|By Steve Neuner, Dan Higgins||
|May 18, 2004 12:00 AM EDT||
Previous notions of limited scalability of Linux were abruptly changed last year by the introduction of the SGI Altix server, which scaled up to 64 processors within a single system image (SSI). Today, large-scale Linux servers with hundreds of processors are being deployed by a variety of businesses, universities, research centers, and governments around the world. NASA Ames Research Center, for example, continues to push the limits even further with their 512-processor system running a single instance of the Linux kernel.
This article examines the challenges in enabling large numbers of processors to work efficiently together to better support Linux system configurations for High- Performance Computing (HPC) environments. We will explain what scaling is, the importance of good hardware design, and the kernel changes that make scaling Linux on systems up to 256 processors and beyond possible. Finally, we will show examples of how these highly scalable Linux systems are being used to solve complex real-world problems more efficiently.
Scaling Within HPC EnvironmentsFirst, let's examine the issues behind system scalability. The term scaling refers to the ability to add more hardware resources, such as processors or memory, to improve the capacity and performance of a system. There are different strategies used for scaling systems depending on the workload requirements. Enterprise business server workloads, for example, often consist of many individual, unrelated tasks that are typically deployed on systems that are smaller in nature and networked together. HPC workloads, on the other hand, are composed of scientific programs that require a high degree of complex processing, process large amounts of data, and have widely fluctuating resource requirements. Because of their demanding resource requirements, HPC programs are written and parallelized to break complex problems down to enable them to leverage system resources in parallel.
One approach used to solve HPC problems is horizontal scaling. With this approach, a program's threads run across a "cluster" of separate systems, and these threads communicate and exchange data over the network. This strategy can be used for workloads that are embarrassingly parallel, where little communication is required between program threads as they perform their computations. However, when program threads need to interact while working on a common set of data, vertical scaling provides a more efficient and better approach. With vertical scaling, threads run on a large number of CPUs all within one system, enabling processors to communicate more efficiently and to also operate upon and exchange data using global shared memory. Adding more processors to the system enables more threads to run simultaneously, thereby enabling more resources to be applied and shared to solve a problem. Vertical scaling also provides an ideal environment for using an HPC system as a central server to dynamically run different HPC programs at the same time when any one program either doesn't actually need all of the system processors or has its own scaling limitations. Whether greater processing capability for a single HPC program is required, or increasing throughput for several different HPC programs running at once, a properly designed vertically scaled system provides a flexible and superior environment for both the most demanding and the widest range of HPC applications.
Hardware Design and ScalabilityPerfect scaling occurs when the number of processors added improves the workload throughput by the same factor. For instance, a four-processor system should theoretically improve processing power fourfold compared to a single processor system. In a multiprocessor system, it is critical to minimize the overhead involved with coordinating among multiple processors and utilizing shared resources. We say, "the system is scaling linearly at 90 percent up to 4 processors" if adding a second processor improves system performance by 1.8X, adding a third processor yields a 2.7X improvement, and adding a fourth processor yields an improvement of 3.6X over a single CPU. As more processors are added to a system, often a point is reached where performance no longer improves or even decreases due to hardware, kernel, or application software limitations. The goal is to improve performance by enabling multiple CPUs to scale as close to perfect as possible, and to the highest possible numbers of CPUs.
One of the keys to obtaining maximum performance is a fast system bus with high bandwidth. The extreme processing power provided by hundreds of high-performance CPUs requires multiple fast paths for handling data between CPUs, caches, memory, and I/O. The system bus found on symmetric multiprocessing systems can quickly become a bottleneck since all traffic from the CPUs uses a single, common bus to access and transfer data. Much higher system performance is available using a non-uniform memory access (NUMA) architecture since CPU accesses to memory within the same node will distribute and reduce the load on the system interconnect (see Figure 1).
A well-designed NUMA system will carefully account for the CPU bus transfer speeds, number of CPUs on any given bus, memory transfer speeds, multiple paths, and other factors to ensure that maximum overall bandwidth can be delivered throughout the system. Drawing an imaginary line through the middle of a system to examine its maximum capacity for transferring data between two halves is called bisectional bandwidth. Figure 2 shows the system bus interconnect for an SGI Altix system designed for overall maximum bisectional bandwidth and performance. In this diagram, each C-brick is a rack-mountable module containing four CPUs and each R-brick is an SGI NUMAlink module used to connect together and make a 128p SGI Altix system.
A computer architecture that is well balanced and built for maximum performance is essential to achieving good system scalability. If the hardware doesn't scale, neither will the Linux kernel or the user's application.
Linux Kernel ScalabilityLinux was originally designed for smaller systems. Extending Linux to scale well on large systems involves extending various sizes and tables managed by the kernel, and then optimizing the performance for high-end technical computing. Thanks to the solid design and wide community support, Linux has adapted well to large systems.
SGI kernel engineers found that while they were clearly the first to run Linux on large system configurations of this kind, the Linux community had already done an excellent job reworking and addressing many of the issues related to Linux scalability. The types of changes made by SGI and others within the community include extending resource counters sizes, extending bit-mask sizes, and fixing commands and tools to support more than double-digit CPU numbers. Other changes included adding NUMA tool commands to help manage larger memory sizes more efficiently, increasing the limit on open file descriptors and on file sizes, and reducing boot time console messages generated by each processor, since administrating and troubleshooting would otherwise be unmanageable on systems with large CPU counts.
Once the kernel was modified to accommodate the resources of a larger system, SGI engineers focused on getting Linux to scale and perform well. One way to find scaling problems for a 256-processor system is to turn up the stress knobs while using a much larger configuration, such as a 512-processor system. Problems that otherwise would be difficult to pinpoint become obvious. Developing and testing on these larger configurations enabled the SGI engineering team to find and fix many problems that affect all multiprocessor systems of all sizes. SGI kernel engineers used several large configurations in this manner to run a variety of different HPC applications, benchmarks, and custom tests to identify and diagnose Linux scaling problems. Figure 3 shows an early 512 processor SGI Altix system, ascender, which was used by SGI kernel engineers to find and fix scaling problems.
Such testing uncovered a number of areas to change for improving scalability. For example, some system-wide kernel variables were converted to per-processor variables. This reduces memory contention on shared data such as global kernel performance statistics, since this data could be maintained separately, then combined only when needed for reporting purposes. Other scaling improvements included finding and eliminating high-contention spinlocks, reducing spinlock contention in timer routines, optimizing process scheduling algorithms, changes in the buffer cache to use per-node data structures, improved translation lookaside buffer algorithms, improved parallelism of page fault and out-of-memory handling, and identifying and removing hot cache lines due to false sharing.
Bringing It All TogetherA well-designed hardware system combined with the Linux optimizations described here enables hundreds of processors within a system to access, use, and manipulate shared resources in the most efficient manner possible, enabling users' HPC programs to fully exploit the available system resources to do real work. The following three examples demonstrate the dramatic scaling and performance improvements being achieved with Linux on systems with processor counts of 128, 256, and larger.
The first example (see Figure 4) shows how adding processors to a system can dramatically reduce the elapsed time for the bioinformatics HPC application HTC-BLAST (High Throughput Computing - Basic Logical Alignment Search Tool) to process 10,000 queries with 4,111,677 total letters on a human genome database with 545 sequences and 2,866,452,029 total letters. In particular, notice that a system with 128 processors ran 1.77X faster than a system with 64 processors.
The next example (see Figure 5) shows the scaling and performance improvements achieved using a computation fluid dynamics application on an automobile external flow problem with a model size of 100 million cells. In this case the total elapsed time continues to decrease as the system configuration is extended from 64 to 256 processors.
Finally, the third example (see Figure 6) shows scaling results for an OpenMP code called Cart3D, developed and used extensively by the NASA Ames Research Center to study flows for the space shuttle. NASA Ames Research Center, known for pushing the limits of computing in pursuit of fundamental science, achieved almost 90% scaling efficiency while running this HPC code on a 512-processor SGI Altix system. SGI and NASA engineers collaborated to identify and fix many Linux scaling issues to achieve a dramatic new breakthrough on system scalability with Linux. The NASA Ames Research Center's system used for this work is shown in Figure 7.
SummaryThe performance and capabilities of Linux for server environments have improved dramatically in just the last year. Scientists and others are now routinely using single-system Linux configurations with hundreds of processors to solve complex problems faster and with greater ease than had been thought possible. Testing and developing on these large configurations have proven invaluable for improving the reliability and performance of Linux on configurations of all sizes. The synergy of these scaling improvements combined with the open development model has enabled the continued advancement of Linux to become the superior operating system choice for delivering performance and stability in all environments.
The Internet of Things will greatly expand the opportunities for data collection and new business models driven off of that data. In her session at Internet of @ThingsExpo, Esmeralda Swartz, CMO of MetraTech, will discuss how for this to be effective you not only need to have infrastructure and operational models capable of utilizing this new phenomenon, but increasingly service providers will need to convince a skeptical public to participate. Get ready to show them the money! Speaker Bio: ...
Oct. 24, 2014 09:30 PM EDT Reads: 1,001
Compute virtualization has been transformational, yet security policy implementation and enforcement has lagged behind in agility and automation. There are a number of key considerations when implementing policy in private and hybrid clouds. In his session at 15th Cloud Expo, Holland Barry, VP of Technology at Catbird, will discuss the impact of this new paradigm and what organizations can do today to safely move to software-defined network and compute architectures, including: How normal ope...
Oct. 24, 2014 07:00 PM EDT Reads: 1,409
Samsung VP Jacopo Lenzi, who headed the company's recent SmartThings acquisition under the auspices of Samsung's Open Innovaction Center (OIC), answered a few questions we had about the deal. This interview was in conjunction with our interview with SmartThings CEO Alex Hawkinson. IoT Journal: SmartThings was developed in an open, standards-agnostic platform, and will now be part of Samsung's Open Innovation Center. Can you elaborate on your commitment to keep the platform open? Jacopo Lenzi: S...
Oct. 23, 2014 11:45 PM EDT Reads: 2,576
How do APIs and IoT relate? The answer is not as simple as merely adding an API on top of a dumb device, but rather about understanding the architectural patterns for implementing an IoT fabric. There are typically two or three trends: Exposing the device to a management framework Exposing that management framework to a business centric logic • Exposing that business layer and data to end users. This last trend is the IoT stack, which involves a new shift in the separation of what stuff hap...
Oct. 23, 2014 07:45 PM EDT Reads: 1,594
SYS-CON Events announced today that SOA Software, an API management leader, will exhibit at SYS-CON's 15th International Cloud Expo®, which will take place on November 4–6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. SOA Software is a leading provider of API Management and SOA Governance products that equip business to deliver APIs and SOA together to drive their company to meet its business strategy quickly and effectively. SOA Software’s technology helps businesses to accel...
Oct. 23, 2014 06:15 PM EDT Reads: 1,620
SYS-CON Events announced today that Utimaco will exhibit at SYS-CON's 15th International Cloud Expo®, which will take place on November 4–6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Utimaco is a leading manufacturer of hardware based security solutions that provide the root of trust to keep cryptographic keys safe, secure critical digital infrastructures and protect high value data assets. Only Utimaco delivers a general-purpose hardware security module (HSM) as a customiz...
Oct. 23, 2014 05:45 PM EDT Reads: 1,543
Almost everyone sees the potential of Internet of Things but how can businesses truly unlock that potential. The key will be in the ability to discover business insight in the midst of an ocean of Big Data generated from billions of embedded devices via Systems of Discover. Businesses will also need to ensure that they can sustain that insight by leveraging the cloud for global reach, scale and elasticity.
Oct. 22, 2014 09:00 PM EDT Reads: 1,451
SYS-CON Events announced today that ElasticBox is holding a Hackathon at DevOps Summit, November 6 from 12 pm -4 pm at the Santa Clara Convention Center in Santa Clara, CA. You can enter as an individual or team of up to 10 developers. A New Star Is Born Every Month! All completed ElasticBoxes will then be sent to a judging panel - 12 winners will be featured on the ElasticBox website in 2015. All entrants will receive five full enterprise licenses for one year + ElasticBox headphones + Elasti...
Oct. 22, 2014 01:00 PM EDT Reads: 1,527
Once the decision has been made to move part or all of a workload to the cloud, a methodology for selecting that workload needs to be established. How do you move to the cloud? What does the discovery, assessment and planning look like? What workloads make sense? Which cloud model makes sense for each workload? What are the considerations for how to select the right cloud model? And how does that fit in with the overall IT tranformation? In his session at 15th Cloud Expo, John Hatem, head of V...
Oct. 22, 2014 12:00 PM EDT Reads: 1,551
Cloud services are the newest tool in the arsenal of IT products in the market today. These cloud services integrate process and tools. In order to use these products effectively, organizations must have a good understanding of themselves and their business requirements. In his session at 15th Cloud Expo, Brian Lewis, Principal Architect at Verizon Cloud, will outline key areas of organizational focus, and how to formalize an actionable plan when migrating applications and internal services to...
Oct. 22, 2014 11:45 AM EDT Reads: 1,576
SAP is delivering break-through innovation combined with fantastic user experience powered by the market-leading in-memory technology, SAP HANA. In his General Session at 15th Cloud Expo, Thorsten Leiduck, VP ISVs & Digital Commerce, SAP, will discuss how SAP and partners provide cloud and hybrid cloud solutions as well as real-time Big Data offerings that help companies of all sizes and industries run better. SAP launched an application challenge to award the most innovative SAP HANA and SAP ...
Oct. 22, 2014 07:00 AM EDT Reads: 1,673
Ixia develops amazing products so its customers can connect the world. Ixia helps its customers provide an always-on user experience through fast, secure delivery of dynamic connected technologies and services. Through actionable insights that accelerate and secure application and service delivery, Ixia's customers benefit from faster time to market, optimized application performance and higher-quality deployments.
Oct. 21, 2014 09:00 PM EDT Reads: 1,510
SYS-CON Events announced today that Calm.io has been named “Bronze Sponsor” of DevOps Summit Silicon Valley, which will take place on November 4–6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Calm.io is a cloud orchestration platform for AWS, vCenter, OpenStack, or bare metal, that runs your CL tools puppet, Chef, shell, git, Jenkins, nagios, and will soon support New Relic and Docker. It can run hosted, or on premise and provides VM automation / expiry, self-service portals,...
Oct. 21, 2014 08:45 PM EDT Reads: 1,456
In her General Session at 15th Cloud Expo, Anne Plese, Senior Consultant, Cloud Product Marketing, at Verizon Enterprise, will focus on finding the right mix of renting vs. buying Oracle capacity to scale to meet business demands, and offer validated Oracle database TCO models for Oracle development and testing environments. Anne Plese is a marketing and technology enthusiast/realist with over 19+ years in high tech. At Verizon Enterprise, she focuses on driving growth for the Verizon Cloud pla...
Oct. 21, 2014 07:30 PM EDT Reads: 1,548
SYS-CON Events announced today that Aria Systems, the recurring revenue expert, has been named "Bronze Sponsor" of SYS-CON's 15th International Cloud Expo®, which will take place on November 4-6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Aria Systems helps leading businesses connect their customers with the products and services they love. Industry leaders like Pitney Bowes, Experian, AAA NCNU, VMware, HootSuite and many others choose Aria to power their recurring revenue bu...
Oct. 21, 2014 06:00 PM EDT Reads: 1,541
The Internet of Things (IoT) is going to require a new way of thinking and of developing software for speed, security and innovation. This requires IT leaders to balance business as usual while anticipating for the next market and technology trends. Cloud provides the right IT asset portfolio to help today’s IT leaders manage the old and prepare for the new. Today the cloud conversation is evolving from private and public to hybrid. This session will provide use cases and insights to reinforce t...
Oct. 21, 2014 05:15 PM EDT Reads: 1,610
As Platform as a Service (PaaS) matures as a category, developers should have the ability to use the programming language of their choice to build applications and have access to a wide array of services. Bluemix is IBM's open cloud development platform that enables users to easily build cloud-based, creative mobile and web applications without having to spend large amounts of time and resources on configuring infrastructure and multiple software licenses. In this track, you will learn about the...
Oct. 21, 2014 05:00 PM EDT Reads: 1,567
Blue Box has closed a $10 million Series B financing. The round was led by a strategic investor and included participation from prior investors including Voyager Capital and Founders Collective, as well as the Blue Box executive team. This round follows a $4.3 million Series A closed in December of 2012 and led by Voyager Capital. In May of this year, the company announced general availability of its private cloud as a service offering, Blue Box Cloud. Since that release, the company has dem...
Oct. 21, 2014 01:45 PM EDT Reads: 1,614
SYS-CON Events announced today that Verizon has been named "Gold Sponsor" of SYS-CON's 15th International Cloud Expo®, which will take place on November 4-6, 2014, at the Santa Clara Convention Center in Santa Clara, CA. Verizon Enterprise Solutions creates global connections that generate growth, drive business innovation and move society forward. With industry-specific solutions and a full range of global wholesale offerings provided over the company's secure mobility, cloud, strategic network...
Oct. 21, 2014 09:30 AM EDT Reads: 1,663
SimpleECM is the only platform to offer a powerful combination of enterprise content management (ECM) services, capture solutions, and third-party business services providing simplified integrations and workflow development for solution providers. SimpleECM is opening the market to businesses of all sizes by reinventing the delivery of ECM services. Our APIs make the development of ECM services simple with the use of familiar technologies for a frictionless integration directly into web applicat...
Oct. 20, 2014 10:00 PM EDT Reads: 1,776