Super-Connecting the Supercomputers

By Gilad Shainer, Mellanox Technologies

June 10, 2019

Supercomputers are the essential tools we need to conduct research, enable scientific discoveries, design new products, and develop self-learning software algorithms. Supercomputing leadership means scientific leadership, which explains the investments made by many governments and research institutes to build faster and more powerful supercomputing platforms.

The heart of a supercomputer is the network that connects the compute elements together, enabling parallel and synchronized computing cycles. Over the past decades, multiple network technologies were created and multiple have disappeared. InfiniBand, an industry standard developed in 1999, continues to show a strong presence in the high-performance computing market. It connected one of the top three supercomputers in 2013 and maintains a strong roadmap into the future.

Many proprietary networks that existed 10 and 15 years ago are no longer in use today; QsNet, Myrinet, Seastar are but a few examples. QSNet technology was later used by Gnodal, which added Ethernet gateways to form an Ethernet switch network, but its development was halted several years ago. Part of that technology and concept is being used in the first generation of Slingshot. Slingshot is planned to replace a former proprietary Aries technology, which replaced Gemini proprietary technology, which replaced Seastar. One of the main disadvantages of a proprietary network is that it requires recreating old concepts again and again—concepts such as congestion control, routing schemes and more.

Being a standard-based interconnect, InfiniBand enjoys the continuous development of new capabilities, better performance, and scalability. It is used in many of the leading supercomputers around the world, demonstrating 96% network utilization with probably the most advanced adaptive routing capabilities (“The Design, Deployment, and Evaluation of the CORAL Pre-Exascale Systems”), and delivering leading performance for the most demanding high compute intensive applications.

InfiniBand technology can be separated into three main pillars: connectivity, network, and communication. The connectivity pillar refers to the elements around the interconnect infrastructure such as topologies. The network pillar refers to the network transport and routing for example. And the communication pillar refers to co-design elements related to communication frameworks such as MPI, SHMEM/PGAS and more.

The Connectivity Pillar

InfiniBand was specified and designed as the ultimate software-defined network. One can define and manage complete routing schemes of the network from a centralized place, and everything is programmable. This advantage enables support for any interconnect topology and optimizes topologies to best fit the applications and workloads needs. Many of today’s supercomputers use the Fat Tree topology as it provides low latency and effectively supports a variety of applications. There are some Torus topologies in use, which best serve stencil applications. Other topologies including Hypercube, Enhanced Hypercube, Dragonfly+ and more are coming in the future.

Dragonfly+ is hybrid topology based on the conventional Dragonfly and extended using the properties of Fat Tree providing the benefit of both. It includes a Fully Progressive Adapting Routing technique, is more scalable than Dragonfly at the same cost, and able to provide the same or better throughput for equivalent Dragonfly and Fat Tree topologies under various traffic patterns (“Dragonfly+: Low Cost Topology for Scaling Datacenters,” Alexander Shpiner, Zachy Haramaty, Saar Eliad, Vladimir Zdornov, Barak Gafni and Eitan Zahavi).

Furthermore, the traditional Dragonfly presents performance limitations for adversarial traffic, as within a group, there is only one route from ingress switch to egress switch. Therefore, network bandwidth decreases with higher switch radix. The more ports on the switch, the lower the data throughput. InfiniBand Dragonfly+ includes multiple routes from ingress switch to egress switch, thereby delivering the highest data throughput. Moreover, due to its hybrid design, Dragonfly+ can simply be extended over time with no need to reroute any of the long cables—an advantage over Fat Trees and traditional Dragonfly networks.

Multi-Host technology enables multiple hosts to connect to a single interconnect adapter by separating the PCIe interface into multiple and independent interfaces, with no performance degradation. This results in lower total cost of ownership (TCO) in the data center by reducing CAPEX requirements from multiple cables, network adapters, and switch ports to only one of each, and by reducing OPEX by cutting down on switch port management and overall power usage.

The Network Pillar

InfiniBand is a pure offload interconnect, managing all network function and transport at the network level, and not imposing overheads on the CPU as other networks such as Ethernet or OmniPath. This results in more CPU cycles being dedicated to the applications and higher overall performance and scalability.

In many networks, a management software utility is responsible for receiving notifications of network errors and in order to modify network routes or change job scheduling to avoid the errors. But this can be time consuming—around 5 seconds for 1000 nodes and 30 seconds for clusters with 10000 or more endpoints—certainly not fast enough to ensure the seamless integrity of a running computation. In fact, no software mechanism can be responsive enough at very large scales to detect and fix fabrics that suffer from a link failure. To address this problem, InfiniBand includes a new and innovative solution called SHIELD (Self-Healing Interconnect Enhancement for Intelligent Datacenters), which takes advantage of the intelligence already built into InfiniBand switches. By providing the fabric with self-healing autonomy, the speed with which communications can be corrected in the face of a link failure can be sped up by 5000x. This is fast enough to save communications from expensive retransmissions or absolute failure.

The Communication Pillar

Mellanox Scalable Hierarchical Aggregation and Reduction Protocol (SHARP)™ technology is included in the EDR and HDR InfiniBand switches. SHARP improves upon the performance of MPI operation by offloading collective operations from the CPU to the switch network, and eliminating the need to send data multiple times between endpoints. This innovative approach decreases the amount of data traversing the network as aggregation nodes are reached, and dramatically reduces the MPI operations time. Implementing collective communication algorithms in the network also has additional benefits, such as freeing up valuable CPU resources for computation rather than using them to process communication.

SHARP provides lower and flat latencies for data aggregation and reduction operations (e.g., MPI Reduce, All-Reduce, Barrier, Broadcast, etc.) compared to other options, so adding more nodes to compute clusters does not adversely affect. SHARP is also the best technology to enable the Exascale supercomputing generation.

Furthermore, SHARP provides key performance enhancement for deep learning and artificial intelligence applications. The combination of SHARP with leading GPUs and the NVIDIA Collective Communications Library (NCCL) deliver leading efficiency and scalability for example.

Another new technology is SNAP (Software-defined Network Accelerated Processing) which enables hardware virtualization of PCIe devices, such as NVMe storage. The NVMe SNAP framework allows users to easily integrate networked storage solutions into their high-performance compute and storage infrastructures. It enables the efficient disaggregation of compute and storage to facilitate fully-optimized resource utilization.

NVMe SNAP logically presents networked storage, such as NVMe over Fabrics (NVMe-oF), as a local NVMe drive. This allows the host operating system to use a standard NVMe-driver instead of a remote networking storage protocol. The host benefits from the performance and simplicity of local NVMe storage, unaware that remote InfiniBand connected storage is being utilized and virtualized by NVMe SNAP.

Furthermore SNAP may apply sophisticated logic and data protection mechanisms (mirroring, compression, data-deduplication, thin-provisioning, encryption, etc.) to the network storage that it virtualizes as local NVMe.

Super-Connecting the #1 Supercomputers

By providing leading data throughput, extremely low latency, and, most importantly, In-Network Computing engines and full programmability, InfiniBand is the leading interconnect technology for compute intensive applications, high performance computing, deep learning and other applications. InfiniBand overtakes proprietary networks and accelerates many of the top supercomputers around the world.

 

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!

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-512 optimizations for the NAMD scalable molecular dynamics cod Read more…

By Rob Farber

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yesterday, Intel reported an Optane and DAOS-based system finishe Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows users to virtually “walk” around the massive supercomputer Read more…

By Oliver Peckham

Supercomputer Simulations Examine Changes in Chesapeake Bay

August 8, 2020

The Chesapeake Bay, the largest estuary in the continental United States, weaves its way south from Maryland, collecting waters from West Virginia, Delaware, DC, Pennsylvania and New York along the way. Like many major e Read more…

By Oliver Peckham

Student Success from ‘Scratch’: CHPC’s Proof is in the Pudding

August 7, 2020

Happy Sithole, who directs the South African Centre for High Performance Computing (SA-CHPC), called the 13th annual CHPC National conference to order on December 1, 2019, at the Birchwood Conference Centre in Kempton Pa Read more…

By Elizabeth Leake

AWS Solution Channel

University of Adelaide Provides Seamless Bioinformatics Training Using AWS

The University of Adelaide, established in South Australia in 1874, maintains a rich history of scientific innovation. For more than 140 years, the institution and its researchers have had an impact all over the world—making vital contributions to the invention of X-ray crystallography, insulin, penicillin, and the Olympic torch. 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…

New GE Simulations on Summit to Advance Offshore Wind Power

August 6, 2020

The wind energy sector is a frequent user of high-power simulations, with researchers aiming to optimize wind flows and energy production from the massive turbines. Now, researchers at GE are preparing to undertake a lar Read more…

By Oliver Peckham

Intel Speeds NAMD by 1.8x: Saves Xeon Processor Users Millions of Compute Hours

August 12, 2020

Potentially saving datacenters millions of CPU node hours, Intel and the University of Illinois at Urbana–Champaign (UIUC) have collaborated to develop AVX-51 Read more…

By Rob Farber

Intel’s Optane/DAOS Solution Tops Latest IO500

August 11, 2020

Intel’s persistent memory technology, Optane, and its DAOS (Distributed Asynchronous Object Storage) stack continue to impress and gain market traction. Yeste Read more…

By John Russell

Summit Now Offers Virtual Tours

August 10, 2020

Summit, the second most powerful publicly ranked supercomputer in the world, now has a virtual tour. The tour, implemented by 3D platform Matterport, allows use Read more…

By Oliver Peckham

Research: A Survey of Numerical Methods Utilizing Mixed Precision Arithmetic

August 5, 2020

Within the past years, hardware vendors have started designing low precision special function units in response to the demand of the machine learning community Read more…

By Hartwig Anzt and Jack Dongarra

Implement Photonic Tensor Cores for Machine Learning?

August 5, 2020

Researchers from George Washington University have reported an approach for building photonic tensor cores that leverages phase change photonic memory to implem Read more…

By John Russell

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

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

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

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

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

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

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

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

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

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

$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

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

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