Like many of you, I attended SC11 in Seattle this year. I have to say, the world’s largest HPC convention has become downright addictive—especially if you happen to be an ex-gamer. I had to extract myself from the “Gaming through the Decades” exhibition before I could even get started with more serious pursuits. Fortunately my willpower was well rewarded. In case you weren’t there, the focus was on big data and visualization, and the strides being made are truly amazing.

The advances made by the Intel Cluster Ready partner community are also very impressive. We held our third annual Partner Appreciation Award ceremony at SC11, and it was gratifying to see the progress we’ve all made in just the past year. The Intel Cluster Ready architecture is now represented across an enormous range of HPC solutions, from SMB clusters to some of the world’s Top500 supercomputers. Hardware and software support has also grown substantially, as has market penetration. For a look at a few of the most impressive developments, check out the award-winning partners below, and follow the links for more information. I think you’ll be intrigued.

We gave awards in three categories:

• The Pathfinder Award honors the vendor who has done the most to forge new paths into a previously unexplored area.
• Explorer Awards distinguish those who have continued to explore and implement programs that significantly advance the portfolio of solutions based on the Intel Cluster Ready architecture.
• Voyager Awards are for those who have contributed to expanding the global reach and overall market growth of Intel Cluster Ready solutions.

Here’s the list of the 2011 award winners. Enjoy!

Pathfinder Award

• Altair continues to drive innovation by making HPC cluster computing simpler and more productive for its customers. Over the past year, Altair integrated Intel Cluster Checker into PBS Professional, its HPC workload management and job scheduling solution, and registered three key applications for design and analysis: RADIOSS, AcuSolve, and OptiStruct.

Explorer Awards

• science+computing took Intel Cluster Ready into the upper reaches of HPC, installing a 292 TFLOP, 1700 node supercomputer at RWTH Aachen University. It’s the largest Intel Cluster Ready certified system to date, and one of the 30 largest supercomputers in the world. A joint success story will be coming soon to highlight the design win and promote Intel Cluster Ready.
• NEC delivered a huge Intel Cluster Ready win, with a certified 500-node cluster for the University of Erlangen. NEC then helped drive visibility and credibility for Intel Cluster Ready solutions with a success story and Web promotions.
• E4 Computer Engineering launched its E-Cluster 7225 platform, certified Intel Cluster Ready, which scales from four to hundreds of nodes! E4 has also integrated Intel Cluster Ready throughout its marketing communications and updated its website based on each new sales quote.

• Fujitsu has demonstrated a strong commitment to Intel Cluster Ready, integrating support throughout its PRIMERGY server product lines, and have achieved the greatest number of certifications in 2011 for certified Intel Cluster Ready clusters shipped in Europe. Starting at Fujitsu Technology Solutions it became a well-integrated part of the technical production workflow—beginning to end. Intel Cluster Ready is now an integral part of the Fujitsu standard cluster software stack for Intel architecture, and allows them to address a multi-geo market with HPC systems that are 'ready to go'.

• Bright Computing has played an integral role in enabling the Intel Cluster Ready ecosystem by fully incorporating support into its workflows and products, including integration of Intel Cluster Checker into Bright Cluster Manager 5.2. The company was instrumental in helping ensure that the complete HPC solution chain will be ready to support the Intel Xeon Processor E5 family at launch.

• The HPC Advisory Council made broad contributions to Intel Cluster Ready by testing, benchmarking and documenting implementation best practices for open-source applications, co-authoring and publishing a technical brief, and partnering in workshops to extend the awareness and value of Intel Cluster Ready solutions to new audiences.

Voyager Awards

• Flow Science created a cluster solutions guide for Silicon Mechanics and other OEMs to simplify the deployment of Flow-3D, a leading computational fluid dynamics (CFD) solution, on Intel Cluster Ready certified systems. Through this and related efforts, Flow Science is helping to bring HPC—and Intel Cluster Ready—into the digital manufacturing market.
• Silicon Mechanics has integrated Intel Cluster Ready into its technical workflows and sales processes to simplify and accelerate cluster implementation. The company also played a pivotal role in supporting the launch of Sandy Bridge EP and partnered with SIMULIA and Flow Science to deliver optimized, turnkey solutions based on the Intel Cluster Ready architecture.
• SIASA (Soluciones Informaticas Argentinas S.A.) was the first Intel Cluster Ready member in Latin America and has delivered more certified clusters than any other vendor in the region. As one example, SIASA helped the University of Cordoba implement the largest cluster in Argentina.
• Platform Computing is a leading Intel Cluster Ready partner and made a major contribution this year by launching Platform Cluster Manager 3.0, which makes it easier for non-technical customers to build, deploy, and manage Intel Cluster Ready certified systems. The company also provided valuable development support for upcoming Intel server platforms.
• ClusterVision – their commitment to Intel Cluster Ready is so strong that they have edited all their marketing materials and website to promote Intel Cluster Ready. They also implemented Intel Cluster Ready training into their annual sales meeting and launched a sales incentive program. The strategy has delivered new cluster solutions, including a cluster deployment for Ceres Power that was documented in a success story.
• Atipa has shipped eight "Rapid Launch" Linux Clusters in the last two years, all Intel Cluster Ready certified. Atipa has played a valuable role in enabling the HPC ecosystem for the launch of Sandy Bridge EP.
• Eurotech launched its Intel Cluster Ready certified Aurora product line. Then, after collaborating with AuroraScience on a dense, green cluster that’s certified Intel Cluster Ready, Eurotech helped produce a success story about the unique 10 Teraflop Aurora cluster that serves a variety of Italian research organizations and provides a basis for scaling to petaflops of performance.
• Univa has been a long-time supporter of Intel Cluster Ready and recently launched its UniCloud middleware, which makes it easy to deploy Intel Cluster Ready certified HPC clusters in private, hybrid, and public clouds (including RightScale and Amazon EC2).

That’s it for this year’s winners. I’d like to add my personal thanks to all of them.

Stay tuned for more information. I’ll be focusing in on some of these technologies and solutions in more detail in future blogs.

Intel Cluster Checker can run a variety of tests depending on what the user is trying to accomplish. For general wellness of a cluster, Intel Cluster Checker offers five levels of thoroughness. For automation, we'll focus on levels one, three, and five.

Wellness Level One is a very short run of tests that check basic connectivity throughout the cluster as well as basic uniformity checks amongst the nodes.  This test focuses on BIOS settings, and processor, memory and system configurations. The level one tests are quick and show that the cluster is online and ready for use.

Wellness Level Three is the default run level for Intel Cluster Checker. It builds on level one and includes more rigorous modules that test parameters like disk and memory bandwidth, MFLOPS, and network performance. It also performs an in-depth hardware uniformity test along with an Intel MPI Collectives and message Integrity test. It takes a bit longer to run this check that assures the performance of the hardware is up to par.

Wellness Level Five adds a packages test, comparing currently installed packages with a generated list of expected packages at a given time. It also runs the HPCC module (a performance benchmark test). The level five tests can take a bit longer but assures the users that all the pieces of the system are working in harmony. This test is useful for the admin to make sure a user hasn’t installed or uninstalled anything that may affect the cluster.

For my clusters, I have set up the following schedule that runs these wellness levels at various times.

• Level One - set to run each weekday
• Level Three - set to run once a week, on Saturday
• Level Five - set to run monthly, on the first Sunday

For our lab with multiple smaller clusters this automation schedule is perfect, allowing users to login to one of the clusters, see when each of the wellness levels passed and know that their jobs will run as expected.

Every cluster has a different purpose and a different load. Running tests at the intervals or frequency I have set may not be feasible or needed for every cluster. However, automating the test runs on a schedule that meets your needs will help assure that your cluster performance remains optimal, and frees up the cluster(s) for jobs during normal business hours.

References:

>> Review Part 1

>> About Intel Cluster Checker

>> Intel Cluster Checker Knowledge Base

Whether you're a cluster user that expects optimal performance and functionality every time you run a job, or a system administrator that needs to keep the cluster in perfect working order for your users, running checks on a regular basis is important!

A great way to ensure that your HPC system, certified Intel Cluster Ready, remains in the same great shape as when it was first built, is to run the Intel® Cluster Checker tool regularly.

While it’s easy enough to run Intel Cluster Checker on your cluster(s) once a week, I've found there are times when I was too busy, or simply forgot to run a check. For this reason, and because I have multiple clusters to check, I developed a method to automate Intel Cluster Checker runs. This automated solution runs Intel Cluster Checker and reports any errors directly to me and/or the system administrator. Not only does automating this process save the administrator a substantial amount of time each week, it will eliminate the chance of missing a run, and ensures that the cluster remains in optimal health.

A Cluster That Checks Itself

In order to automate the process, it is important that your Intel Cluster Checker passes a manual run first. To do this, make sure the configuration file is optimized to ensure the cluster is operating at its best. With the perfect configuration on hand, a script is then needed to setup the system, run Intel Cluster Checker, and report the results.

For the first phase of the process, I wrote a script that sets up the environment and runs the most in-depth wellness check in Intel Cluster Checker. I used cron to schedule my script to execute once a week. After the results are complete, the script updates the message of the day to show when the last check ran and the results. If the check fails, the log file created by Intel Cluster Checker will be copied to the specified directory where it can be accessed and analyzed.

The cluster is now setup to check itself, in the middle of the night, and report its status upon login!

Read Part 2 for more about scheduling test runs, and the different levels of wellness tests in Intel Cluster Checker.

References:

>> About Intel Cluster Checker

>> Intel Cluster Checker Knowledge Base

Check out this paper, Bringing Consistency to a Heterogeneous Research Cluster, related to upgrading the GreenPlanet cluster at UC Irvine to Intel Cluster Ready architecture.  GreenPlanet is an organically grown HPC cluster that went from seven nodes to over three hundred in just a couple years.  The system grew  as principal investigators pooled grants and added more nodes to the system in batches.  Adding nodes in this fashion means the system is comprised of many different types of compute nodes which can become a pretty tough administrative task.  In the paper, Dr. Nathan Crawford states, “We were trying to keep track of all the differences in spreadsheets or in our heads, and like any academic institution, we had the problem of graduate students moving on and taking their knowledge of system details with them.”

Enter Intel Cluster Ready.  UC Irvine combined an equipment move with an upgrade of their software stack using Clustercorp Rocks+ 5.3.  This version has built-in functionality to install the necessary components to meet the Intel Cluster Ready architecture specification including a Roll to install Intel® Cluster Checker.

The result: changes to over 100 nodes in the system.  “The process of getting certified cleaned up a lot of underlying issues, and immediately
made the system much more stable,” said Crawford. "We’ll have more jobs running to completion, and scientists can spend less time trying to
debug underlying hardware and software problems.”

Scientists doing more science.  Nice.

>> Download the full case study

Your hardware vendor may be able to provide the information you need to install and run open source HPC applications. Another great resource is the HPC Advisory Council. The Advisory Council provides best practice recommendations and installation guides for a variety of HPC applications, as well as training opportunities, an online forum for interacting with HPC experts, and cluster resources you can use for testing, optimizing, and benchmarking your applications.

Intel has been working with the HPC Advisory Council to develop best practice recommendations and installation guides for popular open source HPC applications running on Intel Cluster Ready certified systems. Installation guides are available now for Adaptive Mesh Refinement, BQCD, CP2K, CPMD, Espresso, Himeno, LAMMPS, NAMD, NWChem, OpenFOAM, and WRF. If you don’t see the application you’re interested in, stay tuned. More are coming. Or contact the HPC Advisory Council. They’re always looking for input from HPC users.

Update - these installation guides are now available: Amber 11, CESM, GADGET-2, GROMACS, MrBayes, NEMO, Octopus, and OpenMX.

>> View all Intel Cluster Ready Installation Best Practices

For more about the HPC Advisory Council, go to hpcadvisorycouncil.com

For more Intel Cluster Ready information, visit intel.com/go/cluster

Read the HPC Advisory Council and Intel Cluster Ready Technology Brief

As an industry, we need to continue to push HPC technologies into mainstream and make it easier to access for people like Marshall.  Computational simulations can drastically reduce research cost and speed time to results - not just in academia but in commercial environments as well.  HPC is no longer a niche technology but is viable for broad academic and commercial use.  There are a lot more discoveries and advancements out there that we can get to faster with bigger and better simulations.

In case you missed it, read Teen Discovers Promising Cystic Fibrosis Treatment

Seamless Transitions...

I'd add that the Intel Cluster Ready architecture applies in the cloud as well.  In fact, using cloud images based on Intel Cluster Ready architecture allows more seamless transitions between clusters running in the cloud to physical clusters running locally.  As the video points out, cloud provides an entry point into using HPC or even a try-before-buy approach to HPC clusters.  Cloud bursting benefits as well, since the application that runs on the architecture locally would see the same architecture in the cloud.

The common architecture enables the applications to better understand and execute on top of the computing environment without being tied to the exact details of the solution.  In other words, you can get better mileage with a common architecture in both the cloud and local clusters.

The results are then recombined to deliver whatever information design team is looking for, whether it's how the latest chassis protects the driver in a 60 MPH collision, or how a potato chip holds up between factory and bowl.

Intel® Cluster Ready provides an optimized platform for parallel computing, and helps to ensure that registered applications run seamlessly on certified systems. But that's only half the battle. Unless applications make efficient use of all that parallel computing capacity, they aren't going to deliver the kind of value that justifies the cost of a high performance cluster.

In other words, if you build a great cluster they will come, but only if you - or someone else - also builds great, compatible applications. Of course, writing good, parallel software code isn’t easy. It's tough enough writing applications that can efficiently use 12 processor cores in a high-end workstation. Writing code that can fully utilize 120 cores in a 10-node cluster, or 480 cores in a 40-node cluster, takes another level of expertise.

Optimized development tools can help - a lot. I encourage you to take a quick look at this video interview from SC10, or forward it on to one of your software-developing colleagues. Doctor Clay Breshears and Werner Krotz-Vogel, talk about Intel Cluster Studio 2011, a comprehensive bundle of tools for software developers who want to write highly optimized applications for Intel processor-based clusters (compilers, libraries, analyzers, and a lot more). Especially noteworthy in this package is a variety of new threading mechanisms for task, data, and vector parallelism. Clay and Werner provide an overview and discuss some of the features. They also give a shout out to Intel Cluster Ready and the more than 150 vendors who are delivering compatible systems and applications.

Enjoy the video!

Check out the Intel® Cluster Studio 2011 - a tool suite for MPI developers on HPC clusters.

Learn more about Intel® Cluster Ready

Univa Acquires Grid Engine Expertise

Addition of Founding Sun Grid Engine Team Advances Data Center Optimization Strategy

Lisle, IL, January 18, 2010 – Univa, the data center optimization company, today announced that the principal engineers from the Sun/Oracle Grid Engine team, including Grid Engine founder and original project owner Fritz Ferstl, are joining Univa. The company will immediately offer superior engineering support for Grid Engine versions already installed and will publish a Univa version of Grid Engine before the end of Q1 2011. Univa will concentrate on improving Grid Engine for technical computing and HPC use cases in addition to promoting the continuity of the Grid Engine open source community.

As part of this announcement, Mr. Ferstl has been appointed Chief Technology Officer and will direct Univa's technology strategy as well as lead the company's growing EMEA business.

Grid Engine, a policy-driven workload and resource management system that automates workload distribution across a network of servers, is the most widely used system of its kind with over 4 million CPUs under management. The addition of Grid Engine technology and expertise directly supports Univa's data center optimization strategy by bolstering its workload and resource optimization capabilities, which already include the leading desktop management product, Grid MP.

"The first step to data center optimization is effective sharing of systems and workload distribution, and now Univa provides the leading resource management system as a primary element in our optimization stack," said Gary Tyreman, CEO of Univa. "Grid Engine is an area in which Univa has invested significant time and energy over the past 3 years, and we believe we are now best positioned to lead the pursuit of top HPC use cases and requirements that serve our most important customer sets. With this move, Grid Engine users gain a predictable and sustained future for Grid Engine that might not have been available otherwise."

"Combining the Grid Engine and Univa technology offerings was a once-in-a-lifetime opportunity that the new Univa EMEA team and I just couldn't miss," said Ferstl. "Now we'll be able to interact with and serve users worldwide investigating and understanding their data center optimization needs and providing the most innovative and enterprise-strength solutions to meet those needs."

Univa now offers the broadest and most innovative set of product capabilities for optimizing data center efficiency. Univa software continuously and dynamically optimizes an organization's efficiency with respect to workload and resources, people and processes, and application and license usage. This unique approach helps organizations earn rapid ROI through faster time-to-results and by keeping larger costs under control.

"Univa can now claim the most comprehensive set of category-leading products," added Tyreman. "We offer Grid Engine, the leading workload management solution; Grid MP, the leading desktop solution; and UniCloud, the leading dynamic cloud management software stack."

"I'm very excited by Univa providing continuity and ongoing support for Grid Engine," said Wolfgang Gentzsch, former CEO and President of Genias Software which originally developed the Grid Engine software acquired by Sun. "This is clearly a win-win-win situation: GE's thousands of users now have access to enterprise-class support at Univa, Univa customers benefit from the extended capabilities now available for fully optimizing data center efficiency; and the GE open source community can rest assured that robust development will continue thanks to Univa's commitment to the project."

"Univa developing and supporting Grid Engine is welcome news for the GE community," said Ian Foster, Professor of Computer Science and Director of the Computation Institute at the University of Chicago and Argonne National Laboratory. "This move by Univa brings with it a new competitive spirit and sense of innovation to a market that continuously benefits from pushing the envelope."

"This move propels Univa into a lead position in both the data center optimization and workload management spaces," said Steve Tuecke, co-founder of Univa and Deputy Director of the Computation Institute at University of Chicago and Argonne National Laboratory. "We selected Grid Engine as a core part of Univa's software stack almost five years ago due to its market leading feature set, large user community and vibrant open source community, all backed by a fantastic engineering team. Now that key members of the Grid Engine team are part of Univa, it seems a no-brainer for Grid Engine users to go with Univa for ongoing GE technology and services, as well as the broader data center optimization stack Univa has built around GE."

For additional quotes/reactions from the user and technology community, visit: http://www.univa.com/about/quotes.php.

Grid Engine support is available immediately from Univa, and the Univa version of the product will be available by end of Q1 2011. For more information about Univa's Grid Engine offering, including options for current Grid Engine users, visit http://www.univa.com/products/grid-engine.php.

About Univa Corporation

Univa, the Data Center Optimization Company, is the leading provider of optimization and management software for traditional, dynamic and cloud data centers. Our award-winning products are used by Global 2500 companies to improve resource sharing, amplify the efficiency of people and processes, and increase application and license utilization. Univa offers the industry's broadest, most innovative and integrated product set for managing shared, high-demand data center resources. From workload management to policy-driven provisioning across physical, virtual and cloud resources, only Univa provides a proven combination of enterprise-class capabilities, industry expertise, and community sponsorship. Univa is headquartered in Lisle, Illinois with offices worldwide.

SC10 was fascinating…of course. The world's largest supercomputing convention is always a great barometer of the HPC industry. It gives you a look at what's happening now, and where the industry is going (in case you weren't there, the words "cloud" and "exascale" were in wide use.) This year, SC also provided a great barometer of the progress of the Intel Cluster Ready architecture and the ecosystem building around it. That’s because it was the venue for our second annual Partner Appreciation Awards ceremony.

One thing I found particularly gratifying about the presentations this year is that several of the key awards centered around real-world solutions that are having an impact in the marketplace. The awards also highlighted the behind-the-scenes contributions of some HPC vendors that are breaking new ground in the small-to-mid-range HPC market.  These guys are doing some very cool things and they don’t always get the recognition they deserve. Take a look at the award-winning vendors below, and click on the links if you want to know more. I think you’ll be intrigued by the scope and value of their offerings.

Just for the record, we gave awards in three different categories:

• Pioneer Awards, honoring early adopters and promoters of Intel Cluster Ready.
• Pathfinder Awards, to distinguish those who are working with Intel Cluster Ready to forge new paths into previously unexplored markets.
• Explorer Awards, for those who have continued to explore and implement new programs to advance solutions based on the Intel Cluster Ready architecture.

Here’s the list of the 2010 award winners. Enjoy!

Solution 1 - The Seismic Coverage Validation Engine from Landmark is a preconfigured supercomputing solution for oil exploration that is expanding the use of HPC methods into smaller shops. And the award winners are:

• Landmark (Pioneer) delivers the complete appliance, the Seismic Coverage Validation Engine
• Appro (Pathfinder) furnishes the hardware (32 nodes and up) with its Ready-To-Go Clusters

Solution 2 - A number of vendors helped Simpson Strong-Tie deploy a new cluster in just two days, enabling the company’s engineers to run more complex models and get results two to three times faster, while halving the data center footprint and reducing total costs. (Read the case study.)

• SIMULIA (Explorer) provided the simulation software (Abaqus/Explicit) and the pre-sales benchmark testing that closed the deal.
• Silicon Mechanics (Explorer) furnished the hardware with its Hyperform HPCi for Intel Cluster Ready.
• Platform Computing (Pathfinder) has also optimized its PCM middleware for the Intel Cluster Ready architecture, providing a simple cluster management environment for non-expert HPC users.

Solution 3 - Two vendors were particularly instrumental in helping the University of Plymouth deploy a cluster to support ground-breaking research into renewable energy through wave farming.

• Viglen (Explorer) delivered the hardware optimized for out-of-the-box simulations.
• Concurrent Thinking (Pathfinder) provided SmartCluster, designed for complete cluster software provisioning with one-click Intel Cluster Ready validation.

Driving the Market Forward (other behind-the-scenes contributors)

• ANSYS (Pathfinder) is accelerating the adoption of HPC in smaller design shops, by proving the value of its simulation solutions running on Intel Cluster Ready certified clusters through in-house benchmarking.
• Clustercorp (Pathfinder) has optimized its ROCKS+ middleware for the Intel Cluster Ready architecture. ROCKS+ now enables exceptionally simple provisioning and build of certified clusters.
• Mellanox Technologies (Pioneer) and the HPC Advisory Council, which was founded by Mellanox, are delivering a range of compliant fabric solutions, along with installation guides for open source applications on Intel Cluster Ready clusters.
• QLogic (Pathfinder) provides fabric solutions optimized for the Intel Cluster Ready architecture, and has been instrumental in early testing and benchmarking of Intel MPI 4.0 on its InfiniBand hardware.

Honorable Mention
A lot of additional vendors are focused on the Intel Cluster Ready architecture, and are delivering significant new technologies and products. A handful of them received honorable mention awards, including:

• Bright Computing: Bright Cluster Manager for the Intel Cluster Ready architecture
• ClusterVision: Responsible for an array of Intel Cluster Ready cluster deployments
• Fujitsu Technology Solutions: Now providing a range of certified cluster products.
• ICON: Driving new market penetration by promoting Intel Cluster Ready for digital simulation.
• Panasas: High-performance parallel storage solutions
• SGI: A family of Intel Cluster Ready certified solutions, including its innovative Octane III desk-side cluster.
• Transtec: Responsible for a significant number of critical, real-world implementations.

That's it for this year's winners. I'd like to add my personal thanks to all of them. Stay tuned for more information. I’ll be focusing in on some of these technologies and solutions in more detail in future blogs.

>> Learn more about Intel Cluster Ready HPC solutions