Advancing Modular Supercomputing with DEEP and DEEP-ER Architectures

By Sean Thielen

February 24, 2017

Editor’s note: In this contributed feature, Sean Thielen details the innovative architectural concepts coming out of the DEEP and DEEP-ER projects, and follows the evolution of the Cluster-Booster architecture, a heterogeneous hardware design developed at the Jülich Supercomputing Centre.

Knowing that the jump to exascale will require novel architectural approaches capable of delivering dramatic efficiency and performance gains, researchers around the world are hard at work on next-generation HPC systems.

In Europe, the DEEP project has successfully built a next-generation heterogeneous architecture based on an innovative “cluster-booster” approach. The new architecture can dynamically assign individual code parts in a simulation to different hardware components based on which component can deliver the highest computational efficiency. It also provides a foundation for a modular type of supercomputing where a variety of top-level system components, such as a memory module or a data analytics module for example, could be swapped in and out based on workload characteristics. Recently, Norbert Eicker, head of the Cluster Computing research group at Jülich Supercomputing Centre (JSC), explained how the DEEP and DEEP-ER projects are advancing the idea of “modular supercomputing” in pursuit of exascale performance.

Why go DEEP?

Eicker says that the use of vectorization or multi-core processors have become the two main strategies for acceleration. He noted that the main advantages in general purpose multi-core processors include high single-thread performance due to relatively high frequency along with their ability to do out-of-order processing. Their downsides include limited energy efficiency and a higher cost per FLOP. Accelerators, such as the Intel Xeon Phi coprocessor or GPUs, on the other hand are more energy efficient but harder to program.

Given the different characteristics of general purpose processors and accelerators, it was only a matter for time before researchers began looking for ways to integrate different types of compute modules into an overall HPC system. Eicker said that most efforts have involved building heterogeneous clusters wherein standard cluster nodes are connected using a fabric and then accelerators are attached to each cluster node.

Figure 1: An example of a basic architecture for a heterogeneous cluster.

Per Eicker, this heterogeneous approach has drawbacks, including the need for static assignment of accelerators to CPUs. Since some applications benefit greatly from accelerators and others not at all, getting the ratio of CPUs to accelerators right is tricky and inevitably leads to inefficiencies. Eicker explained that the idea behind the DEEP project was to combine compute resources into a common fabric and make the accelerating resources more autonomous. The goal was to not only enable dynamic assignments between cluster nodes and the accelerator, but also to enable the accelerators to run a kind of MPI so the system could offload more complex kernels to the accelerators rather than needing to always rely on the CPU.

The building blocks of a successful prototype

Work on the prototype Dynamical Exascale Entry Platform (DEEP) system began in 2011, and was mostly finalized toward the end of 2015. It took the combined efforts of 20 partners to complete the European Commission funded project. The 500 TFLOP/s DEEP prototype system includes a “cluster” component with general-purpose Intel Xeon processors and a “booster” component with Intel Xeon Phi coprocessors along with a software stack capable of dynamically separating code parts in a simulation based on concurrency levels and sending them to the appropriate hardware component. The University of Heidelberg developed the fabric, which has been commercialized by EXTOLL and dubbed the EXTOLL 3D Torus Network.

Figure 2: The DEEP cluster-booster hardware architecture. The cluster is based on an Aurora HPC system from Eurotech. The booster includes 384 Intel Xeon Phi processors interconnected by Extoll fabric.

Given the unusual architecture, the project team knew it would need to modify and test applications from a variety of HPC fields on the DEEP system to prove its viability. The team analyzed each selected application to determine which parts would run better on the cluster and which would run better on the booster, and modified the applications accordingly. One example is a climate application from Cyprus Institute. The standard climate model part of the application runs on the cluster side while an atmospheric chemical simulation runs on the booster side, with both sides interacting with each other from time to time to exchange data.

The new software architecture

One of the most important developments of the DEEP project is a software architecture that includes new communication protocols for transferring data between network technologies, programming model extensions and other important advancements.

Figure 3: The DEEP software architecture includes standard software stack components along with some new components developed specifically for the project.

While left- and right-hand sides of the architecture in figure 3 are identical to the standard MPI-based software-stacks of most present day HPC architectures, the components in the middle add some important new capabilities. Eicker explained that in the DEEP software architecture, the main part of applications and less scalable code are only run on the cluster nodes and everything starts on the cluster side. What’s different is that the cluster part of the application can collectively start a crowd of MPI-processes on the right-hand side using a global MPI.

The spawn for the booster is a collective operation of cluster processes that creates an inter-communicator containing all parents on one side and all children on the other. For example, the MPI_COMM_WORLD or a subset of processes on the cluster side, collectively called the MPI_Comm_spawn function, can create a new MPI_COMM WORLD on the booster side that is capable of standard MPI communication. Once started, the processes on the booster side can communicate amongst each other and exchange messages, making it possible to offload complex kernels to the booster.

Using MPI to bridge between the different fabrics in the cluster and booster may seem like it would significantly complicate the lives of application developers. However, Barcelona Supercomputing Center invented what is basically a source-to-source compiler, called the OmpSs Offload Abstraction compiler that does much of the work. Developers see a familiar looking cluster side with an Infiniband-based MPI and a booster side with an EXTOLL-based MPI. Their job is to annotate the code to tell the compiler which parts should run on the cluster versus the booster. The OmpSs compiler introduces the MPI_Comm_spawn call and the other required communication calls for sharing data between the two code parts.

Eicker explained that the flexible DEEP approach has many advantages, including options for multiple operational modes that enable much more efficient use of system resources. Beyond the specialized symmetric mode described above, the booster can be used discretely, or as a pool of accelerators. He used applications that could scale on the Blue Gene system as an example, noting they be run entirely on the booster side with no cluster interaction.

From DEEP to DEEP-ER

Plans for the DEEP-ER (Dynamical Exascale Entry Platform – Extended Reach) phase include updating the booster to include the latest generation of Intel Xeon Phi processors. The team is also exploring how on-node Non-Volatile Memory (NVM), network attached memory and a simplified interface can improve the overall system capabilities.

Figure 4: The DEEP-ER cluster-booster hardware architecture.

Eicker said that since Xeon Phi processors are self-booting, the upgrade will make the hardware implementation easier. The team also significantly simplified the interface by using the EXTOLL fabric throughout the entire system. The global use of the EXTOLL fabric enabled the team to eliminate the booster interface nodes and the DEEP cluster-booster protocol. The DEEP-ER system will use a standard EXTOLL protocol running the two types of nodes. The EXTOLL interconnect also enables the system to take advantage of the network attached memory.

One of the main objectives of the DEEP-ER project is to explore scalable I/O. To that end, the project team is investigating the integration of different storage types, starting from the disks using NVM while also making use of the network attached memory. Eicker said the team is using the BeeGFS file system and extensions that enable smart caching to local NVMe devices in the common namespace of the file system to help improve performance as well as SIONlib, a scalable I/O library developed by JSC for parallel access to task-local files, to enable more efficient local tasking of I/O. Exascale10 I/O software from Seagate also sits on top of the BeeGFS file system, enabling the MPI I/O to make use of the file system cache extensions.

Beyond I/O, the DEEP-ER project is also exploring how to improve resiliency. Eicker noted that because the offloaded parts of programs are stateless in the DEEP approach, it’s possible to improve the overall resiliency of the software and make functions like checkpoint restart a lot more efficient than standard approaches.

Toward modular supercomputing

Each phase of the DEEP project is an important step forward toward modular supercomputing. Eicker said that the DEEP cluster-booster concept showed that it’s possible to integrate heterogeneous systems in new ways. With DEEP-ER, the combination of the NAM and network attached storage add what is essentially a memory booster module. Moving forward, there are all kinds of possibilities for new modules, according to Eicker. He mentioned an analytics module that might look like a cluster, but include more memory or different types of processors, or a module that acts as a graphics cluster for online visualization.

Figure 5: The end goal of the DEEP project is to create a truly modular supercomputer, which could pave the way for increasingly specialized modules for solving different types of supercomputing challenges.

The ultimate goal of the DEEP project is to build a flexible modular supercomputer that allows users to organize applications for efficient use of the various system modules. Eicker said that the DEEP-ER team hopes to extend its JURECA cluster with the next-generation Xeon Phi processor-based booster. Then the team will begin exploring new possibilities for the system, which could include adding new modules, such as a graphics, storage and data analytics modules. The next steps could even include a collaboration with the Human Brain Project on neuromorphic computing. And these ideas are only the beginning. The DEEP approach could enable scientists to dream up new modules for tackling their specific challenges. Eicker acknowledges that there is much work to be done, but he believes the co-design approach used by the DEEP team will continue to drive significant steps forward.

Watch a short video capturing highlights of Eicker’s presentation.

About the Author

Sean Thielen, the founder and owner of Sprocket Copy, is a freelance writer from Portland, Oregon who specializes in high-tech subject matter.

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