. As a reflection of its grassroots heritage, nine sessions were planned by more than a dozen thought leaders from seven organizations, including three U.S. national Department of Energy (DOE) laboratories and Sylabs... Read more…

By Elizabeth Leake

Intel’s New Hyderabad Design Center Targets Exascale Era Technologies

December 3, 2019

Intel's Raja Koduri was in India this week to help launch a new 300,000 square foot design and engineering center in Hyderabad, which will focus on advanced com Read more…

By Tiffany Trader

AWS Debuts 7nm 2nd-Gen Graviton Arm Processor

December 3, 2019

The “x86 Big Bang,” in which market dominance of the venerable Intel CPU has exploded into fragments of processor options suited to varying workloads, has n Read more…

By Doug Black

Ride on the Wild Side – Squyres SC19 Mars Rovers Keynote

December 2, 2019

Reminding us of the deep and enabling connection between HPC and modern science is an important part of the SC Conference mission. And yes, HPC is a science its Read more…

By John Russell

NSCI Update – Adapting to a Changing Landscape

December 2, 2019

It was November of 2017 when we last visited the topic of the National Strategic Computing Initiative (NSCI). As you will recall, the NSCI was started with an Executive Order (E.O. No. 13702), that was issued by President Obama in July of 2015 and was followed by a Strategic Plan that was released in July of 2016. The question for November of 2017... Read more…

By Alex R. Larzelere

Tsinghua University Racks Up Its Ninth Student Cluster Championship Win at SC19

November 27, 2019

Tsinghua University has done it again. At SC19 last week, the eight-time gold medal-winner team took home the top prize in the 2019 Student Cluster Competition Read more…

By Oliver Peckham

SC19: IBM Changes Its HPC-AI Game Plan

November 25, 2019

It’s probably fair to say IBM is known for big bets. Summit supercomputer – a big win. Red Hat acquisition – looking like a big win. OpenPOWER and Power processors – jury’s out? At SC19, long-time IBMer Dave Turek sketched out a different kind of bet for Big Blue – a small ball strategy, if you’ll forgive the baseball analogy... Read more…

By John Russell

How the Gordon Bell Prize Winners Used Summit to Illuminate Transistors

November 22, 2019

At SC19, the Association for Computing Machinery (ACM) awarded the prestigious Gordon Bell Prize to the Swiss Federal Institute of Technology (ETH) Zurich. The Read more…

By Oliver Peckham

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

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

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

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

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

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

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

SC19: IBM Changes Its HPC-AI Game Plan

November 25, 2019

It’s probably fair to say IBM is known for big bets. Summit supercomputer – a big win. Red Hat acquisition – looking like a big win. OpenPOWER and Power processors – jury’s out? At SC19, long-time IBMer Dave Turek sketched out a different kind of bet for Big Blue – a small ball strategy, if you’ll forgive the baseball analogy... Read more…

By John Russell

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

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

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

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann 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

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

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