Dragonfly+ Delivers Performance for Canada’s Fastest Supercomputer

July 9, 2018

Introducing the Niagara supercomputer

The need to analyze massive amount of data and solve complex computational problems drives the increasing use of high performance computing (HPC) systems and is leading to innovation in networking technology. Canadian academics and scientists across Canada use supercomputers at SciNet, Canada’s largest supercomputer center located at the University of Toronto to process their data. Researchers run big data workloads in areas such as artificial intelligence, biomedical sciences, aerospace engineering, astrophysics and climate science that requires major data processing time—up to thousands of hours.

SciNet recently installed a new high-performance computing system named Niagara that is now Canada’s fastest supercomputer as shown in Figure 1. Niagara uses the latest cutting-edge innovations developed by an ecosystem of partners to deliver performance at a cost performance price. The Niagara system is a partnership between Lenovo, Mellanox and Excelero to deliver Canada’s fastest supercomputer based on world’s first implementation of DragonFly+ architecture.

Figure 1. Lenovo Niagara supercomputer housed at Canada’s University of Toronto.
Figure 1. Lenovo Niagara supercomputer housed at Canada’s University of Toronto.

According to Scot Schultz, Sr. Director, HPC / Artificial Intelligence and Technical Computing – Mellanox Technologies, “Niagara runs on a Lenovo designed supercomputer using the latest Mellanox EDR InfiniBand technology, DragonFly+ network topology and InfiniBand-based burst buffer leveraging Mellanox interconnect accelerations and Excelero’s NVMesh solution. Niagara was designed using multiple technology innovations and networking accelerations to deliver state-of-the-art performance to tackle the most compute intense processing tasks.”

Lenovo—powering many of the world’s fastest supercomputers

Lenovo is now the global leader in powering leading HPC systems with the most supercomputers on the Top500 list. The Niagara supercomputer is a Lenovo ThinkSystem SD530 system built with input from SciNet, the University of Toronto, Compute Ontario and Compute Canada. The SciNet Lenovo Niagara HPC system contains 1,500 dense Lenovo ThinkSystem SD530 high-performance compute nodes and uses Lenovo Scalable Infrastructure (LeSI). It also contains two Intel® Xeon® 20-core Gold 6148 (2.4Ghz) CPUs fitting into 21 racks along with Lenovo DSS-G high performance storage. Currently, Niagara ranks among the top 10 percent of fastest publicly benchmarked computers in the world with a peak theoretical speed of 4.61 petaflops and a Linpack Rmax of 3 petaflops.

DragonFly+ networking topology enables high levels of compute performance

Current research and big data processing drives the need for higher data throughput to enable detailed analysis and network topology has a significant impact on distributed application performance. In typical, and probably the most popular networking scenarios, servers are connected and based on fat-tree network topology. While this topology maximizes throughput for a variety of communication patterns, it is relatively costly due to the large number of routers and links.

The Dragonfly topology was originally introduced as an alternative to show good performance of various traffic patterns while reducing the cost, compared to other topologies as well as reducing the number of long links. Mellanox introduced DragonFly+, which is a very cost-effective performance-based topology and allows connecting a larger number of hosts to the network. DragonFly+ is a concept of connecting groups of compute nodes in an all-to-all way where each group has at least one direct link to another group as shown in Figure 2.

Figure 2. Example of DragonFly and DragonFly+ topology
Figure 2. Example of DragonFly and DragonFly+ topology

Dragonfly+ also implements Fully Progressive Adaptive Routing (FPAR) with the advantage that routing decisions are evaluated in every switch in the network packets path. In addition, Adaptive Routing Notification (ARN) is implemented where messages are sent between routers to notify of distant congestion that can be resolved before it becomes an issue.

DragonFly+ uses open standard interconnect to provide low latency communication and high bandwidth resulting in expandability and cost reduction. DragonFly+ also allows extending the cluster without the need to reserve ports (which on standard DragonFly provides less bandwidth).  In a more traditional FAT Tree network topology, expanding the network cluster almost always requires a significant amount of re-cabling, and often the cables are often cut and wasted and new cables are installed. According to Schultz, “The DragonFly+ system installed in the Niagara system has a reduced number of switches and provides a better value between performance and cost, and allows for flexible growth of the system.”

Excelero NVMesh burst buffers achieve unprecedented bandwidth

HPC systems use checkpointing and checkpoint restart during processing to make sure compute jobs are not interrupted. When a computer system is tracking checkpointing, it is not computing which leads to a performance slow down. Niagara combines Excelero’s NVMesh burst buffer with Mellanox’s world-leading, end-to-end InfiniBand networking solution to resolve the performance issue.

A burst buffer is a fast and intermediate storage layer between the nonpersistent memory of the compute nodes and persistent storage (parallel file system). Niagara uses a built-in low-latency network fabric and the solution adds commodity flash drives and NVMesh software to compute nodes. NVMesh provides redundancy without impacting target central processing units which enables standard servers to also act as file servers. This enables Niagara to use the full performance capacity and processing power of underlying servers and storage.

“In supercomputing any unavailability wastes time, reduces the availability score of the system and impedes the progress of scientific exploration. In working with partners at Lenovo and Mellanox, we were able to provide SciNet and its researchers with important storage functionality that achieves the highest performance available in the industry at a significantly reduced price – while assuring vital scientific research can progress swiftly,” said Lior Gal, CEO and co-founder at Excelero.

Summary

Canada’s fastest supercomputer named Niagara, located at the SciNet computing center, uses innovative networking technology based on a partnership of Lenovo, Mellanox and Excelero. Niagara is a Lenovo ThinkSystem SD530 system designed with world-class architecture and is currently ranked one of the fastest supercomputers in the world. The Niagara system uses the world’s first implementation of Mellanox DragonFly+ networking architecture which provides hyperscale processing capabilities while reducing the need to buy additional hardware—the solution uses industry standard hardware, commercial and open source software. Excelero’s NVMesh burst buffers allow Niagara to use the full performance capacity and processing power of underlying servers and storage. The partnership resulted in unprecedented bandwidth processing on Niagara which results in fast performance at a low-cost point.

Resources

The SciNet Niagara system is already being used in research as described in: “SciNet Launches Niagara, Canada’s Fastest Supercomputer, Tabor Communications, March 5, 2018.
https://www.hpcwire.com/2018/03/05/scinet-launches-niagara-canadas-fastest-supercomputer/

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!

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has been unveiled in upstate New York that will be used by IBM Read more…

By Doug Black

At SC19: Developing a Digital Twin

December 11, 2019

In the not too distant future, we can expect to see our skies filled with unmanned aerial vehicles (UAVs) delivering packages, maybe even people, from location to location. In such a world, there will also be a digita Read more…

By Aaron Dubrow

Supercomputers Help Predict Carbon Dioxide Levels

December 10, 2019

The Earth’s terrestrial ecosystems – its lands, forests, jungles and so on – are crucial “sinks” for atmospheric carbon, holding nearly 30 percent of our annual CO2 emissions as they breathe in the carbon-rich Read more…

By Oliver Peckham

Finally! SC19 Competitors Live and in Color!

December 10, 2019

You know the saying “better late than never”? That’s how my cluster competition coverage is faring this year. With SC19 coming late in November, quickly followed by my annual trip to South Africa to cover their clu Read more…

By Dan Olds

Intel’s Jim Clarke on its New Cryo-controller and why Intel isn’t Late to the Quantum Party

December 9, 2019

Intel today introduced the ‘first-of-its-kind’ cryo-controller chip for quantum computing and previewed a cryo-prober tool for characterizing quantum processor chips. The new controller is a mixed-signal SoC named Ho 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

GPU Scheduling and Resource Accounting: The Key to an Efficient AI Data Center

[Connect with LSF users and learn new skills in the IBM Spectrum LSF User Community!]

GPUs are the new CPUs

GPUs have become a staple technology in modern HPC and AI data centers. Read more…

What’s New in HPC Research: Natural Gas, Precision Agriculture, Neural Networks and More

December 6, 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

RPI Powers Up ‘AiMOS’ AI Supercomputer

December 11, 2019

Designed to push the frontiers of computing chip and systems performance optimized for AI workloads, an 8 petaflops (Linpack) IBM Power9-based supercomputer has Read more…

By Doug Black

Intel’s Jim Clarke on its New Cryo-controller and why Intel isn’t Late to the Quantum Party

December 9, 2019

Intel today introduced the ‘first-of-its-kind’ cryo-controller chip for quantum computing and previewed a cryo-prober tool for characterizing quantum proces Read more…

By John Russell

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

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

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

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

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

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

Leading Solution Providers

SC 2019 Virtual Booth Video Tour

AMD
AMD
CEJN
CJEN
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
SIX NINES IT
SIX NINES IT
VERNE GLOBAL
VERNE GLOBAL
WEKAIO
WEKAIO

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

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

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

Cerebras to Supply DOE with Wafer-Scale AI Supercomputing Technology

September 17, 2019

Cerebras Systems, which debuted its wafer-scale AI silicon at Hot Chips last month, has entered into a multi-year partnership with Argonne National Laboratory and Lawrence Livermore National Laboratory as part of a larger collaboration with the U.S. Department of Energy... Read more…

By Tiffany Trader

Jensen Huang’s SC19 – Fast Cars, a Strong Arm, and Aiming for the Cloud(s)

November 20, 2019

We’ve come to expect Nvidia CEO Jensen Huang’s annual SC keynote to contain stunning graphics and lively bravado (with plenty of examples) in support of GPU 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