Building an HPC cluster with AWS ParallelCluster and Amazon FSx for Lustre

By Pierre-Yves Aquilanti, Sr. HPC Specialized Solution Architect, AWS and Jeff Bartley, Sr. Storage Solution Architect, AWS

July 23, 2019

High performance computing (HPC) customers love the breadth of services offered by AWS and the flexibility offered by the cloud to address their computational challenges. AWS provides you with the opportunity to innovate quickly and accelerate your workflow thanks to a virtually unlimited capacity. For more information, see the following posts:

However, building an HPC system can be complex, which is one reason AWS created AWS ParallelCluster. This tool offers a simple method to create an automatically scaling HPC system in the AWS Cloud, utilizing services such as Amazon EC2, AWS Batch, and Amazon FSx for Lustre. AWS Parallel Cluster configures the compute and storage resources necessary to run your HPC workloads. Settings based on your specific storage, compute, and network requirements all help optimize its functionality.

You can manage an HPC cluster with AWS ParallelCluster through a simple set of commands: create, update, and delete. The compute portion of the cluster automatically scales when jobs have to be processed. As a result, you only pay for what you use. Additionally, to provide shared storage to the cluster, AWS ParallelCluster can use Amazon FSx for Lustre as a high-performance file system that can be accessed by all compute nodes.

In this post, I show how easy it is to spin up a fully functioning compute cluster with a shared, high-performance file system in a matter of minutes using AWS ParallelCluster and Amazon FSx for Lustre. To test file system throughput, which is a common performance metric for sizing HPC clusters, you’ll use the SGE scheduler (pre-installed with AWS ParallelCluster) once your cluster is up to run a quick I/O benchmark job. The I/O benchmark will also verify that the compute cluster can achieve the expected level of file system performance. If you’re new to AWSParallelCluster, review this post detailing how to get started before continuing.

Overview

AWS recently announced AWS ParallelCluster support for FSx for Lustre. AWS ParallelCluster is a cluster-management tool for AWS that makes it easy for scientists, researchers, and IT administrators to deploy and manage HPC clusters in the AWS Cloud. This tool also facilitates both quick-start proofs of concept (POCs) and production deployments.

FSx for Lustre provides a high-performance file system that makes it easy to process data stored on Amazon S3 or on premises. With FSx for Lustre, you can launch and run a file system that provides sub-millisecond access to your data. It allows you to read and write data at speeds of up to hundreds of gigabytes per second of throughput and millions of IOPS. By integrating AWS ParallelCluster with FSx for Lustre, HPC customers can now spin up clusters with thousands of compute instances, and shared storage that scales performance for the most demanding workloads so that compute instances never have to wait for data and you get to the answers faster.

To test the performance of your FSx for Lustre file system, you can use IOR, a commonly used HPC benchmarking tool. IOR provides a number of options that approximate workload performance. However, I always recommend that you benchmark with your own workload to get full visibility into performance characteristics.

Right-sizing

Use IOR to generate a sequential read/write I/O pattern to test the high-throughput capabilities of FSx for Lustre. This means that you begin your sizing at the storage layer, and then determine how many compute nodes should drive your desired I/O performance.

When sizing FSx for Lustre performance, a good rule of thumb is to plan for 200 MB/s of throughput per 1 TiB allocated. FSx for Lustre allocates file systems in 3.6-TiB increments, which provide around 720 MB/s per increment. A 39.6-TiB file system, should give you around 7.92 GB/s of total file system throughput.

After you know the storage performance target, you can figure out how many compute nodes you need. Each compute node communicates with FSx for Lustre over the network, making the workload throughput-based, and so network bandwidth is the primary sizing factor for compute nodes.

Amazon EC2 instances provide different levels of network bandwidth, depending upon the instance type. In this case, I selected the c4.4xlarge instance type because it is widely available in all Regions and, in testing, provides about 500-MB/s peak network bandwidth. To reach 7.92 GB/s of performance, you want sixteen c4.4xlarge compute nodes in your cluster.

Prerequisites

You must have the AWS CLI installed and configured on a system with Python and PIP. This could be on your laptop, a desktop computer, or an Amazon EC2 bastion host running in AWS.

Read the complete blog and follow along with step-by-step instructions here.

Return to Solution Channel Homepage
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!

China’s Tencent Server Design Will Use AMD Rome

November 13, 2019

Tencent, the Chinese cloud giant, said it would use AMD’s newest Epyc processor in its internally-designed server. The design win adds further momentum to AMD’s bid to erode rival Intel Corp.’s dominance of the glo Read more…

By George Leopold

NCSA Industry Conference Recap – Part 1

November 13, 2019

Industry Program Director Brendan McGinty welcomed guests to the annual National Center for Supercomputing Applications (NCSA) Industry Conference, October 8-10, on the University of Illinois campus in Urbana (UIUC). On Read more…

By Elizabeth Leake, STEM-Trek

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 components with Intel Xeon, AMD Epyc, IBM Power, and Arm server ch Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. Read more…

By Doug Black

SIA Recognizes Robert Dennard with 2019 Noyce Award

November 12, 2019

If you don’t know what Dennard Scaling is, the chances are strong you don’t labor in electronics. Robert Dennard, longtime IBM researcher, inventor of the DRAM and the fellow for whom Dennard Scaling was named, is th 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

Leveraging Exaflops Performance to Remediate Nuclear Waste

November 12, 2019

Nuclear waste storage sites are a subject of intense controversy and debate; nobody wants the radioactive remnants in their backyard. Now, a collaboration between Berkeley Lab, Pacific Northwest National University (PNNL Read more…

By Oliver Peckham

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

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

Tackling HPC’s Memory and I/O Bottlenecks with On-Node, Non-Volatile RAM

November 8, 2019

On-node, non-volatile memory (NVRAM) is a game-changing technology that can remove many I/O and memory bottlenecks and provide a key enabler for exascale. Th Read more…

By Jan Rowell

MLPerf Releases First Inference Benchmark Results; Nvidia Touts its Showing

November 6, 2019

MLPerf.org, the young AI-benchmarking consortium, today issued the first round of results for its inference test suite. Among organizations with submissions wer Read more…

By John Russell

Azure Cloud First with AMD Epyc Rome Processors

November 6, 2019

At Ignite 2019 this week, Microsoft's Azure cloud team and AMD announced an expansion of their partnership that began in 2017 when Azure debuted Epyc-backed ins Read more…

By Tiffany Trader

Nvidia Launches Credit Card-Sized 21 TOPS Jetson System for Edge Devices

November 6, 2019

Nvidia has launched a new addition to its Jetson product line: a credit card-sized (70x45mm) form factor delivering up to 21 trillion operations/second (TOPS) o Read more…

By Doug Black

In Memoriam: Steve Tuecke, Globus Co-founder

November 4, 2019

HPCwire is deeply saddened to report that Steve Tuecke, longtime scientist at Argonne National Lab and University of Chicago, has passed away at age 52. Tuecke Read more…

By Tiffany Trader

Spending Spree: Hyperscalers Bought $57B of IT in 2018, $10B+ by Google – But Is Cloud on Horizon?

October 31, 2019

Hyperscalers are the masters of the IT universe, gravitational centers of increasing pull in the emerging age of data-driven compute and AI.  In the high-stake Read more…

By Doug Black

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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