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Full-Text Articles in Computer Engineering
Exploration Of Dynamic Memory, Delvin Curvin Defoe
Exploration Of Dynamic Memory, Delvin Curvin Defoe
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Since the advent of the Java programming language and the development of real-time garbage collection, Java has become an option for implementing real-time applications. The memory management choices provided by real-time garbage collection allow for real-time eJava developers to spend more of their time implementing real-time solutions. Unfortunately, the real-time community is not convinced that real-time garbage collection works in managing memory for Java applications deployed in a real-time context. Consequently, the Real-Time for Java Expert Group formulated the Real-Time Specification for Java (RTSJ) standards to make Java a real-time programming language. In lieu of garbage collection, the RTSJ proposed …
Unwoven Aspect Analysis, Morgan G. Deters
Unwoven Aspect Analysis, Morgan G. Deters
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Various languages and tools supporting advanced separation of concerns (such as aspect-oriented programming) provide a software developer with the ability to separate functional and non-functional programmatic intentions. Once these separate pieces of the software have been specified, the tools automatically handle interaction points between separate modules, relieving the developer of this chore and permitting more understandable, maintainable code. Many approaches have left traditional compiler analysis and optimization until after the composition has been performed; unfortunately, analyses performed after composition cannot make use of the logical separation present in the original program. Further, for modular systems that can be configured with …
Comparing Features Of Three-Dimensional Object Models Using Registration Based On Surface Curvature Signatures, Timothy David Gatzke, Cindy M. Grimm
Comparing Features Of Three-Dimensional Object Models Using Registration Based On Surface Curvature Signatures, Timothy David Gatzke, Cindy M. Grimm
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This dissertation presents a technique for comparing local shape properties for similar three-dimensional objects represented by meshes. Our novel shape representation, the curvature map, describes shape as a function of surface curvature in the region around a point. A multi-pass approach is applied to the curvature map to detect features at different scales. The feature detection step does not require user input or parameter tuning. We use features ordered by strength, the similarity of pairs of features, and pruning based on geometric consistency to efficiently determine key corresponding locations on the objects. For genus zero objects, the corresponding locations are …
Performance Evaluation For Hybrid Architectures, Praveen Krishnamurthy
Performance Evaluation For Hybrid Architectures, Praveen Krishnamurthy
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In this dissertation we discuss methologies for estimating the performance of applications on hybrid architectures, systems that include various types of computing resources (e.g. traditional general-purpose processors, chip multiprocessors, reconfigurable hardware). A common use of hybrid architectures will be to deploy coarse pipeline stages of application on "suitable" compute units with communication path for transferring data. The first problem we focus on relates to the sizing the data queues between the different processing elements of an hybrid system. Much of the discussion centers on our analytical models that can be used to derive performance metrics of interest such as, throughput …
The Effect Of Object Color On Depth Ordering, Reynold Bailey, Cindy Grimm, Christopher Davoli, Richard Abrams
The Effect Of Object Color On Depth Ordering, Reynold Bailey, Cindy Grimm, Christopher Davoli, Richard Abrams
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The relationship between color and perceived depth for realistic, colored objects with varying shading was explored. Background: Studies have shown that warm-colored stimuli tend to appear nearer in depth than cool-colored stimuli. The majority of these studies asked human observers to view physically equidistant, colored stimuli and compare them for relative depth. However, in most cases, the stimuli presented were rather simple: straight colored lines, uniform color patches, point light sources, or symmetrical objects with uniform shading. Additionally, the colors were typically highly saturated. Although such stimuli are useful for isolating and studying depth cues in certain contexts, they leave …
Emergent Task Allocation For Mobile Robots Through Intentions And Directives, Nuzhet Atay, Burchan Bayazit
Emergent Task Allocation For Mobile Robots Through Intentions And Directives, Nuzhet Atay, Burchan Bayazit
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Multi-robot systems require efficient and accurate planning in order to perform mission-critical tasks. However, algorithms that find the optimal solution are usually computationally expensive and may require a large number of messages between the robots as the robots need to be aware of the global spatiotemporal information. In this paper, we introduce an emergent task allocation approach for mobile robots. Each robot uses only the information obtained from its immediate neighbors in its decision. Our technique is general enough to be applicable to any task allocation scheme as long as a utilization criteria is given. We demonstrate that our approach …
Expression Profiling Of Human Donor Lungs To Understand Primary Graft Dysfunction After Lung Transplantation, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson
Expression Profiling Of Human Donor Lungs To Understand Primary Graft Dysfunction After Lung Transplantation, Monika Ray, Sekhar Dharmarajan, Johannes Freudenberg, Weixiong Zhang, Alexander G. Patterson
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Lung transplantation is the treatment of choice for end-stage pulmonary diseases. A limited donor supply has resulted in 4000 patients on the waiting list. Currently, 10-20% of donor organs offered for transplantation are deemed suitable under the selection criteria, of which 15-25% fails due to primary graft dysfunction (PGD). This has resulted in increased efforts to search for alternative donor lungs selection criteria. In this study, we attempt to further our understanding of PGD by observing the changes in gene expression across donor lungs that developed PGD versus those that did not. Our second goal is to use a machine …
Determining Alpha-Helix Correspondence For Protein Structure Prediction From Cryo-Em Density Maps, Master's Thesis, May 2007, Sasakthi S. Abeysinghe
Determining Alpha-Helix Correspondence For Protein Structure Prediction From Cryo-Em Density Maps, Master's Thesis, May 2007, Sasakthi S. Abeysinghe
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Determining protein structure is an important problem for structural biologists, which has received a significant amount of attention in the recent years. In this thesis, we describe a novel, shape-modeling approach as an intermediate step towards recovering 3D protein structures from volumetric images. The input to our method is a sequence of alpha-helices that make up a protein, and a low-resolution volumetric image of the protein where possible locations of alpha-helices have been detected. Our task is to identify the correspondence between the two sets of helices, which will shed light on how the protein folds in space. The central …
Splice: A Standardized Peripheral Logic And Interface Creation Engine, Justin Thiel
Splice: A Standardized Peripheral Logic And Interface Creation Engine, Justin Thiel
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Recent advancements in FPGA technology have allowed manufacturers to place general-purpose processors alongside user-configurable logic gates on a single chip. At first glance, these integrated devices would seem to be the ideal deployment platform for hardware-software co-designed systems, but some issues, such as incompatibility across vendors and confusion over which bus interfaces to support, have impeded adoption of these platforms. This thesis describes the design and operation of Splice, a software-based code generation tool intended to address these types of issues by providing a bus-independent structure that allows end-users to easily integrate their customized peripheral logic into embedded systems. To …
Improving Individual Flow Performance With Multiple Queue Fair Queuing, Manfred Georg, Christopher Jechlitschek, Sergey Gorinsky
Improving Individual Flow Performance With Multiple Queue Fair Queuing, Manfred Georg, Christopher Jechlitschek, Sergey Gorinsky
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Fair Queuing (FQ) algorithms provide isolation between packet flows, allowing max-min fair sharing of a link even when flows misbehave. However, fairness comes at the expense of per-flow state. To keep the memory requirement independent of the flow count, the router can isolate aggregates of flows, rather than individual flows. We investigate the feasibility of protecting individual flows under such aggregate isolation in the context of Multiple Queue Fair Queuing (MQFQ), where the router maintains a fixed number of queues and associates multiple queues with each flow. MQFQ places packets in the shortest queue associated with their flow. The redundancy …
Scheduling Induced Bounds And The Verification Of Preemptive Real-Time Systems, Terry Tidwell, Christopher Gill, Venkita Subramonian
Scheduling Induced Bounds And The Verification Of Preemptive Real-Time Systems, Terry Tidwell, Christopher Gill, Venkita Subramonian
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Distributed real-time and embedded (DRE) systems have stringent constraints on timeliness and other properties whose assurance is crucial to correct system behavior. Our previous research has shown that detailed models of essential middleware mechanisms can be developed, composed, and for constrained examples verified tractably, using state of the art timed automata model checkers. However, to apply model checking to a wider range of real-time systems, particularly those involving more general forms of preemptive concurrency, new techniques are needed to address decidability and tractability concerns. This paper makes three contributions to research on formal verification and validation of DRE systems. First, …
Single Cell Expression Profiling Reveals Major Disruption Of Dna Repair Capacity In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang
Single Cell Expression Profiling Reveals Major Disruption Of Dna Repair Capacity In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang
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Understanding the pathogenesis in the early stages of late-onset Alzheimer's disease (LOAD) can help in gaining important mechanistic insights into this devastating neurodegenerative disorder. Alzheimer's disease (AD) is characterised by extensive cell death with disease progression. In this paper laser capture microdissection (LCM) based gene expression profiling, which is able to profile gene expression in a single cell type, is employed to analyse the gene expression regulation of incipient AD. Our analysis shows that LCM based gene expression profiling of neurons has a critical advantage over the conventional gene expression profiling method which uses samples of mixed cell types and …
Control Of A Robotic Arm Using Low-Dimensional Emg And Ecog Biofeedback, Timothy M. Blackely, William D. Smart
Control Of A Robotic Arm Using Low-Dimensional Emg And Ecog Biofeedback, Timothy M. Blackely, William D. Smart
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In this dissertation we describe a system that uses a low dimensional input derived from electromyography and electrocorticography data to control a robot. The work involves creating a system that allows signals recorded directly from a human body to allow control of a small robot arm. We compare direct joystick control with electromyogram (EMG) input to determine if one input system is superior, or if the quality of control between them is comparable. We also verify the system that is used to record the electromyogram signals is adaptable to other forms of biosignal input; in particular, direct connection to a …
Implementing Legba: Fine-Grained Memory Protection, Sheffield, Sowell, Wilson
Implementing Legba: Fine-Grained Memory Protection, Sheffield, Sowell, Wilson
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Fine-grained hardware protection could provide a powerful and effective means for isolating untrusted code. However, previous techniques for providing fine-grained protection in hardware have lead to poor performance. Legba has been proposed as a new caching architecture, designed to reduce the granularity of protection, without slowing down the processor. Unfortunately, the designers of Legba have not attempted an implementation. Instead, all of their analysis is based purely on simulations. We present an implementation of the Legba design on a MIPS Core Processor, along with an analysis of our observations and results.
Byzantine Fault-Tolerant Web Services For N-Tier And Service Oriented Architectures, Sajeeva L. Pallemulle, Kenneth J. Goldman
Byzantine Fault-Tolerant Web Services For N-Tier And Service Oriented Architectures, Sajeeva L. Pallemulle, Kenneth J. Goldman
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Web Services that provide mission-critical functionality must be replicated to guarantee correct execution and high availability in spite of arbitrary (Byzantine) faults. Existing approaches for Byzantine fault-tolerant execution of Web Services are inadequate to guarantee correct execution due to several major limitations. Some approaches do not support interoperability between replicated Web Services. Other approaches do not provide fault isolation guarantees that are strong enough to prevent cascading failures across organizational and application boundaries. Moreover, existing approaches place impractical limitations on application development by not supporting long-running active threads of computation, fully asynchronous communication, and access to host specific information. We …
A Duality Theory With Zero Duality Gap For Nonlinear Programming, Yixin Chen
A Duality Theory With Zero Duality Gap For Nonlinear Programming, Yixin Chen
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Duality is an important notion for constrained optimization which provides a theoretical foundation for a number of constraint decomposition schemes such as separable programming and for deriving lower bounds in space decomposition algorithms such as branch and bound. However, the conventional duality theory has the fundamental limit that it leads to duality gaps for nonconvex optimization problems, especially discrete and mixed-integer problems where the feasible sets are nonconvex. In this paper, we propose a novel extended duality theory for nonlinear optimization that overcomes some limitations of previous dual methods. Based on a new dual function, the extended duality theory leads …
Extending Bpel For Interoperable Pervasive Computing, Gregory Hackmann, Christopher Gill, Christopher Gill, Gruia-Catalin Roman
Extending Bpel For Interoperable Pervasive Computing, Gregory Hackmann, Christopher Gill, Christopher Gill, Gruia-Catalin Roman
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The widespread deployment of mobile devices like PDAs and mobile phones has created a vast computation and communication platform for pervasive computing applications. However, these devices feature an array of incompatible hardware and software architectures, discouraging ad-hoc interactions among devices. The Business Process Execution Language (BPEL) allows users in wired computing settings to model applications of significant complexity, leveraging Web standards to guarantee interoperability. However, BPEL's inflexible communication model effectively prohibits its deployment on the kinds of dynamic wireless networks used by most pervasive computing devices. This paper presents extensions to BPEL that address these restrictions, transforming BPEL into a …
Optimal Discrete Rate Adaptation For Distributed Real-Time Systems With End-To-End Tasks, Yingming Chen, Chenyang Lu, Xenofon Koutsoukos
Optimal Discrete Rate Adaptation For Distributed Real-Time Systems With End-To-End Tasks, Yingming Chen, Chenyang Lu, Xenofon Koutsoukos
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Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload changes such as dynamic task arrivals. Through oline preprocessing MPRA transforms a NP-hard utility optimization problem to a set of simple linear functions in different regions expressed in term of CPU utilization changes caused by workload variations. At run time MPRA produces optimal …
Curing Regular Expressions Matching Algorithms From Insomnia, Amnesia, And Acalulia, Sailesh Kumar, Balakrishnan Chandrasekaran, Jonathan Turner, George Varghese
Curing Regular Expressions Matching Algorithms From Insomnia, Amnesia, And Acalulia, Sailesh Kumar, Balakrishnan Chandrasekaran, Jonathan Turner, George Varghese
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The importance of network security has grown tremendously and a collection of devices have been introduced, which can improve the security of a network. Network intrusion detection systems (NIDS) are among the most widely deployed such system; popular NIDS use a collection of signatures of known security threats and viruses, which are used to scan each packet's payload. Today, signatures are often specified as regular expressions; thus the core of the NIDS comprises of a regular expressions parser, such parsers are traditionally implemented as finite automata. Deterministic Finite Automata (DFA) are fast, therefore they are often desirable at high network …
Optimal Discrete Rate Adaptation For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu, Xenofon Kutsoukos
Optimal Discrete Rate Adaptation For Distributed Real-Time Systems, Yingming Chen, Chenyang Lu, Xenofon Kutsoukos
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Many distributed real-time systems face the challenge of dynamically maximizing system utility in response to fluctuations in system workload. We present the MultiParametric Rate Adaptation (MPRA) algorithm for discrete rate adaptation in distributed real-time systems with end-to-end tasks. The key novelty and advantage of MPRA is that it can efficiently produce optimal solutions in response to workload variations such as dynamic task arrivals. Through offline preprocessing MPRA transforms an NP-hard utility optimization problem to the evaluation of a piecewise linear function of the CPU utilization. At run time MPRA produces optimal solutions by evaluating the function based on the CPU …
Mercury Blast Dictionaries: Analysis And Performance Measurement, Jeremy Buhler
Mercury Blast Dictionaries: Analysis And Performance Measurement, Jeremy Buhler
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This report describes a hashing scheme for a dictionary of short bit strings. The scheme, which we call near-perfect hashing, was designed as part of the construction of Mercury BLAST, an FPGA-based accelerator for the BLAST family of biosequence comparison algorithms. Near-perfect hashing is a heuristic variant of the well-known displacement hashing approach to building perfect hash functions. It uses a family of hash functions composed from linear transformations on bit vectors and lookups in small precomputed tables, both of which are especially appropriate for implementation in ardware logic. We show empirically that for inputs derived from genomic DNA sequences, …
Configurable Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu
Configurable Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu
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Many distributed real-time applications must handle mixed periodic and aperiodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both periodic and aperiodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for and effectiveness of our configurable component middleware approach in supporting different applications with periodic and aperiodic tasks.
Configuring Low Cost Metanetworks On A Shared Substrate, Jing Lu, Jonathan Turner
Configuring Low Cost Metanetworks On A Shared Substrate, Jing Lu, Jonathan Turner
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In a diversified internet, meta-networks (“metanets?for short) share a common substrate and offer value-added services to millions of users around the globe. Therefore, configuring low-cost metanets with links having enough bandwidth to accommodate all anticipated user traffic is critical to the success of the metanets. In this paper, we propose a novel pruning algorithm that configures metanets on any given substrate in a cost-efficient way. In contrast to other testbed configuration systems, we solve the metanet configuration problem from a higher level specification and produces a network that is dimensioned to handle the specified traffic. To the best of our …
Mobile Wireless Sensor Network Connectivity Repair With K-Redundanc, Nuzhet Atay, Burchan Bayazit
Mobile Wireless Sensor Network Connectivity Repair With K-Redundanc, Nuzhet Atay, Burchan Bayazit
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Connectivity is an important requirement for wireless sensor networks especially in real-time monitoring and data transfer applications. However, node movements and failures change the topology of the initial deployed network, which can result in partitioning of the communication graph. In this paper, we present a method for maintaining and repairing the communication network of a dynamic mobile wireless sensor network. We assume that we cannot control the motion of wireless sensor nodes, but there are robots whose motion can be controlled by the wireless sensor nodes to maintain and repair the connectivity of the network. At the heart of our …
Dna Repair In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang
Dna Repair In Incipient Alzheimer's Disease, Monika Ray, Weixiong Zhang
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Alzheimer’s disease (AD) is a progressive neurodegenerative disorder currently with no cure. Understanding the pathogenesis in the early stages of late-onset AD can help gain important mechanistic insights into this disease as well as aid in effective drug development. The analysis of incipient AD is steeped in difficulties due to its slight pathological and genetic differences from normal ageing. The difficulty also lies in the choice of analysis techniques as statistical power to analyse incipient AD with a small sample size, as is common in pilot studies, can be low if the proper analytical tool is not employed. In this …
Customizing Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu
Customizing Component Middleware For Distributed Real-Time Systems With Aperiodic And Periodic Tasks, Yuanfang Zhang, Christopher Gill, Chenyang Lu
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Many distributed real-time applications must handle mixed aperiodic and periodic tasks with diverse requirements. However, existing middleware lacks flexible configuration mechanisms needed to manage end-to-end timing easily for a wide range of different applications with both aperiodic and periodic tasks. The primary contribution of this work is the design, implementation and performance evaluation of the first configurable component middleware services for admission control and load balancing of aperiodic and periodic tasks in distributed real-time systems. Empirical results demonstrate the need for, and the effectiveness of, our configurable component middleware approach in supporting different applications with aperiodic and periodic tasks.
Combined Controllers That Follow Imperfect Input Motions For Humanoid Robots, Gazihan Alankus, Burchan O. Bayazit
Combined Controllers That Follow Imperfect Input Motions For Humanoid Robots, Gazihan Alankus, Burchan O. Bayazit
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Humanoid robots have the potential to become a part of everyday life as their hardware and software challenges are being solved. In this paper we present a system that gets as input a motion trajectory in the form of motion capture data, and produces a controller that controls a humanoid robot in real-time to achieve a motion trajectory that is similar to the input motion data. The controller expects the input motion data not to be dynamically feasible for the robot and employs a combined controller with corrective components to keep the robot balanced while following the motion. Since the …
Gigabit Concept Mining: A Sensitivity Analysis, Masters Thesis, December 2006, Andrew Levine
Gigabit Concept Mining: A Sensitivity Analysis, Masters Thesis, December 2006, Andrew Levine
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Massive amounts of data are passed over public networks. There is a need for network administrators to analyze this traffic, but it was not previously possible to analyze live network data at high speed. It has been shown that streaming computation and deep packet analysis are possible at very high rates through the use of hardware acceleration. This work provides analysis for a larger project that involves digesting large amounts of network traffic. In this system, we process the traffic using hardware that has constraints. The workings of the system are first discussed. Tradeoffs in the design of hardware and …
Experimental Evaluation Of A Coarse-Grained Switch Scheduler, Charlie Wiseman, Jon Turner, Ken Wong, Brandon Heller
Experimental Evaluation Of A Coarse-Grained Switch Scheduler, Charlie Wiseman, Jon Turner, Ken Wong, Brandon Heller
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Modern high performance routers rely on sophisticated interconnection networks to meet ever increasing demands on capacity. Regulating the flow of packets through these interconnects is critical to providing good performance, particularly in the presence of extreme traffic patterns that result in sustained overload at output ports. Previous studies have used a combination of analysis and idealized simulations to show that coarse-grained scheduling of traffic flows can be effective in preventing congestion, while ensuring high utilization. In this paper, we study the performance of a coarse-grained scheduler in a real router with a scalable architecture similar to those found in high …
Strong Performance Guarantees For Asynchronous Buffered Crossbar Schedulers, Jonathon Turner
Strong Performance Guarantees For Asynchronous Buffered Crossbar Schedulers, Jonathon Turner
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Crossbar-based switches are commonly used to implement routers with throughputs up to about 1 Tb/s. The advent of crossbar scheduling algorithms that provide strong performance guarantees now makes it possible to engineer systems that perform well, even under extreme traffic conditions. Until recently, such performance guarantees have only been developed for crossbars that switch cells rather than variable length packets. Cell-based crossbars incur a worst-case bandwidth penalty of up to a factor of two, since they must fragment variable length packets into fixed length cells. In addition, schedulers for cell-based crossbars may fail to deliver the expected performance guarantees when …