Stanford HPC Center Rocks with Intel Cluster Ready Solution

By Steve Jones

March 28, 2008

In just eleven days during 2007, the Stanford University High-Performance Computing (HPC) Center nearly doubled the performance of its existing compute system. The center leveraged certification methodology from the Intel Cluster Ready Program to fully implement a 1,696-core cluster solution. The solution integrates Clustercorp, Dell and Panasas technologies to give the center the flexibility to meet ever-expanding computational and application requirements and to enable Stanford researchers to achieve faster time-to-results. Steve Jones, the founder and manager of the Stanford HPC Center, writes about the design and deployment of this system.

Mission: Enable CFD on Demand

The goal of our expansion was simple: acquire sufficient compute power to facilitate School of Engineering coursework and research efforts and to support the university’s industrial affiliates program.

The system would need to support more than 200 researchers and effectively enable CFD on demand. Two departments in particular require large-scale, massively parallel computing resources for their work. Researchers in the mechanical engineering and aeronautics and astronautics departments leverage HPC Center resources to analyze the details of flow and acoustics created by helicopters in forward flight. Critical applications include two major in-house-developed simulation codes: Stanford University multiblock (SUmb) and CDP, named for the late Charles David Pierce. Commercial applications include ANSYS, Gaussian, MatLab, and VASP. Stanford’s post-processing programs include EnSight for distributed rendering and Tecplot for visualization.

Objective: Extend In-House Support for Complex Code Verification and Validation

To address Stanford researchers’ increasing needs for code validation, our team opted to bolster local compute resources. The goal was to build a cluster-based solution capable of scaling to thousands of nodes and supporting our large user base. The minimum expectation for the cluster was to run routine jobs in-house and to allow researchers to do more extensive verification and validation of code destined for the national labs. In addition to the large compute capacity and scalability requirements, the system needed to be capable of sustained performance with a file system fast enough to cope with massive I/O load and to deliver the granularity of results researchers require.

Challenge: Overcome Limitations in Space, Time, and Staff

While our plan was to dramatically expand compute resources, the project was bound by constraints of space, time and staff. The Stanford HPC Center has limited square footage in which to operate, so footprint was an issue, not only in terms of the system size and density, but also in how it would impact general HVAC requirements. Extensive project demands also applied scheduling pressures that propelled the deployment team to implement a more aggressive rollout than the three- to six-month timeframe more typically allotted for implementations of this scope. The final challenge was the center’s requirements to grow overall services delivery while maintaining the existing support staff.

We felt that taking advantage of an integrated solution would help us meet our compute and deployment objectives without exceeding our space, time, and staffing limitations. In particular, we were sold on the idea of the Intel Cluster Ready (ICR) program where certification of the Clustercorp/Dell/Panasas solution had been completed upfront. The certification provides cluster components validation to ensure accurate configuration, optimal performance, and a system that is easy to manage and seamlessly expand.

Solution: Use Certified Best-of-Breed Compute, Distribution, and Storage Components

With the assistance of the Dell Advanced Systems Group and following extensive review of available technologies, we began to solidify plans. Specifically, the Dell team worked with us to design and build the final cluster-based solution architecture that incorporates Dell Power Edge Servers using Intel Quad-Core Xeon processors and compilers with Clustercorp Rocks+ cluster distribution software, and Panasas ActiveStor Parallel storage. The design includes:

  • Dell PowerEdge 1950 servers. Standards-based product, a 1U form-factor, remote management and diagnostic functionality, scalability, and parts availability were important factors in the selection of Dell servers for the HPC Center compute nodes.
  • Cisco 7024 InfiniBand switch. High-speed, full nonblocking internode communications help ensure that compute nodes do not waste cycles waiting for messages.
  • Panasas ActiveStor AS3000 parallel storage (with object-based Panasas PanFS parallel file system). Determining factors included Intel Cluster ready certification (Panasas ActiveStor Storage Clusters were actually the first parallel storage solution to be certified as part of the ICR program), MPI I/O optimization, and bandwidth per storage shelf.
  • Clustercorp Rocks+ 4.3 (with CentOS 4.5) and Clustercorp Intel Developer, Fluent, Moab, Cisco OFED, and Panasas Rolls. Rocks+ cluster distribution offers comprehensive application integration packages (i.e. Rocks+Rolls) that are essential for large-cluster configuration. Using Rolls to add software stacks with “checkbox” application distribution is a nice relief for system administrators who remember the old days of installation, distribution, configuration, scripting, and testing for every application added to the system. Rolls for Fluent, EnSight, and other higher-level applications greatly add to the simplicity of building an end-to-end solution.
  • Dell Deployment Services. The Dell Advanced Systems Group and the company’s ecosystem of partners, including APC, Cisco, Clustercorp, Intel, and Panasas, came together to architect and implement the solution seamlessly and in record time. Expertise and comprehensive planning were critical to the rapid deployment.
  • APC Hot Aisle Containment System. This chilled-water, row-cooling system enables greater rack density (and therefore smaller footprint) than would be possible using traditional room cooling.

In terms of the selection of the storage component, let me add further explanation of our selection of the Panasas parallel solution. Unlike NFS appliances and other clustered-storage products we considered, the Panasas storage system enhanced application performance to deliver the parallel I/O efficiency and stability our researchers require. Our experience with NFS has been that as we start to increase the number of processors or processes writing in parallel to the file system, we overwhelm the appliance and cannot successfully run a large simulation. That’s why we looked for a storage solution specifically optimized for parallel processing environments.

We did run direct comparisons of Panasas PanFS parallel file system against an array of other file systems, including those commonly targeted to HPC clusters. The PanFS parallel file system consistently outperformed them–in fact, when we ran our simulation and modeling applications, Panasas parallel storage allowed it to run significantly faster. We’ve used Panasas parallel storage in-house for more than three years now because we find it to be the highest-performing, most manageable, and most reliable of the leading storage solutions designed for high-performance computing.

Result: Achieve 2-14X Performance Improvement After an 11-Day Deployment

The entire deployment, including implementation of an entirely new power and cooling infrastructure, took a total of eleven days. The Dell Enterprise Deployment team played an integral role in this feat, coordinating the efforts of all participating vendors. The power, cooling, and system build-out were completed in parallel. We used the Rocks+ Linux cluster distribution to configure master and compute nodes, and by day eleven our researchers were able to submit jobs that were flawlessly executed and producing scientific code and operations with unprecedented fidelity. The new cluster easily handles ten times the workload of the original 48-node configuration. Testing results show performance of 15.8 teraflops performance compared to 1.1 teraflops delivered by the smaller cluster.

The Stanford HPC Center currently supports fifteen different types of HPC systems, including the Intel Cluster Ready system based on the Clustercorp/Dell/Panasas solution. The original 48-node system is now used by students and researchers working on smaller-scale problems. The ease-of-use of commodity-based hardware, efficient cluster distribution, and appliance-like ease of storage management allow the center to maintain a small support staff.

Research Impact: Achieve Faster and More Accurate Time-To-Results

The new cluster is paying off well for our center. It has delivered faster time-to-results by:

  • Allowing researchers to run more simulations and other heavy-compute jobs in-house.
  • Delivering finer detail or higher fidelity so that scientists more quickly and easily recognize salient features or other important phenomena.
  • Enabling more thorough verification and validation of complex codes destined to be submitted to the 10,000-65,000-processor systems at the National Labs.

With this new, more powerful, stable and manageable cluster in place, our researchers are better able to focus on their science and deliver consistent, meaningful results to project sponsors. Deployment of the new cluster has also brought added recognition to the Stanford High Performance Computing Center, helping us achieve a ranking of 130 on the Top 500 list in November 2007.

Meanwhile, our compute infrastructure continues to grow — the HPC Center is currently doubling the size of the existing cluster and designing an additional system based on a similar architecture. The integrated, standards-based solution and the Intel Cluster Ready certification combine to give the Stanford High Performance Computing Center the flexibility to add or change cluster elements to meet specific computational and application requirements. Stanford’s industrial partners are also able take advantage of the system to enable more traditional operations and expand their own research and computing services.

About the Author

Steve Jones currently runs the High Performance Computing Center at Stanford University, supporting sponsored research for The Department of Energy Advanced Simulation and Computing Program (ASC), and the next-generation Predictive Science Academic Alliance Program (PSAAP). The HPC Center also supports the computational needs of sponsored research for National Aeronautics and Space Administration (NASA), Air Force Office of Scientific Research (AFOSR) and Defense Advanced Research Projects Agency (DARPA). Jones is the chair of the annual Stanford High Performance Computing Conference, has designed and currently administers numerous Top 500 Supercomputers, and speaks regularly about the management of High Performance Computing Clusters. More information can be found at and

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!

What’s New in Computing vs. COVID-19: Fugaku, Congress, De Novo Design & More

July 2, 2020

Supercomputing, big data and artificial intelligence are crucial tools in the fight against the coronavirus pandemic. Around the world, researchers, corporations and governments are urgently devoting their computing reso Read more…

By Oliver Peckham

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time last year, IBM announced open sourcing its Power instructio Read more…

By John Russell

HPC Career Notes: July 2020 Edition

July 1, 2020

In this monthly feature, we'll keep you up-to-date on the latest career developments for individuals in the high-performance computing community. Whether it's a promotion, new company hire, or even an accolade, we've got Read more…

By Mariana Iriarte

Supercomputers Enable Radical, Promising New COVID-19 Drug Development Approach

July 1, 2020

Around the world, innumerable supercomputers are sifting through billions of molecules in a desperate search for a viable therapeutic to treat COVID-19. Those molecules are pulled from enormous databases of known compoun Read more…

By Oliver Peckham

HPC-Powered Simulations Reveal a Looming Climatic Threat to Vital Monsoon Seasons

June 30, 2020

As June draws to a close, eyes are turning to the latter half of the year – and with it, the monsoon and hurricane seasons that can prove vital or devastating for many of the world’s coastal communities. Now, climate Read more…

By Oliver Peckham

AWS Solution Channel

Maxar Builds HPC on AWS to Deliver Forecasts 58% Faster Than Weather Supercomputer

When weather threatens drilling rigs, refineries, and other energy facilities, oil and gas companies want to move fast to protect personnel and equipment. And for firms that trade commodity shares in oil, precious metals, crops, and livestock, the weather can significantly impact their buy-sell decisions. 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…

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This year is no different though the conversion of ISC to a digital Read more…

By John Russell

OpenPOWER Reboot – New Director, New Silicon Partners, Leveraging Linux Foundation Connections

July 2, 2020

Earlier this week the OpenPOWER Foundation announced the contribution of IBM’s A21 Power processor core design to the open source community. Roughly this time Read more…

By John Russell

Hyperion Forecast – Headwinds in 2020 Won’t Stifle Cloud HPC Adoption or Arm’s Rise

June 30, 2020

The semiannual taking of HPC’s pulse by Hyperion Research – late fall at SC and early summer at ISC – is a much-watched indicator of things come. This yea Read more…

By John Russell

Racism and HPC: a Special Podcast

June 29, 2020

Promoting greater diversity in HPC is a much-discussed goal and ostensibly a long-sought goal in HPC. Yet it seems clear HPC is far from achieving this goal. Re Read more…

Top500 Trends: Movement on Top, but Record Low Turnover

June 25, 2020

The 55th installment of the Top500 list saw strong activity in the leadership segment with four new systems in the top ten and a crowning achievement from the f Read more…

By Tiffany Trader

ISC 2020 Keynote: Hope for the Future, Praise for Fugaku and HPC’s Pandemic Response

June 24, 2020

In stark contrast to past years Thomas Sterling’s ISC20 keynote today struck a more somber note with the COVID-19 pandemic as the central character in Sterling’s annual review of worldwide trends in HPC. Better known for his engaging manner and occasional willingness to poke prickly egos, Sterling instead strode through the numbing statistics associated... Read more…

By John Russell

ISC 2020’s Student Cluster Competition Winners Announced

June 24, 2020

Normally, the Student Cluster Competition involves teams of students building real computing clusters on the show floors of major supercomputer conferences and Read more…

By Oliver Peckham

Hoefler’s Whirlwind ISC20 Virtual Tour of ML Trends in 9 Slides

June 23, 2020

The ISC20 experience this year via livestreaming and pre-recordings is interesting and perhaps a bit odd. That said presenters’ efforts to condense their comments makes for economic use of your time. Torsten Hoefler’s whirlwind 12-minute tour of ML is a great example. Hoefler, leader of the planned ISC20 Machine Learning... Read more…

By John Russell

At ISC, the Fight Against COVID-19 Took the Stage – and Yes, Fugaku Was There

June 23, 2020

With over nine million infected and nearly half a million dead, the COVID-19 pandemic has seized the world’s attention for several months. It has also dominat Read more…

By Oliver Peckham

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

[email protected] Turns Its Massive Crowdsourced Computer Network Against COVID-19

March 16, 2020

For gamers, fighting against a global crisis is usually pure fantasy – but now, it’s looking more like a reality. As supercomputers around the world spin up Read more…

By Oliver Peckham

[email protected] Rallies a Legion of Computers Against the Coronavirus

March 24, 2020

Last week, we highlighted [email protected], a massive, crowdsourced computer network that has turned its resources against the coronavirus pandemic sweeping the globe – but [email protected] isn’t the only game in town. The internet is buzzing with crowdsourced computing... Read more…

By Oliver Peckham

Global Supercomputing Is Mobilizing Against COVID-19

March 12, 2020

Tech has been taking some heavy losses from the coronavirus pandemic. Global supply chains have been disrupted, virtually every major tech conference taking place over the next few months has been canceled... Read more…

By Oliver Peckham

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

DoE Expands on Role of COVID-19 Supercomputing Consortium

March 25, 2020

After announcing the launch of the COVID-19 High Performance Computing Consortium on Sunday, the Department of Energy yesterday provided more details on its sco Read more…

By John Russell

Steve Scott Lays Out HPE-Cray Blended Product Roadmap

March 11, 2020

Last week, the day before the El Capitan processor disclosures were made at HPE's new headquarters in San Jose, Steve Scott (CTO for HPC & AI at HPE, and former Cray CTO) was on-hand at the Rice Oil & Gas HPC conference in Houston. He was there to discuss the HPE-Cray transition and blended roadmap, as well as his favorite topic, Cray's eighth-gen networking technology, Slingshot. Read more…

By Tiffany Trader

Honeywell’s Big Bet on Trapped Ion Quantum Computing

April 7, 2020

Honeywell doesn’t spring to mind when thinking of quantum computing pioneers, but a decade ago the high-tech conglomerate better known for its control systems waded deliberately into the then calmer quantum computing (QC) waters. Fast forward to March when Honeywell announced plans to introduce an ion trap-based quantum computer whose ‘performance’ would... Read more…

By John Russell

Leading Solution Providers


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

‘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

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

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

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

Summit Supercomputer is Already Making its Mark on Science

September 20, 2018

Summit, now the fastest supercomputer in the world, is quickly making its mark in science – five of the six finalists just announced for the prestigious 2018 Read more…

By John Russell

TACC Supercomputers Run Simulations Illuminating COVID-19, DNA Replication

March 19, 2020

As supercomputers around the world spin up to combat the coronavirus, the Texas Advanced Computing Center (TACC) is announcing results that may help to illumina Read more…

By Staff report

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