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!

Talk to Me: Nvidia Claims NLP Inference, Training Records

August 15, 2019

Nvidia says it’s achieved significant advances in conversation natural language processing (NLP) training and inference, enabling more complex, immediate-response interchanges between customers and chatbots. And the co Read more…

By Doug Black

Trump Administration and NIST Issue AI Standards Development Plan

August 14, 2019

Efforts to develop AI are gathering steam fast. On Monday, the White House issued a federal plan to help develop technical standards for AI following up on a mandate contained in the Administration’s AI Executive Order Read more…

By John Russell

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a good understanding of the early universe, its fate billions Read more…

By Rob Johnson

AWS Solution Channel

Efficiency and Cost-Optimization for HPC Workloads – AWS Batch and Amazon EC2 Spot Instances

High Performance Computing on AWS leverages the power of cloud computing and the extreme scale it offers to achieve optimal HPC price/performance. With AWS you can right size your services to meet exactly the capacity requirements you need without having to overprovision or compromise capacity. Read more…

HPE Extreme Performance Solutions

Bring the combined power of HPC and AI to your business transformation

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

Cloudy with a Chance of Mainframes

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

Rapid rates of change sometimes result in unexpected bedfellows. Read more…

Argonne Supercomputer Accelerates Cancer Prediction Research

August 13, 2019

In the fight against cancer, early prediction, which drastically improves prognoses, is critical. Now, new research by a team from Northwestern University – and accelerated by supercomputing resources at Argonne Nation Read more…

By Oliver Peckham

Scientists to Tap Exascale Computing to Unlock the Mystery of our Accelerating Universe

August 14, 2019

The universe and everything in it roared to life with the Big Bang approximately 13.8 billion years ago. It has continued expanding ever since. While we have a Read more…

By Rob Johnson

AI is the Next Exascale – Rick Stevens on What that Means and Why It’s Important

August 13, 2019

Twelve years ago the Department of Energy (DOE) was just beginning to explore what an exascale computing program might look like and what it might accomplish. Today, DOE is repeating that process for AI, once again starting with science community town halls to gather input and stimulate conversation. The town hall program... Read more…

By Tiffany Trader and 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

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

Lenovo Drives Single-Socket Servers with AMD Epyc Rome CPUs

August 7, 2019

No summer doldrums here. As part of the AMD Epyc Rome launch event in San Francisco today, Lenovo announced two new single-socket servers, the ThinkSystem SR635 Read more…

By Doug Black

Building Diversity and Broader Engagement in the HPC Community

August 7, 2019

Increasing diversity and inclusion in HPC is a community-building effort. Representation of both issues and individuals matters - the more people see HPC in a w Read more…

By AJ Lauer

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

Upcoming NSF Cyberinfrastructure Projects to Support ‘Long-Tail’ Users, AI and Big Data

August 5, 2019

The National Science Foundation is well positioned to support national priorities, as new NSF-funded HPC systems to come online in the upcoming year promise to Read more…

By Ken Chiacchia, Pittsburgh Supercomputing Center/XSEDE

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

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

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... 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

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

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl 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

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

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

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

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

Qualcomm Invests in RISC-V Startup SiFive

June 7, 2019

Investors are zeroing in on the open standard RISC-V instruction set architecture and the processor intellectual property being developed by a batch of high-flying chip startups. Last fall, Esperanto Technologies announced a $58 million funding round. Read more…

By George Leopold

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