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Chapter: Distributed and Cloud Computing: From Parallel Processing to the Internet of Things : Computer Clusters for Scalable Parallel Computing

Computer Clusters and MPP Architectures

1. Cluster Organization and Resource Sharing 2. Node Architectures and MPP Packaging 3. Cluster System Interconnects 4. Hardware, Software, and Middleware Support 5. GPU Clusters for Massive Parallelism



Most clusters emphasize higher availability and scalable performance. Clustered systems evolved from the Microsoft Wolfpack and Berkeley NOW to the SGI Altix Series, IBM SP Series, and IBM Roadrunner. NOW was a UC Berkeley research project designed to explore new mechanisms for clustering of UNIX workstations. Most clusters use commodity networks such as Gigabit Ethernet, Myrinet switches, or InfiniBand networks to interconnect the compute and storage nodes. The clustering trend moves from supporting large rack-size, high-end computer systems to high-volume, desktop or deskside computer systems, matching the downsizing trend in the computer industry.


1. Cluster Organization and Resource Sharing


In this section, we will start by discussing basic, small-scale PC or server clusters. We will discuss how to construct large-scale clusters and MPPs in subsequent sections.


1.1 A Basic Cluster Architecture


Figure 2.4 shows the basic architecture of a computer cluster over PCs or workstations. The figure shows a simple cluster of computers built with commodity components and fully supported with desired SSI features and HA capability. The processing nodes are commodity workstations, PCs, or servers. These commodity nodes are easy to replace or upgrade with new generations of hardware. The node operating systems should be designed for multiuser, multitasking, and multithreaded applications. The nodes are interconnected by one or more fast commodity networks. These net-works use standard communication protocols and operate at a speed that should be two orders of magnitude faster than that of the current TCP/IP speed over Ethernet.


The network interface card is connected to the nodes standard I/O bus (e.g., PCI). When the processor or the operating system is changed, only the driver software needs to change. We desire to have a platform-independent cluster operating system, sitting on top of the node platforms. But such a cluster OS is not commercially available. Instead, we can deploy some cluster middleware to glue together all node platforms at the user space. An availability middleware offers HA services. An SSI layer provides a single entry point, a single file hierarchy, a single point of control, and a

single job management system. Single memory may be realized with the help of the compiler or a runtime library. A single process space is not necessarily supported.


In general, an idealized cluster is supported by three subsystems. First, conventional databases and OLTP monitors offer users a desktop environment in which to use the cluster. In addition to running sequential user programs, the cluster supports parallel programming based on standard languages and communication libraries using PVM, MPI, or OpenMP. The programming environment also includes tools for debugging, profiling, monitoring, and so forth. A user interface sub-system is needed to combine the advantages of the web interface and the Windows GUI. It should also provide user-friendly links to various programming environments, job management tools, hypertext, and search support so that users can easily get help in programming the computer cluster.



1.2 Resource Sharing in Clusters


Supporting clusters of smaller nodes will increase computer sales. Clustering improves both avail-ability and performance. These two clustering goals are not necessarily in conflict. Some HA clusters use hardware redundancy for scalable performance. The nodes of a cluster can be connected in one of three ways, as shown in Figure 2.5. The shared-nothing architecture is used in most clusters, where the nodes are connected through the I/O bus. The shared-disk architecture is in favor of small-scale availability clusters in business applications. When one node fails, the other node takes over.


The shared-nothing configuration in Part (a) simply connects two or more autonomous computers via a LAN such as Ethernet. A shared-disk cluster is shown in Part (b). This is what most business clusters desire so that they can enable recovery support in case of node failure. The shared disk can hold checkpoint files or critical system images to enhance cluster availability. Without shared disks, checkpointing, rollback recovery, failover, and failback are not possible in a cluster. The shared-memory cluster in Part (c) is much more difficult to realize. The nodes could be connected by a scalable coherence interface (SCI) ring, which is connected to the memory bus of each node through an NIC module. In the other two architectures, the interconnect is attached to the I/O bus. The memory bus operates at a higher frequency than the I/O bus.


There is no widely accepted standard for the memory bus. But there are such standards for the I/O buses. One recent, popular standard is the PCI I/O bus standard. So, if you implement an NIC card to attach a faster Ethernet network to the PCI bus you can be assured that this card can be used in other systems that use PCI as the I/O bus. The I/O bus evolves at a much slower rate than the memory bus. Consider a cluster that uses connections through the PCI bus. When the processors are upgraded, the interconnect and the NIC do not have to change, as long as the new system still uses PCI. In a shared-memory cluster, changing the processor implies a redesign of the node board and the NIC card.


2. Node Architectures and MPP Packaging


In building large-scale clusters or MPP systems, cluster nodes are classified into two categories: compute nodes and service nodes. Compute nodes appear in larger quantities mainly used for large-scale searching or parallel floating-point computations. Service nodes could be built with different processors mainly used to handle I/O, file access, and system monitoring. For MPP clusters, the

compute nodes dominate in system cost, because we may have 1,000 times more compute nodes than service nodes in a single large clustered system. Table 2.3 introduces two example compute node architectures: homogeneous design and hybrid node design.


In the past, most MPPs are built with a homogeneous architecture by interconnecting a large number of the same compute nodes. In 2010, the Cray XT5 Jaguar system was built with 224,162 AMD Opteron processors with six cores each. The Tiahe-1A adopted a hybrid node design using two Xeon CPUs plus two AMD GPUs per each compute node. The GPU could be replaced by special floating-point accelerators. A homogeneous node design makes it easier to program and maintain the system.


Example 2.1 Modular Packaging of the IBM Blue Gene/L System

The Blue Gene/L is a supercomputer jointly developed by IBM and Lawrence Livermore National Labora-tory. The system became operational in 2005 with a 136 Tflops performance at the No. 1 position in the

Top-500 list—toped the Japanese Earth Simulator. The system was upgraded to score a 478 Tflops speed in 2007. By examining the architecture of the Blue Gene series, we reveal the modular construction of a scalable MPP system as shown in Figure 2.6. With modular packaging, the Blue Gene/L system is con-structed hierarchically from processor chips to 64 physical racks. This system was built with a total of 65,536 nodes with two PowerPC 449 FP2 processors per node. The 64 racks are interconnected by a huge 3D 64 x 32 x 32 torus network.


In the lower-left corner, we see a dual-processor chip. Two chips are mounted on a computer card. Sixteen computer cards (32 chips or 64 processors) are mounted on a node board. A cabinet houses 32 node boards with an 8 x 8 x 16 torus interconnect. Finally, 64 cabinets (racks) form the total system at the upper-right corner. This packaging diagram corresponds to the 2005 configuration. Cus-tomers can order any size to meet their computational needs. The Blue Gene cluster was designed to achieve scalable performance, reliability through built-in testability, resilience by preserving locality of failures and checking mechanisms, and serviceability through partitioning and isolation of fault locations.


3. Cluster System Interconnects


3.1 High-Bandwidth Interconnects


Table 2.4 compares four families of high-bandwidth system interconnects. In 2007, Ethernet used a 1 Gbps link, while the fastest InfiniBand links ran at 30 Gbps. The Myrinet and Quadrics perform in between. The MPI latency represents the state of the art in long-distance message passing. All four technologies can implement any network topology, including crossbar switches, fat trees, and torus networks. The InfiniBand is the most expensive choice with the fastest link speed. The Ethernet is still the most cost-effective choice. We consider two example cluster interconnects over 1,024 nodes in Figure 2.7 and Figure 2.9. The popularity of five cluster interconnects is compared in Figure 2.8.

Example 2.2 Crossbar Switch in Google Search Engine Cluster


Google has many data centers using clusters of low-cost PC engines. These clusters are mainly used to support Google’s web search business. Figure 2.7 shows a Google cluster interconnect of 40 racks of PC engines via two racks of 128 x 128 Ethernet switches. Each Ethernet switch can handle 128 one Gbps Ethernet links. A rack contains 80 PCs. This is an earlier cluster of 3,200 PCs. Google’s search engine clusters are built with a lot more nodes. Today’s server clusters from Google are installed in data centers with container trucks.


Two switches are used to enhance cluster availability. The cluster works fine even when one switch fails to provide the links among the PCs. The front ends of the switches are connected to the Internet via 2.4 Gbps OC 12 links. The 622 Mbps OC 12 links are connected to nearby data-center networks. In case of failure of the OC 48 links, the cluster is still connected to the outside world via the OC 12 links. Thus, the Google cluster eliminates all single points of failure.


3.2 Share of System Interconnects over Time


Figure 2.8 shows the distribution of large-scale system interconnects in the Top 500 systems from 2003 to 2008. Gigabit Ethernet is the most popular interconnect due to its low cost and market readiness. The InfiniBand network has been chosen in about 150 systems for its high-bandwidth performance. The Cray interconnect is designed for use in Cray systems only. The use of Myrinet and Quadrics networks had declined rapidly in the Top 500 list by 2008.

Example 2.3 Understanding the InfiniBand Architecture


The InfiniBand has a switch-based point-to-point interconnect architecture. A large InfiniBand has a layered architecture. The interconnect supports the virtual interface architecture (VIA) for distributed mes-saging. The InfiniBand switches and links can make up any topology. Popular ones include crossbars, fat trees, and torus networks. Figure 2.9 shows the layered construction of an InfiniBand network. According to Table 2.5, the InfiniBand provides the highest speed links and the highest bandwidth in reported large-scale systems. However, InfiniBand networks cost the most among the four interconnect technologies.


Each end point can be a storage controller, a network interface card (NIC), or an interface to a host system. A host channel adapter (HCA) connected to the host processor through a standard peripheral component inter-connect (PCI), PCI extended (PCI-X), or PCI express bus provides the host interface. Each HCA has more than one InfiniBand port. A target channel adapter (TCA) enables I/O devices to be loaded within the network. The TCA includes an I/O controller that is specific to its particular device’s protocol such as SCSI, Fibre Channel, or Ethernet. This architecture can be easily implemented to build very large scale cluster interconnects that con-nect thousands or more hosts together. Supporting the InfiniBand in cluster applications can be found in.


4. Hardware, Software, and Middleware Support


Realistically, SSI and HA features in a cluster are not obtained free of charge. They must be sup-ported by hardware, software, middleware, or OS extensions. Any change in hardware design and OS extensions must be done by the manufacturer. The hardware and OS support could be cost-prohibitive to ordinary users. However, programming level is a big burden to cluster users. There-fore, the middleware support at the application level costs the least to implement. As an example, we show in Figure 2.10 the middleware, OS extensions, and hardware support needed to achieve HA in a typical Linux cluster system.


Close to the user application end, middleware packages are needed at the cluster management level: one for fault management to support failover and failback, to be discussed in Section 2.3.3. Another desired feature is to achieve HA using failure detection and recovery and packet switching. In the middle of Figure 2.10, we need to modify the Linux OS to support HA, and we need special drivers to support HA, I/O, and hardware devices. Toward the bottom, we need special hardware to support hot-swapped devices and provide router interfaces. We will discuss various supporting mechanisms in subsequent sections.


5. GPU Clusters for Massive Parallelism


Commodity GPUs are becoming high-performance accelerators for data-parallel computing. Modern GPU chips contain hundreds of processor cores per chip. Based on a 2010 report [19], each GPU

chip is capable of achieving up to 1 Tflops for single-precision (SP) arithmetic, and more than 80 Gflops for double-precision (DP) calculations. Recent HPC-optimized GPUs contain up to 4 GB of on-board memory, and are capable of sustaining memory bandwidths exceeding 100 GB/second. GPU clusters are built with a large number of GPU chips. GPU clusters have already demonstrated their capability to achieve Pflops performance in some of the Top 500 systems. Most GPU clusters are structured with homogeneous GPUs of the same hardware class, make, and model. The software used in a GPU cluster includes the OS, GPU drivers, and clustering API such as an MPI.


The high performance of a GPU cluster is attributed mainly to its massively parallel multicore architecture, high throughput in multithreaded floating-point arithmetic, and significantly reduced time in massive data movement using large on-chip cache memory. In other words, GPU clusters already are more cost-effective than traditional CPU clusters. GPU clusters result in not only a quantum jump in speed performance, but also significantly reduced space, power, and cooling demands. A GPU cluster can operate with a reduced number of operating system images, compared with CPU-based clusters. These reductions in power, environment, and management complexity make GPU clusters very attractive for use in future HPC applications.


5.1 The Echelon GPU Chip Design


Figure 2.11 shows the architecture of a future GPU accelerator that was suggested for use in build-ing a NVIDIA Echelon GPU cluster for Exascale computing. This Echelong project led by Bill Dally at NVIDIA is partially funded by DARPA under the Ubiquitous High-Performance Computing (UHPC) program. This GPU design incorporates 1024 stream cores and 8 latency-optimized CPU-like cores (called latency processor) on a single chip. Eight stream cores form a stream multi-processor (SM) and there are 128 SMs in the Echelon GPU chip.


Each SM is designed with 8 processor cores to yield a 160 Gflops peak speed. With 128 SMs, the chip has a peak speed of 20.48 Tflops. These nodes are interconnected by a NoC (network on chip) to 1,024 SRAM banks (L2 caches). Each cache band has a 256 KB capacity. The MCs (memory controllers) are used to connect to off-chip DRAMs and the NI (network interface) is to scale the size of the GPU cluster hierarchically, as shown in Figure 2.14. At the time of this writing, the Echelon is only a research project. With permission from Bill Dally, we present the design for

academic interest to illustrate how one can explore the many-core GPU technology to achieve Exascale computing in the future GPU technology to achieve Exascale computing in the future.


5.2 GPU Cluster Components


A GPU cluster is often built as a heterogeneous system consisting of three major components: the CPU host nodes, the GPU nodes and the cluster interconnect between them. The GPU nodes are formed with general-purpose GPUs, known as GPGPUs, to carry out numerical calculations. The host node controls program execution. The cluster interconnect handles inter-node communications. To guarantee the per-formance, multiple GPUs must be fully supplied with data streams over high-bandwidth network and memory. Host memory should be optimized to match with the on-chip cache bandwidths on the GPUs. Figure 2.12 shows the proposed Echelon GPU clusters using the GPU chips shown in Figure 2.11 as building blocks interconnected by a hierarchically constructed network.


5.3 Echelon GPU Cluster Architecture


The Echelon system architecture is shown in Figure 2.11, hierarchically. The entire Echelon system is built with N cabinets, labeled C0, C1, ... , CN. Each cabinet is built with 16 compute module labeled as M0, M1, ... , M15. Each compute module is built with 8 GPU nodes labeled as N0, N1, ... , N7. Each GPU node is the innermost block labeled as PC in Figure 2.12 (also detailed in Figure 2.11).

Each compute module features a performance of 160 Tflops and 12.8 TB/s over 2 TB of memory. Thus, a single cabinet can house 128 GPU nodes or 16,000 processor cores. Each cabinet has the potential to deliver 2.6 Pflops over 32 TB memory and 205 TB/s bandwidth. The N cabinets are interconnected by a Dragonfly network with optical fiber.


To achieve Eflops performance, we need to use at least N = 400 cabinets. In total, an Exascale system needs 327,680 processor cores in 400 cabinets. The Echelon system is supported by a self-aware OS and runtime system. The Echelon system is also designed to preserve locality with the support of compiler and autotuner. At present, NVIDIA Fermi (GF110) chip has 512 stream proces-sors. Thus the Echelon design is about 25 times faster. It is highly likely that the Echelon will employ post-Maxwell NVIDIA GPU planned to appear in 2013 ~ 2014 time frame.


5.4 CUDA Parallel Programming


CUDA (Compute Unified Device Architecture) offers a parallel computing architecture developed by NVIDIA. CUDA is the computing engine in NVIDIA GPUs. This software is accessible to developers through standard programming languages. Programmers use C for CUDA C with NVIDIA extensions and certain restrictions. This CUDA C is compiled through a PathScale Open64 C com-piler for parallel execution on a large number of GPU cores. Example 2.4 shows the advantage of using CUDA C in parallel processing.



Example 2.4 Parallel SAXPY Execution Using CUDA C Code on GPUs


SAXPY is a kernel operation frequently performed in matrix multiplication. It essentially performs repeated mul-tiply and add operations to generate the dot product of two long vectors. The following saxpy_serial routine is written in standard C code. This code is only suitable for sequential execution on a single processor core.



Void saxpy_serial (int n, float a, float*x, float *


{ for (int i = 0; i < n; ++i), y[i] = a*x[i] + y[i] }


//    Invoke the serial SAXPY kernel


saxpy_serial (n, 2.0, x, y);


The following saxpy_parallel routine is written in CUDA C code for parallel execution by 256 threads/block on many processing cores on the GPU chip. Note that n blocks are handled by n pro-cessing cores, where n could be on the order of hundreds of blocks.


_global__void saxpy_parallel (int n, float a, float*x, float *y)


{ Int i = blockIndex.x*blockDim.x + threadIndex.x; if (i < n) y [i] = a*x[i] + y[i] }


// Invoke the parallel SAXPY kernel with 256 threads/block int nblocks = (n + 255)/256; saxpy_parallel <<< nblocks, 256 >>> (n, 2.0, x, y);


This is a good example of using CUDA C to exploit massive parallelism on a cluster of multi-core and multithreaded processors using the CODA GPGPUs as building blocks.


5.5 CUDA Programming Interfaces


CUDA architecture shares a range of computational interfaces with two competitors: the Khronos Group’s Open Computing Language and Microsofts DirectCompute. Third-party wrappers are also available for using Python, Perl, FORTRAN, Java, Ruby, Lua, MATLAB, and IDL. CUDA has been used to accelerate nongraphical applications in computational biology, cryptography, and other fields by an order of magnitude or more. A good example is the BOINC distributed computing cli-ent. CUDA provides both a low-level API and a higher-level API. CUDA works with all NVIDIA GPUs from the G8X series onward, including the GeForce, Quadro, and Tesla lines. NVIDIA states that programs developed for the GeForce 8 series will also work without modification on all future NVIDIA video cards due to binary compatibility.


5.6 Trends in CUDA Usage


Tesla and Fermi are two generations of CUDA architecture released by NVIDIA in 2007 and 2010, respectively. The CUDA version 3.2 is used for using a single GPU module in 2010. A newer CUDA version 4.0 will allow multiple GPUs to address use an unified virtual address space of shared memory. The next NVIDIA GPUs will be Kepler-designed to support C++. The Fermi has eight times the peak double-precision floating-point performance of the Tesla GPU (5.8 Gflops/W versus 0.7 Gflops/W). Currently, the Fermi has up to 512 CUDA cores on 3 billion transistors.


Future applications of the CUDA GPUs and the Echelon system may include the following:


    The search for extraterrestrial intelligence (SETI@Home)


    Distributed calculations to predict the native conformation of proteins


    Medical analysis simulations based on CT and MRI scan images


    Physical simulations in fluid dynamics and environment statistics


    Accelerated 3D graphics, cryptography, compression, and interconversion of video file formats


    Building the single-chip cloud computer (SCC) through virtualization in many-core architecture.


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