3D Torus Topology with InfiniBand at San Diego Supercomputing Center

By Nicole Hemsoth

January 30, 2012

The San Diego Supercomputing Center Gordon Supercomputer was built in response to a call from the National Science Foundation (NSF) to deploy a “data intensive” computer.     With this in mind, Gordon was designed for running data-intensive applications spanning domains such as genomics, graph problems, geophysics, and data mining. Scientific researches will include the analysis of individual genomes to tailor drugs to specific patients, the development of more accurate models to predict the impact of earthquakes on buildings and other structures, and simulations that offer greater insight into what’s happening to the planet’s climate.

CAPABILITIES OF THE GORDON SUPERCOMPUTER

The SDSC Gordon cluster is composed of over 1,000 compute nodes based on the Intel Xeon processor E5 family.   The supercomputer also employs a number of unique capabilities to provide the data-intensive applications it was built to run.   One of these features is very fast access to storage via 64 I/O nodes incorporating 300TB of high performance SSD flash-based memory connected over the InfiniBand fabric.  This flash memory will help speed access to storage that is traditionally limited by the slower spinning disk-based storage.      One benefit of this fast storage is to enable the manipulation of massive graphs that arise in many data-intensive fields, including bioinformatics, social networks and neuroscience. In these applications, large databases could be loaded into flash memory and queried with much lower latency than if they were resident on disk.

Each of these I/O nodes is capable of more than 560K IOPS, or 35M IOPS for the full system, making it what SDSC believes is the fastest supercomputer ever commissioned by the NSF in terms of I/O operations.   For comparison purposes, the flash storage is large enough to store the entire 100,000 Netflix movie catalog (and still have room to spare), and is fast enough to deliver more than 200 Netflix movies in a single second.  

Another concept unique to the Gordon cluster is the ‘Supernode’ architecture.    Each Gordon supernode consists of 32 HPC compute nodes and is capable of 240 GFLOPS/node and 64 GBof RAM per node.   Each supernode also incorporates 2 of the high speed I/O nodes detailed above.   When tied together by virtual shared memory, each of the system’s 32 supernodes has the potential of 7.7 TFLOP of compute power and 10 TB of memory.    An additional benefit of the cluster is the use of the supernodes are completely programmable, so the nodes can be allocated either as traditional HPC nodes, as supernodes, or as combinations of the two.  

A 3D TORUS TOPOLOGY

SDSC chose to deploy a 3D Torus topology for the Gordon fabric.   There are considerations to take into account when selecting between a 3D Torus and alternate topologies, but in some clusters there are key characteristics of a 3D Torus that make it a good choice.     When comparing the 3D Torus to other topologies, the most often considered alternative is a fat-tree topology, which is the most commonly used topology for InfiniBand fabrics today.    With a fat-tree topology, every node has equal access bandwidth to every other node in the cluster.   Fat-tree is a great topology for running large scale applications where nodes do a lot of communication with each other, e.g., large MPI jobs.   In contrast, a 3D Torus topology is best used for applications that use communications between localized compute nodes, as this locality is usually a requirement to achieve optimal performance with a torus.   Given the data intensive applications that are targeted for Gordon, and the nature of these applications where in many cases localization constraints within the application are employed, the 3D Torus architecture made sense from a performance perspective.  

There are additional advantages to be gained by using a 3D Torus topology that make it appealing for certain installations.   In general the cabling of the cluster can be simpler, and also shorter cables can be utilized to build the cluster.   This provides for a cost effective, power efficient and resilient design.    Also, if future expansion is a requirement, the 3D Torus can be added to with very little re-cabling necessary.   The ends of the torus are simply disconnected, servers are added, and then the torus is reconnected at the end points.

3D TORUS IMPLEMENTATION

To build their 3D Torus network, SDSC relied on InfiniBand hardware and software from Mellanox Technologies.    The 3D Torus was built using 36-port switch nodes in a 4x4x4 configuration, for a total of 64 torus junctions.   Each of these junctions connects to 16 compute nodes, and 2 IO nodes, with inter-node links using 3 switch ports in each of the +/- X, Y, and Z directions.   Utilizing 40Gb/s QDR technology, this delivers over 12 GB/s of bandwidth in each direction.    The cluster also employs a dual-rail technology, meaning two independent HCAs are populate in each server, and each HCA is connected to a separate 4x4x4 torus network.   This provides the applications double the throughput from a server, or over 7 GB/s injection rate into the network.  

 

 

Fig. 1   4x4x4 3D-Torus Logical Deployment Diagram

Mellanox used a unique algorithm called ‘Torus-2QOS’ to provide the packet routing configuration through the switching fabric.    This algorithm, originally developed at Sandia National Laboratories, is based on Direct Ordered Routing (DOR) routing principles, but has the unique capability of being able to handle the loop wiring nature of a torus, and to also provide a level of Quality of Service (QOS) within the torus.   QOS in important as it allows different traffic types, or service levels,  their own dedicated network resources that won’t interfere with traffic from other service levels.   This is especially useful in a cluster like Gordon, as the storage traffic from the IO nodes can run on their own service level from the compute traffic, giving each of these traffic types their own set of resources within the network where they won’t interfere with each other.    

The Torus-2QOS algorithm that was deployed also has many advanced features, including its level of resiliency.   The routing is setup in such a way that it can ‘self-heal’ and reroute around multiple cable failures as well as a complete switch failure.   This rerouting is done automatically by the subnet management entity that is managing the fabric, and is done independently and without the knowledge of the applications running over the fabric.  

While the details and interworking’s of the 3D Torus algorithm are beyond the scope of this article, from a simple conceptual view, separate ‘virtual fabric’ are employed in the switching network and used by the applications to avoid the credit loops discussed above.   For example, a dateline is drawn in each plane of the torus, and if the packets cross this dateline they run over a different ‘virtual fabric’ from packets that do not cross the dateline.    In this way, no loops are can be formed across the torus.  Applications need to be aware of the correct ‘virtual fabrics’ to use when communicating to another server.   Because InfiniBand uses a centralized management scheme, it is a rather straightforward process for the application to be given the ‘virtual fabric’ information from this centralized manager whenever setting up a connection to another server.    Since most applications use this mechanism anyways, no changes to the application were necessary to be able to use the 3D Torus.  

THE FUTURE OF 3D TORUS WITH INFINIBAND

The software that Mellanox deployed on the cluster is now industry standard and part of the open source community Open Fabric stack.   This includes the subnet management routing algorithms, the management tools, and the application support to run over a 3D Torus topology.   The San Diego Supercomputing Gordon cluster shows that it is feasible and practical to run a 3D Torus topology with InfiniBand.   It also shows the power and flexibility of InfiniBand to be able to run different topologies depending on the performance goals, architecture and cost targets of the supercomputer. 

http://www.mellanox.com

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!

World Cup is Lame Compared to This Competition

June 18, 2018

So you think World Cup soccer is a big deal? While I’m sure it’s very compelling to watch a bunch of athletes kick a ball around, World Cup misses the boat because it doesn’t include teams putting together their ow Read more…

By Dan Olds

IBM Demonstrates Deep Neural Network Training with Analog Memory Devices

June 18, 2018

From smarter, more personalized apps to seemingly-ubiquitous Google Assistant and Alexa devices, AI adoption is showing no signs of slowing down – and yet, the hardware used for AI is far from perfect. Currently, GPUs Read more…

By Oliver Peckham

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPC and AI Convergence is Accelerating New Levels of Intelligence

Data analytics is the most valuable tool in the digital marketplace – so much so that organizations are employing high performance computing (HPC) capabilities to rapidly collect, share, and analyze endless streams of data. Read more…

IBM Accelerated Insights

Banks Boost Infrastructure to Tackle GDPR

As banks become more digital and data-driven, their IT managers are challenged with fast growing data volumes and lines-of-businesses’ (LoBs’) seemingly limitless appetite for analytics. Read more…

Challenges Face Astroinformatics as It Sorts Through the Stars

June 15, 2018

You might have seen one of those YouTube videos: they begin on Earth, slowly zooming out to the Moon, the Solar System, the Milky Way, beyond – and suddenly, you’re looking at trillions of stars. It’s a lot to take Read more…

By Oliver Peckham

Sandia to Take Delivery of World’s Largest Arm System

June 18, 2018

While the enterprise remains circumspect on prospects for Arm servers in the datacenter, the leadership HPC community is taking a bolder, brighter view of the x86 server CPU alternative. Amongst current and planned Arm HPC installations – i.e., the innovative Mont-Blanc project, led by Bull/Atos, the 'Isambard’ Cray XC50 going into the University of Bristol, and commitments from both Japan and France among others -- HPE is announcing that it will be supply the United States National Nuclear Security Administration (NNSA) with a 2.3 petaflops peak Arm-based system, named Astra. Read more…

By Tiffany Trader

The Machine Learning Hype Cycle and HPC

June 14, 2018

Like many other HPC professionals I’m following the hype cycle around machine learning/deep learning with interest. I subscribe to the view that we’re probably approaching the ‘peak of inflated expectation’ but not quite yet starting the descent into the ‘trough of disillusionment. This still raises the probability that... Read more…

By Dairsie Latimer

Xiaoxiang Zhu Receives the 2018 PRACE Ada Lovelace Award for HPC

June 13, 2018

Xiaoxiang Zhu, who works for the German Aerospace Center (DLR) and Technical University of Munich (TUM), was awarded the 2018 PRACE Ada Lovelace Award for HPC for her outstanding contributions in the field of high performance computing (HPC) in Europe. Read more…

By Elizabeth Leake

U.S Considering Launch of National Quantum Initiative

June 11, 2018

Sometime this month the U.S. House Science Committee will introduce legislation to launch a 10-year National Quantum Initiative, according to a recent report by Read more…

By John Russell

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

Exascale USA – Continuing to Move Forward

June 6, 2018

The end of May 2018, saw several important events that continue to advance the Department of Energy’s (DOE) Exascale Computing Initiative (ECI) for the United Read more…

By Alex R. Larzelere

Exascale for the Rest of Us: Exaflops Systems Capable for Industry

June 6, 2018

Enterprise advanced scale computing – or HPC in the enterprise – is an entity unto itself, situated between (and with characteristics of) conventional enter Read more…

By Doug Black

Fracas in Frankfurt: ISC18 Cluster Competition Teams Unveiled

June 6, 2018

The Student Cluster Competition season heats up with the seventh edition of the ISC Student Cluster Competition, slated to begin on June 25th in Frankfurt, Germ Read more…

By Dan Olds

MLPerf – Will New Machine Learning Benchmark Help Propel AI Forward?

May 2, 2018

Let the AI benchmarking wars begin. Today, a diverse group from academia and industry – Google, Baidu, Intel, AMD, Harvard, and Stanford among them – releas Read more…

By John Russell

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

ORNL Summit Supercomputer Is Officially Here

June 8, 2018

Oak Ridge National Laboratory (ORNL) together with IBM and Nvidia celebrated the official unveiling of the Department of Energy (DOE) Summit supercomputer toda Read more…

By Tiffany Trader

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

HPE Wins $57 Million DoD Supercomputing Contract

February 20, 2018

Hewlett Packard Enterprise (HPE) today revealed details of its massive $57 million HPC contract with the U.S. Department of Defense (DoD). The deal calls for HP Read more…

By Tiffany Trader

Leading Solution Providers

SC17 Booth Video Tours Playlist

Altair @ SC17

Altair

AMD @ SC17

AMD

ASRock Rack @ SC17

ASRock Rack

CEJN @ SC17

CEJN

DDN Storage @ SC17

DDN Storage

Huawei @ SC17

Huawei

IBM @ SC17

IBM

IBM Power Systems @ SC17

IBM Power Systems

Intel @ SC17

Intel

Lenovo @ SC17

Lenovo

Mellanox Technologies @ SC17

Mellanox Technologies

Microsoft @ SC17

Microsoft

Penguin Computing @ SC17

Penguin Computing

Pure Storage @ SC17

Pure Storage

Supericro @ SC17

Supericro

Tyan @ SC17

Tyan

Univa @ SC17

Univa

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Sympo Read more…

By Staff

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

Google I/O 2018: AI Everywhere; TPU 3.0 Delivers 100+ Petaflops but Requires Liquid Cooling

May 9, 2018

All things AI dominated discussion at yesterday’s opening of Google’s I/O 2018 developers meeting covering much of Google's near-term product roadmap. The e Read more…

By John Russell

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Pattern Computer – Startup Claims Breakthrough in ‘Pattern Discovery’ Technology

May 23, 2018

If it weren’t for the heavy-hitter technology team behind start-up Pattern Computer, which emerged from stealth today in a live-streamed event from San Franci Read more…

By John Russell

Part One: Deep Dive into 2018 Trends in Life Sciences HPC

March 1, 2018

Life sciences is an interesting lens through which to see HPC. It is perhaps not an obvious choice, given life sciences’ relative newness as a heavy user of H Read more…

By John Russell

Intel Pledges First Commercial Nervana Product ‘Spring Crest’ in 2019

May 24, 2018

At its AI developer conference in San Francisco yesterday, Intel embraced a holistic approach to AI and showed off a broad AI portfolio that includes Xeon processors, Movidius technologies, FPGAs and Intel’s Nervana Neural Network Processors (NNPs), based on the technology it acquired in 2016. Read more…

By Tiffany Trader

Google Charts Two-Dimensional Quantum Course

April 26, 2018

Quantum error correction, essential for achieving universal fault-tolerant quantum computation, is one of the main challenges of the quantum computing field and it’s top of mind for Google’s John Martinis. At a presentation last week at the HPC User Forum in Tucson, Martinis, one of the world's foremost experts in quantum computing, emphasized... 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