Generalized database index structures on massively parallel processor architectures

Height-balanced search trees are ubiquitous in database management systems as well as in other applications that require efficient access methods in order to identify entries in large data volumes. They can be configured with various strategies for structuring the search space for a given data set and for pruning it when different kinds of search queries are answered. In order to facilitate the development of application-specific tree variants, index frameworks, such as GiST, exist that provide a reusable library of commonly shared tree management functionality. By specializing internal data organization strategies, the framework can be customized to create an index that is efficient for an application's data access characteristics. Because the majority of the framework's code can be reused development and testing efforts are significantly lower, compared to an implementation from scratch. However, none of the existing frameworks supports the execution of index operations on massively parallel processor architectures, such as GPUs. Enabling the use of such processors for generalized index frameworks is the goal of this thesis. By compiling state-of-the-art techniques from a wide range of CPU- and GPU-optimized indexes, a GiST extension is developed that abstracts the physical execution aspect of generic, tree-based search queries. Tree traversals are broken-down into vectorized processing primitives that can be scheduled to one of the available (co-)processors for execution. Further, a CPU-based implementation is provided as well as a new GPU-based algorithm that, unlike prior art in this area, does not require that the index is fully stored inside a GPU's main memory buffer. The applicability of the extended framework is assessed for image rendering engines and, based on microbenchmarks, the parallelized algorithm performance is compared for different CPU and GPU generations. It will be shown that cases exist, where the GPU clearly outperforms the CPU and vice versa. In order to leverage the strengths of each processor type, an adaptive scheduler is presented that can be calibrated to schedule index operations to the best-fitting device in a hybrid system. With the help of a tree traversal simulation different scheduling strategies are evaluated and it will be shown that the adaptive scheduler can be used to make near-optimal decisions.Suchbäume sind allgegenwärtig in Datenbanksystemen und anderen Anwendungen, die eine effiziente Möglichkeit benötigen um in großen Datensätzen nach Einträgen zu suchen, die bestimmte Suchkriterien erfüllen. Sie können mit verschiedenen Strategien konfiguriert werden um den Suchraum zu strukturieren und die für ein Suchergebnis irrelevante Bereiche von der Bearbeitung auszuschließen. Die Entwicklung von anwendungsspezifischen Indexen wird durch Frameworks wie GiST unterstützt. Jedoch unterstützt keines der heute bereits existierenden Frameworks die Verwendung von hochgradig parallelen Prozessorarchitekturen wie GPUs. Solche Prozessoren für generische Index Frameworks nutzbar zu machen, ist Ziel dieser Arbeit. Dazu werden Techniken aus verschiedensten CPU- und GPU-optimierten Indexen analysiert und für die Entwicklung einer GiST-Erweiterung verwendet, welche die für eine Suche in Suchbäumen nötigen Berechnungen abstrahiert. Traversierungsoperationen werden dabei auf vektorisierte Primitive abgebildet, die auf parallelen Prozessoren implementiert werden können. Die Verwendung dieser Erweiterung wird beispielhaft an einem CPU Algorithmus demonstriert. Weiterhin wird ein neuer GPU-basierter Algorithmus vorgestellt, der im Vergleich zu bisherigen Verfahren, ein dynamisches Nachladen der Index Daten in den Hauptspeicher der GPU unterstützt. Die Praktikabilität des erweiterten Frameworks wird am Beispiel von Anwendungen aus der Computergrafik untersucht und die Performanz der verwendeten Algorithmen mit Hilfe eines Benchmarks auf verschiedenen CPU- und GPU-Modellen analysiert. Dabei wird gezeigt, unter welchen Bedingungen die parallele GPU-basierte Ausführung schneller ist als die CPU-basierte Variante - und umgekehrt. Um die Stärken beider Prozessortypen in einem hybriden System ausnutzen zu können, wird ein Scheduler entwickelt, der nach einer Kalibrierungsphase für eine gegebene Operation den geeignetsten Prozessor wählen kann. Mit Hilfe eines Simulators für Baumtraversierungen werden verschiedenste Scheduling Strategien verglichen. Dabei wird gezeigt, dass die Entscheidungen des Schedulers kaum vom Optimum abweichen und, abhängig von der simulierten Last, die erzielbaren Durchsätze für die parallele Ausführung mehrerer Suchoperationen durch hybrides Scheduling um eine Größenordnung und mehr erhöht werden können

Graph Processing in Main-Memory Column Stores

Evermore, novel and traditional business applications leverage the advantages of a graph data model, such as the offered schema flexibility and an explicit representation of relationships between entities. As a consequence, companies are confronted with the challenge of storing, manipulating, and querying terabytes of graph data for enterprise-critical applications. Although these business applications operate on graph-structured data, they still require direct access to the relational data and typically rely on an RDBMS to keep a single source of truth and access. Existing solutions performing graph operations on business-critical data either use a combination of SQL and application logic or employ a graph data management system. For the first approach, relying solely on SQL results in poor execution performance caused by the functional mismatch between typical graph operations and the relational algebra. To the worse, graph algorithms expose a tremendous variety in structure and functionality caused by their often domain-specific implementations and therefore can be hardly integrated into a database management system other than with custom coding. Since the majority of these enterprise-critical applications exclusively run on relational DBMSs, employing a specialized system for storing and processing graph data is typically not sensible. Besides the maintenance overhead for keeping the systems in sync, combining graph and relational operations is hard to realize as it requires data transfer across system boundaries. A basic ingredient of graph queries and algorithms are traversal operations and are a fundamental component of any database management system that aims at storing, manipulating, and querying graph data. Well-established graph traversal algorithms are standalone implementations relying on optimized data structures. The integration of graph traversals as an operator into a database management system requires a tight integration into the existing database environment and a development of new components, such as a graph topology-aware optimizer and accompanying graph statistics, graph-specific secondary index structures to speedup traversals, and an accompanying graph query language. In this thesis, we introduce and describe GRAPHITE, a hybrid graph-relational data management system. GRAPHITE is a performance-oriented graph data management system as part of an RDBMS allowing to seamlessly combine processing of graph data with relational data in the same system. We propose a columnar storage representation for graph data to leverage the already existing and mature data management and query processing infrastructure of relational database management systems. At the core of GRAPHITE we propose an execution engine solely based on set operations and graph traversals. Our design is driven by the observation that different graph topologies expose different algorithmic requirements to the design of a graph traversal operator. We derive two graph traversal implementations targeting the most common graph topologies and demonstrate how graph-specific statistics can be leveraged to select the optimal physical traversal operator. To accelerate graph traversals, we devise a set of graph-specific, updateable secondary index structures to improve the performance of vertex neighborhood expansion. Finally, we introduce a domain-specific language with an intuitive programming model to extend graph traversals with custom application logic at runtime. We use the LLVM compiler framework to generate efficient code that tightly integrates the user-specified application logic with our highly optimized built-in graph traversal operators. Our experimental evaluation shows that GRAPHITE can outperform native graph management systems by several orders of magnitude while providing all the features of an RDBMS, such as transaction support, backup and recovery, security and user management, effectively providing a promising alternative to specialized graph management systems that lack many of these features and require expensive data replication and maintenance processes

Hardware Acceleration for Unstructured Big Data and Natural Language Processing.

The confluence of the rapid growth in electronic data in recent years, and the renewed interest in domain-specific hardware accelerators presents exciting technical opportunities. Traditional scale-out solutions for processing the vast amounts of text data have been shown to be energy- and cost-inefficient. In contrast, custom hardware accelerators can provide higher throughputs, lower latencies, and significant energy savings. In this thesis, I present a set of hardware accelerators for unstructured big-data processing and natural language processing. The first accelerator, called HAWK, aims to speed up the processing of ad hoc queries against large in-memory logs. HAWK is motivated by the observation that traditional software-based tools for processing large text corpora use memory bandwidth inefficiently due to software overheads, and, thus, fall far short of peak scan rates possible on modern memory systems. HAWK is designed to process data at a constant rate of 32 GB/s—faster than most extant memory systems. I demonstrate that HAWK outperforms state-of-the-art software solutions for text processing, almost by an order of magnitude in many cases. HAWK occupies an area of 45 sq-mm in its pareto-optimal configuration and consumes 22 W of power, well within the area and power envelopes of modern CPU chips. The second accelerator I propose aims to speed up similarity measurement calculations for semantic search in the natural language processing space. By leveraging the latency hiding concepts of multi-threading and simple scheduling mechanisms, my design maximizes functional unit utilization. This similarity measurement accelerator provides speedups of 36x-42x over optimized software running on server-class cores, while requiring 56x-58x lower energy, and only 1.3% of the area.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/116712/1/prateekt_1.pd

A High-Performance Domain-Specific Language and Code Generator for General N-body Problems

General N-body problems are a set of problems in which an update to a single element in the system depends on every other element. N-body problems are ubiquitous, with applications in various domains ranging from scientific computing simulations in molecular dynamics, astrophysics, acoustics, and fluid dynamics all the way to computer vision, data mining and machine learning problems. Different N-body algorithms have been designed and implemented in these various fields. However, there is a big gap between the algorithm one designs on paper and the code that runs efficiently on a parallel system. It is time-consuming to write fast, parallel, and scalable code for these problems. On the other hand, the sheer scale and growth of modern scientific datasets necessitate exploiting the power of both parallel and approximation algorithms where there is a potential to trade-off accuracy for performance. The main problem that we are tackling in this thesis is how to automatically generate asymptotically optimal N-body algorithms from the high-level specification of the problem. We combine the body of work in performance optimizations, compilers and the domain of N-body problems to build a unified system where domain scientists can write programs at the high level while attaining performance of code written by an expert at the low level.In order to generate a high-performance, scalable code for this group of problems, we take the following steps in this thesis; first, we propose a unified algorithmic framework named PASCAL in order to address the challenge of designing a general algorithmic template to represent the class of N-body problems. PASCAL utilizes space-partitioning trees and user-controlled pruning/approximations to reduce the asymptotic runtime complexity from linear to logarithmic in the number of data points. In PASCAL, we design an algorithm that automatically generates conditions for pruning or approximation of an N-body problem considering the problem's definition. In order to evaluate PASCAL, we developed tree-based algorithms for six well-known problems: k-nearest neighbors, range search, minimum spanning tree, kernel density estimation, expectation maximization, and Hausdorff distance. We show that applying domain-specific optimizations and parallelization to the algorithms written in PASCAL achieves 10x to 230x speedup compared to state-of-the-art libraries on a dual-socket Intel Xeon processor with 16 cores on real-world datasets. Second, we extend the PASCAL framework to build PASCAL-X that adds support for NUMA-aware parallelization. PASCAL-X also presents insights on the influence of tuning parameters. Tuning parameters such as leaf size (influences the shape of the tree) and cut-off level (controls the granularity of tasks) of the space-partitioning trees result in performance improvement of up to 4.6x. A key goal is to generate scalable and high-performance code automatically without sacrificing productivity. That implies minimizing the effort the users have to put in to generate the desired high-performance code. Another critical factor is the adaptivity, which indicates the amount of effort that is required to extend the high-performance code generation to new N-body problems. Finally, we consider these factors and develop a domain-specific language and code generator named Portal, which is built on top of PASCAL-X. Portal's language design is inspired by the mathematical representation of N-body problems, resulting in an intuitive language for rapid implementation of a variety of problems. Portal's back-end is designed and implemented to generate optimized, parallel, and scalable implementations for multi-core systems. We demonstrate that the performance achieved by using Portal is comparable to that of expert hand-optimized code while providing productivity for domain scientists. For instance, using Portal for the k-nearest neighbors problem gains performance that is similar to the hand-optimized code, while reducing the lines of code by 68x. To the best of our knowledge, there are no known libraries or frameworks that implement parallel asymptotically optimal algorithms for the class of general N-body problems and this thesis primarily aims to fill this gap. Finally, we present a case study of Portal for the real-world problem of face clustering. In this case study, we show that Portal not only provides a fast solution for the face clustering problem with similar accuracy as the state-of-the-art algorithm, but also it provides productivity by implementing the face clustering algorithm in only 14 lines of Portal code

Efficient and Reliable Task Scheduling, Network Reprogramming, and Data Storage for Wireless Sensor Networks

Wireless sensor networks (WSNs) typically consist of a large number of resource-constrained nodes. The limited computational resources afforded by these nodes present unique development challenges. In this dissertation, we consider three such challenges. The first challenge focuses on minimizing energy usage in WSNs through intelligent duty cycling. Limited energy resources dictate the design of many embedded applications, causing such systems to be composed of small, modular tasks, scheduled periodically. In this model, each embedded device wakes, executes a task-set, and returns to sleep. These systems spend most of their time in a state of deep sleep to minimize power consumption. We refer to these systems as almost-always-sleeping (AAS) systems. We describe a series of task schedulers for AAS systems designed to maximize sleep time. We consider four scheduler designs, model their performance, and present detailed performance analysis results under varying load conditions. The second challenge focuses on a fast and reliable network reprogramming solution for WSNs based on incremental code updates. We first present VSPIN, a framework for developing incremental code update mechanisms to support efficient reprogramming of WSNs. VSPIN provides a modular testing platform on the host system to plug-in and evaluate various incremental code update algorithms. The framework supports Avrdude, among the most popular Linux-based programming tools for AVR microcontrollers. Using VSPIN, we next present an incremental code update strategy to efficiently reprogram wireless sensor nodes. We adapt a linear space and quadratic time algorithm (Hirschberg\u27s Algorithm) for computing maximal common subsequences to build an edit map specifying an edit sequence required to transform the code running in a sensor network to a new code image. We then present a heuristic-based optimization strategy for efficient edit script encoding to reduce the edit map size. Finally, we present experimental results exploring the reduction in data size that it enables. The approach achieves reductions of 99.987% for simple changes, and between 86.95% and 94.58% for more complex changes, compared to full image transmissions - leading to significantly lower energy costs for wireless sensor network reprogramming. The third challenge focuses on enabling fast and reliable data storage in wireless sensor systems. A file storage system that is fast, lightweight, and reliable across device failures is important to safeguard the data that these devices record. A fast and efficient file system enables sensed data to be sampled and stored quickly and batched for later transmission. A reliable file system allows seamless operation without disruptions due to hardware, software, or other unforeseen failures. While flash technology provides persistent storage by itself, it has limitations that prevent it from being used in mission-critical deployment scenarios. Hybrid memory models which utilize newer non-volatile memory technologies, such as ferroelectric RAM (FRAM), can mitigate the physical disadvantages of flash. In this vein, we present the design and implementation of LoggerFS, a fast, lightweight, and reliable file system for wireless sensor networks, which uses a hybrid memory design consisting of RAM, FRAM, and flash. LoggerFS is engineered to provide fast data storage, have a small memory footprint, and provide data reliability across system failures. LoggerFS adapts a log-structured file system approach, augmented with data persistence and reliability guarantees. A caching mechanism allows for flash wear-leveling and fast data buffering. We present a performance evaluation of LoggerFS using a prototypical in-situ sensing platform and demonstrate between 50% and 800% improvements for various workloads using the FRAM write-back cache over the implementation without the cache

Flexible Scheduling in Middleware for Distributed rate-based real-time applications - Doctoral Dissertation, May 2002

Distributed rate-based real-time systems, such as process control and avionics mission computing systems, have traditionally been scheduled statically. Static scheduling provides assurance of schedulability prior to run-time overhead. However, static scheduling is brittle in the face of unanticipated overload, and treats invocation-to-invocation variations in resource requirements inflexibly. As a consequence, processing resources are often under-utilized in the average case, and the resulting systems are hard to adapt to meet new real-time processing requirements. Dynamic scheduling offers relief from the limitations of static scheduling. However, dynamic scheduling offers relief from the limitations of static scheduling. However, dynamic scheduling often has a high run-time cost because certain decisions are enforced on-line. Furthermore, under conditions of overload tasks can be scheduled dynamically that may never be dispatched, or that upon dispatch would miss their deadlines. We review the implications of these factors on rate-based distributed systems, and posits the necessity to combine static and dynamic approaches to exploit the strengths and compensate for the weakness of either approach in isolation. We present a general hybrid approach to real-time scheduling and dispatching in middleware, that can employ both static and dynamic components. This approach provides (1) feasibility assurance for the most critical tasks, (2) the ability to extend this assurance incrementally to operations in successively lower criticality equivalence classes, (3) the ability to trade off bounds on feasible utilization and dispatching over-head in cases where, for example, execution jitter is a factor or rates are not harmonically related, and (4) overall flexibility to make more optimal use of scarce computing resources and to enforce a wider range of application-specified execution requirements. This approach also meets additional constraints of an increasingly important class of rate-based systems, those with requirements for robust management of real-time performance in the face of rapidly and widely changing operating conditions. To support these requirements, we present a middleware framework that implements the hybrid scheduling and dispatching approach described above, and also provides support for (1) adaptive re-scheduling of operations at run-time and (2) reflective alternation among several scheduling strategies to improve real-time performance in the face of changing operating conditions. Adaptive re-scheduling must be performed whenever operating conditions exceed the ability of the scheduling and dispatching infrastructure to meet the critical real-time requirements of the system under the currently specified rates and execution times of operations. Adaptive re-scheduling relies on the ability to change the rates of execution of at least some operations, and may occur under the control of a higher-level middleware resource manager. Different rates of execution may be specified under different operating conditions, and the number of such possible combinations may be arbitrarily large. Furthermore, adaptive rescheduling may in turn require notification of rate-sensitive application components. It is therefore desirable to handle variations in operating conditions entirely within the scheduling and dispatching infrastructure when possible. A rate-based distributed real-time application, or a higher-level resource manager, could thus fall back on adaptive re-scheduling only when it cannot achieve acceptable real-time performance through self-adaptation. Reflective alternation among scheduling heuristics offers a way to tune real-time performance internally, and we offer foundational support for this approach. In particular, run-time observable information such as that provided by our metrics-feedback framework makes it possible to detect that a given current scheduling heuristic is underperforming the level of service another could provide. Furthermore we present empirical results for our framework in a realistic avionics mission computing environment. This forms the basis for guided adaption. This dissertation makes five contributions in support of flexible and adaptive scheduling and dispatching in middleware. First, we provide a middle scheduling framework that supports arbitrary and fine-grained composition of static/dynamic scheduling, to assure critical timeliness constraints while improving noncritical performance under a range of conditions. Second, we provide a flexible dispatching infrastructure framework composed of fine-grained primitives, and describe how appropriate configurations can be generated automatically based on the output of the scheduling framework. Third, we describe algorithms to reduce the overhead and duration of adaptive rescheduling, based on sorting for rate selection and priority assignment. Fourth, we provide timely and efficient performance information through an optimized metrics-feedback framework, to support higher-level reflection and adaptation decisions. Fifth, we present the results of empirical studies to quantify and evaluate the performance of alternative canonical scheduling heuristics, across a range of load and load jitter conditions. These studies were conducted within an avionics mission computing applications framework running on realistic middleware and embedded hardware. The results obtained from these studies (1) demonstrate the potential benefits of reflective alternation among distinct scheduling heuristics at run-time, and (2) suggest performance factors of interest for future work on adaptive control policies and mechanisms using this framework

Energy Demand Response for High-Performance Computing Systems

The growing computational demand of scientific applications has greatly motivated the development of large-scale high-performance computing (HPC) systems in the past decade. To accommodate the increasing demand of applications, HPC systems have been going through dramatic architectural changes (e.g., introduction of many-core and multi-core systems, rapid growth of complex interconnection network for efficient communication between thousands of nodes), as well as significant increase in size (e.g., modern supercomputers consist of hundreds of thousands of nodes). With such changes in architecture and size, the energy consumption by these systems has increased significantly. With the advent of exascale supercomputers in the next few years, power consumption of the HPC systems will surely increase; some systems may even consume hundreds of megawatts of electricity. Demand response programs are designed to help the energy service providers to stabilize the power system by reducing the energy consumption of participating systems during the time periods of high demand power usage or temporary shortage in power supply. This dissertation focuses on developing energy-efficient demand-response models and algorithms to enable HPC system\u27s demand response participation. In the first part, we present interconnection network models for performance prediction of large-scale HPC applications. They are based on interconnected topologies widely used in HPC systems: dragonfly, torus, and fat-tree. Our interconnect models are fully integrated with an implementation of message-passing interface (MPI) that can mimic most of its functions with packet-level accuracy. Extensive experiments show that our integrated models provide good accuracy for predicting the network behavior, while at the same time allowing for good parallel scaling performance. In the second part, we present an energy-efficient demand-response model to reduce HPC systems\u27 energy consumption during demand response periods. We propose HPC job scheduling and resource provisioning schemes to enable HPC system\u27s emergency demand response participation. In the final part, we propose an economic demand-response model to allow both HPC operator and HPC users to jointly reduce HPC system\u27s energy cost. Our proposed model allows the participation of HPC systems in economic demand-response programs through a contract-based rewarding scheme that can incentivize HPC users to participate in demand response

Dynamic Rule-Based Reasoning in Smart Environments

Slimme huizen en andere soorten slimme omgevingen kunnen worden gedefinieerd door verschillende belangrijke karakteristieken. De belangrijkste hiervan is ongetwijfeld de mogelijkheid om omgevingsbewust te zijn, om de fysieke omgeving te ervaren en om de context van de huidige situatie te begrijpen. Slimme omgevingen zouden in staat moeten zijn om met deze informatie te kunnen redeneren en waardevolle kennis te kunnen afleiden. Daarnaast zullen ze de mogelijkheid moeten hebben om intelligent te reageren in reactie op veranderende situaties, volgens bepaalde doelstellingen. Slimme omgevingen zijn vaak ubiquitous, wat betekent dat hun capaciteiten voor waarnemen en handelen berusten op apparaten die zijn ingebed in de fysieke wereld. De meeste van de huidige commerciele slimme omgevingsproducten presenteren slechts gedeeltelijke oplossingen, zoals automatische verlichting of energiebewustzijn. Verschillende factoren vertragen de commercialisering van volledig slimme huizen, waaronder de noodzaak om de oplossing op iedere nieuwe locatie opnieuw zeer nauwkeurig af te stellen, de inspanningen rondom de integratie en co'ordinatie van verschillende componenten, handelingen om een consistent model over verschillende subsystemen van verschillende bronnen samen te stellen, enzovoorts. Samenvattend, de grote hoeveelheid aan inspanningen die benodigd zijn om de oplossing van een locatie naar een andere te verplaatsen hindert de mogelijkheden voor het stroomlijnen van de uitrol. Wat zijn de overeenkomsten in het ontwerp en het ontwikkelproces van een slimme omgeving? Wat is een effectieve aanpak om een redeneringsmotor voor slimme omgevingen te ontwerpen die aan alle belangrijke vereisten voldoet? Hoe kan het effect van sensorfouten voor wat betreft de besluitvorming worden geminimaliseerd? Hoe kan een slim systeem het bestaan van verschillende energieleveranciers gebruiken om de energiekosten in de tijd te minimaliseren? In dit proefschrift bespreken we en geven we antwoord op een aantal belangrijke onderzoeksvraagstukken voor huidige pervasieve systemen, slimme omgevingen in het bijzonder

Virtual Reality Games for Motor Rehabilitation

This paper presents a fuzzy logic based method to track user satisfaction without the need for devices to monitor users physiological conditions. User satisfaction is the key to any product’s acceptance; computer applications and video games provide a unique opportunity to provide a tailored environment for each user to better suit their needs. We have implemented a non-adaptive fuzzy logic model of emotion, based on the emotional component of the Fuzzy Logic Adaptive Model of Emotion (FLAME) proposed by El-Nasr, to estimate player emotion in UnrealTournament 2004. In this paper we describe the implementation of this system and present the results of one of several play tests. Our research contradicts the current literature that suggests physiological measurements are needed. We show that it is possible to use a software only method to estimate user emotion