Open Source Cloud Authors: Zakia Bouachraoui, Elizabeth White, Liz McMillan, Yeshim Deniz, Pat Romanski

Related Topics: Open Source Cloud

Open Source Cloud: Article

Achieving High Performance at Low Cost

The Dual Core Commodity Cluster Advantage

Advances in clustering technology have redefined the price-to-performance curve for many High Performance Computing (HPC) application areas. The use of specialized high-speed interconnects and fast commodity processors have pushed the envelope to where it is today.

Not all applications need this level of hardware (and cost) to achieve leading-edge price to performance. Indeed, there have been several technological advances that may invite a step back from the traditional edge-of-technology approach to HPC clustering. These advances include the following developments:

  • Introduction of low-cost high-performance multi-core processors
  • Introduction of high-density motherboards and packaging solutions
  • Introduction of optimized Linux Gigabit Ethernet performance
Of particular importance is the fact that these advances are in the commodity sector where high demand and economies of scale have created reasonable price points. Furthermore, alternative high-cost approaches that employ enhanced interconnects and multi-socket motherboards may not be required for certain application classes. Users in this category can expect the commodity approach to deliver new levels of industry-leading price to performance.

In this article, we will discuss how these advances can be used to optimize cluster performance. In addition, we will highlight application areas where these types of clusters are expected to provide optimum performance.

Gaining the Multi-Core Advantage
The multi-core revolution is here. All major processor families have begun using multiple CPU cores to enhance performance. Currently, dual core processors are available at various performance and price levels. Remarkably, most HPC users can immediately benefit from these advances, as most HPC cluster software is designed to use multiple processors.

Specifically, current dual core designs allow HPC users to effectively double the number of processing units while still enjoying traditional commodity price points. In the HPC market, more CPUs are always welcome, but the right design (choice of processor, motherboard, and packaging) is critical to achieving the desired performance.

The recently introduced Pentium D (Presler) processor and Xeon 3000 processers from Intel are examples of commodity high-performance processors. The Presler series is a dual core processor manufactured using the latest 65nm process and is currently available at speeds up to 3.40 GHz. More important for HPC users is that each Presler has a total of 4MB of on-chip cache that it divides evenly between the two cores (2MB each). These caches are fed using an 800MHz FSB and DDR2 memory.

In the HPC cluster sector, the processor battle has typically been between the high-end Intel Xeon or the AMD Opteron. Little consideration has been given to "lesser processors" in the HPC space. As this report will show, this assumption may not hold when actual price and performance numbers are determined.

Check the Numbers - Presler Is on Top
The SPEC benchmarks are usually a good rating of overall processors performance. Table 1 shows the SPEC benchmarks for an Intel Pentium D (model 940) and an AMD Opteron (model 270). Pentium D 940 performs at a level 10% greater than the Opteron 270, yet at this point in time, it's priced at half the cost of an Opteron 270.

While the SPEC benchmarks are an important yardstick, real application benchmarks often provide a second data point with which to compare processors. The GROMACS molecular dynamics package is known to push processors very hard and is therefore a good test of overall number-crunching capability. The results shown in Table 2 are for the Gromacs Benchmark Suite (Linux Version 3.3). See the references at the end of this article for more information on GROMACS. All results are normalized to the Pentium D (lower means slower) and were run using one processor.

The results show a substantial performance advantage over the Opteron 270 processor. The Opteron 270 numbers were taken from the Gromacs Web site (www.gromacs.org).

Breakthrough Design - The Caretta Motherboard
When designing clusters, the "more is better" model often works. However, the number of processors (and hence cores) that can be placed on a motherboard needs to be considered carefully. Modern cluster designs currently take advantage of dual socket motherboards and single core processors. While this approach has helped improve processor density, extending this design with dual cores may have some unexpected results. Using dual core processors on dual socket motherboards requires that the memory subsystems and interconnect now service four cores (instead of two) at the same time.

This situation can, in certain cases, seriously degrade the maximum achievable performance of each core. Optimizing onboard memory subsystems is one way to mitigate memory contention, but this approach also introduces a "nonlocal" or NUMA (Non-uniform Memory Access) type of memory structure. In the end, the application determines the best approach, but rethinking the dense core motherboard approach may have some advantages.

A potentially more optimal solution for many applications would be a small single socket motherboard on which a dual core processor can reside. Such a system would resemble current dual socket motherboards/single core clusters designs in use today, on which memory and interconnect contention is well understood.

The recent introduction of the Intel Caretta motherboard (S3000PT) has been designed to fill this need. The Caretta motherboard supports the Intel Xeon 3000, Pentium D, and Pentium 4 processors, four DIMM slots (DDR2 533/667 with ECC, two-way interleaved, unbuffered), Integrated two port SATA 3.0Gb/s with RAID 0 &1, an ATI ES1000 (16MB), Dual Gigabit Ethernet LAN, and a 5.95 inch x13 inch Form Factor. Interestingly, the Form Factor is one half the size of an Extended ATX motherboard (12"x13"). These dimensions allow a standard Rack Mount ATX enclosure to hold two Caretta motherboards.

The Caretta allows the density found on dualcore/dualsocket motherboards, but provides each processor with its own local memory environment.

This approach has further advantages as well. As more cores/processors are placed on the motherboard, a node failure (motherboard/power supply/hard drive) removes all the cores/processors from the cluster. By using a separate motherboard for each processor, failures are limited to two cores (one processor).

The HyperBlade Advantage
When deploying a high density production HPC cluster, correct system packaging will ensure continuous operation. While many users find utility in deploying 1U server packaging solutions, blade systems are designed with a higher level of custom integration. Blades are typically easier to manage, but more expensive that 1U servers. A hybrid solution where commodity components can be packaged in a blade-like fashion has been developed by Appro International. The advantages of this solution include the use of commodity components inside the "blade" and the integration and manageability of bladed systems.

Like blades, the Appro HyperBlades are modular servers plugged into a common backplane that eliminates cable clutter. By using a vertical mount approach, the Appro HyperBlade offers an enhanced density, providing up to 50 servers in a standard 42U rack cabinet. Large and smaller rack systems are available as well. Because the HyperBlade is designed to include the flexibility of a typical 1U server, high speed interconnects options - including Myrinet, Dolphin, Quadrics and InfiniBand™ - are easily deployed.

In addition, HyperBlades offer the power advantage of 1U servers while, at the same time, they provide an integrated power control and serial management capability found in more expensive blade systems. Finally, each Appro HyperBlade can hold two Caretta motherboards, thus providing excellent processor density (four cores per HyperBlade) and easy management.

The Gigabit Ethernet Advantage
While there are many choices for cluster interconnects, the preferred and lowest cost option is Gigabit Ethernet. While often dismissed as underpowered for today's clusters, actual tests show the exact opposite is true for some application classes. Shown in Figure 1 is a NetPIPE TCP throughput graph for a Gigabit Ethernet link between two Pentium D 940 processors.

The connection used an onboard Intel 82573 chipset, an e1000 driver, and a 1500 byte MTU. It should be noted that the single byte latency was 36 microseconds. Not all applications can scale well with this level of performance. However, there are many that will find commodity Gigabit Ethernet more than adequate for their computing needs.

More Stories By Douglas Eadline

Dr. Douglas Eadline has over 25 years of experience in high-performance computing. You can contact him through Basement Supercomputing (http://basement-supercomputing.com).

Comments (0)

Share your thoughts on this story.

Add your comment
You must be signed in to add a comment. Sign-in | Register

In accordance with our Comment Policy, we encourage comments that are on topic, relevant and to-the-point. We will remove comments that include profanity, personal attacks, racial slurs, threats of violence, or other inappropriate material that violates our Terms and Conditions, and will block users who make repeated violations. We ask all readers to expect diversity of opinion and to treat one another with dignity and respect.

IoT & Smart Cities Stories
The challenges of aggregating data from consumer-oriented devices, such as wearable technologies and smart thermostats, are fairly well-understood. However, there are a new set of challenges for IoT devices that generate megabytes or gigabytes of data per second. Certainly, the infrastructure will have to change, as those volumes of data will likely overwhelm the available bandwidth for aggregating the data into a central repository. Ochandarena discusses a whole new way to think about your next...
CloudEXPO | DevOpsSUMMIT | DXWorldEXPO are the world's most influential, independent events where Cloud Computing was coined and where technology buyers and vendors meet to experience and discuss the big picture of Digital Transformation and all of the strategies, tactics, and tools they need to realize their goals. Sponsors of DXWorldEXPO | CloudEXPO benefit from unmatched branding, profile building and lead generation opportunities.
DXWorldEXPO LLC announced today that Big Data Federation to Exhibit at the 22nd International CloudEXPO, colocated with DevOpsSUMMIT and DXWorldEXPO, November 12-13, 2018 in New York City. Big Data Federation, Inc. develops and applies artificial intelligence to predict financial and economic events that matter. The company uncovers patterns and precise drivers of performance and outcomes with the aid of machine-learning algorithms, big data, and fundamental analysis. Their products are deployed...
All in Mobile is a place where we continually maximize their impact by fostering understanding, empathy, insights, creativity and joy. They believe that a truly useful and desirable mobile app doesn't need the brightest idea or the most advanced technology. A great product begins with understanding people. It's easy to think that customers will love your app, but can you justify it? They make sure your final app is something that users truly want and need. The only way to do this is by ...
Digital Transformation and Disruption, Amazon Style - What You Can Learn. Chris Kocher is a co-founder of Grey Heron, a management and strategic marketing consulting firm. He has 25+ years in both strategic and hands-on operating experience helping executives and investors build revenues and shareholder value. He has consulted with over 130 companies on innovating with new business models, product strategies and monetization. Chris has held management positions at HP and Symantec in addition to ...
Dynatrace is an application performance management software company with products for the information technology departments and digital business owners of medium and large businesses. Building the Future of Monitoring with Artificial Intelligence. Today we can collect lots and lots of performance data. We build beautiful dashboards and even have fancy query languages to access and transform the data. Still performance data is a secret language only a couple of people understand. The more busine...
Cell networks have the advantage of long-range communications, reaching an estimated 90% of the world. But cell networks such as 2G, 3G and LTE consume lots of power and were designed for connecting people. They are not optimized for low- or battery-powered devices or for IoT applications with infrequently transmitted data. Cell IoT modules that support narrow-band IoT and 4G cell networks will enable cell connectivity, device management, and app enablement for low-power wide-area network IoT. B...
The hierarchical architecture that distributes "compute" within the network specially at the edge can enable new services by harnessing emerging technologies. But Edge-Compute comes at increased cost that needs to be managed and potentially augmented by creative architecture solutions as there will always a catching-up with the capacity demands. Processing power in smartphones has enhanced YoY and there is increasingly spare compute capacity that can be potentially pooled. Uber has successfully ...
SYS-CON Events announced today that CrowdReviews.com has been named “Media Sponsor” of SYS-CON's 22nd International Cloud Expo, which will take place on June 5–7, 2018, at the Javits Center in New York City, NY. CrowdReviews.com is a transparent online platform for determining which products and services are the best based on the opinion of the crowd. The crowd consists of Internet users that have experienced products and services first-hand and have an interest in letting other potential buye...
When talking IoT we often focus on the devices, the sensors, the hardware itself. The new smart appliances, the new smart or self-driving cars (which are amalgamations of many ‘things'). When we are looking at the world of IoT, we should take a step back, look at the big picture. What value are these devices providing. IoT is not about the devices, its about the data consumed and generated. The devices are tools, mechanisms, conduits. This paper discusses the considerations when dealing with the...