Dynamic Orchestration of Massively Data Parallel Execution.

Graphics processing units (GPUs) are specialized hardware accelerators capable of rendering graphics much faster than conventional general-purpose processors. They are widely used in personal computers, tablets, mobile phones, and game consoles. Modern GPUs are not only efficient at manipulating computer graphics, but also are more effective than CPUs for algorithms where processing of large data blocks can be done in parallel. This is mainly due to their highly parallel architecture. While GPUs provide low-cost and efficient platforms for accelerating massively parallel applications, tedious performance tuning is required to maximize application execution efficiency. Achieving high performance requires the programmers to manually manage the amount of on-chip memory used per thread, the total number of threads per multiprocessor, the pattern of off-chip memory accesses, etc. In addition to a complex programming model, there is a lack of performance portability across various systems with different runtime properties. Programmers usually make assumptions about runtime properties when they write code and optimize that code based on those assumptions. However, if any of these properties changes during execution, the optimized code performs poorly. To alleviate these limitations, several implementations of the application are needed to maximize performance for different runtime properties. However, it is not practical for the programmer to write several different versions of the same code which are optimized for each individual runtime condition. In this thesis, we propose a static and dynamic compiler framework to take the burden of fine tuning different implementations of the same code off the programmer. This framework enables the programmer to write the program once and allow a static compiler to generate different versions of a data parallel application with several tuning parameters. The runtime system selects the best version and fine tunes its parameters based on runtime properties such as device configuration, input size, dependency, and data values.PhDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/108805/1/mehrzads_1.pd

Running stream-like programs on heterogeneous multi-core systems

All major semiconductor companies are now shipping multi-cores. Phones, PCs, laptops, and mobile internet devices will all require software that can make effective use of these cores. Writing high-performance parallel software is difficult, time-consuming and error prone, increasing both time-to-market and cost. Software outlives hardware; it typically takes longer to develop new software than hardware, and legacy software tends to survive for a long time, during which the number of cores per system will increase. Development and maintenance productivity will be improved if parallelism and technical details are managed by the machine, while the programmer reasons about the application as a whole. Parallel software should be written using domain-specific high-level languages or extensions. These languages reveal implicit parallelism, which would be obscured by a sequential language such as C. When memory allocation and program control are managed by the compiler, the program's structure and data layout can be safely and reliably modified by high-level compiler transformations. One important application domain contains so-called stream programs, which are structured as independent kernels interacting only through one-way channels, called streams. Stream programming is not applicable to all programs, but it arises naturally in audio and video encode and decode, 3D graphics, and digital signal processing. This representation enables high-level transformations, including kernel unrolling and kernel fusion. This thesis develops new compiler and run-time techniques for stream programming. The first part of the thesis is concerned with a statically scheduled stream compiler. It introduces a new static partitioning algorithm, which determines which kernels should be fused, in order to balance the loads on the processors and interconnects. A good partitioning algorithm is crucial if the compiler is to produce efficient code. The algorithm also takes account of downstream compiler passes---specifically software pipelining and buffer allocation---and it models the compiler's ability to fuse kernels. The latter is important because the compiler may not be able to fuse arbitrary collections of kernels. This thesis also introduces a static queue sizing algorithm. This algorithm is important when memory is distributed, especially when local stores are small. The algorithm takes account of latencies and variations in computation time, and is constrained by the sizes of the local memories. The second part of this thesis is concerned with dynamic scheduling of stream programs. First, it investigates the performance of known online, non-preemptive, non-clairvoyant dynamic schedulers. Second, it proposes two dynamic schedulers for stream programs. The first is specifically for one-dimensional stream programs. The second is more general: it does not need to be told the stream graph, but it has slightly larger overhead. This thesis also introduces some support tools related to stream programming. StarssCheck is a debugging tool, based on Valgrind, for the StarSs task-parallel programming language. It generates a warning whenever the program's behaviour contradicts a pragma annotation. Such behaviour could otherwise lead to exceptions or race conditions. StreamIt to OmpSs is a tool to convert a streaming program in the StreamIt language into a dynamically scheduled task based program using StarSs.Totes les empreses de semiconductors produeixen actualment multi-cores. Mòbils,PCs, portàtils, i dispositius mòbils d’Internet necessitaran programari quefaci servir eficientment aquests cores. Escriure programari paral·lel d’altrendiment és difícil, laboriós i propens a errors, incrementant tant el tempsde llançament al mercat com el cost. El programari té una vida més llarga queel maquinari; típicament pren més temps desenvolupar nou programi que noumaquinari, i el programari ja existent pot perdurar molt temps, durant el qualel nombre de cores dels sistemes incrementarà. La productivitat dedesenvolupament i manteniment millorarà si el paral·lelisme i els detallstècnics són gestionats per la màquina, mentre el programador raona sobre elconjunt de l’aplicació.El programari paral·lel hauria de ser escrit en llenguatges específics deldomini. Aquests llenguatges extrauen paral·lelisme implícit, el qual és ocultatper un llenguatge seqüencial com C. Quan l’assignació de memòria i lesestructures de control són gestionades pel compilador, l’estructura iorganització de dades del programi poden ser modificades de manera segura ifiable per les transformacions d’alt nivell del compilador.Un dels dominis de l’aplicació importants és el que consta dels programes destream; aquest programes són estructurats com a nuclis independents queinteractuen només a través de canals d’un sol sentit, anomenats streams. Laprogramació de streams no és aplicable a tots els programes, però sorgeix deforma natural en la codificació i descodificació d’àudio i vídeo, gràfics 3D, iprocessament de senyals digitals. Aquesta representació permet transformacionsd’alt nivell, fins i tot descomposició i fusió de nucli.Aquesta tesi desenvolupa noves tècniques de compilació i sistemes en tempsd’execució per a programació de streams. La primera part d’aquesta tesi esfocalitza amb un compilador de streams de planificació estàtica. Presenta unnou algorisme de partició estàtica, que determina quins nuclis han de serfusionats, per tal d’equilibrar la càrrega en els processadors i en lesinterconnexions. Un bon algorisme de particionat és fonamental per tal de queel compilador produeixi codi eficient. L’algorisme també té en compte elspassos de compilació subseqüents---específicament software pipelining il’arranjament de buffers---i modela la capacitat del compilador per fusionarnuclis. Aquesta tesi també presenta un algorisme estàtic de redimensionament de cues.Aquest algorisme és important quan la memòria és distribuïda, especialment quanles memòries locals són petites. L’algorisme té en compte latències ivariacions en els temps de càlcul, i considera el límit imposat per la mida deles memòries locals.La segona part d’aquesta tesi es centralitza en la planificació dinàmica deprogrames de streams. En primer lloc, investiga el rendiment dels planificadorsdinàmics online, non-preemptive i non-clairvoyant. En segon lloc, proposa dosplanificadors dinàmics per programes de stream. El primer és específicament pera programes de streams unidimensionals. El segon és més general: no necessitael graf de streams, però els overheads són una mica més grans.Aquesta tesi també presenta un conjunt d’eines de suport relacionades amb laprogramació de streams. StarssCheck és una eina de depuració, que és basa enValgrind, per StarSs, un llenguatge de programació paral·lela basat en tasques.Aquesta eina genera un avís cada vegada que el comportament del programa estàen contradicció amb una anotació pragma. Aquest comportament d’una altra manerapodria causar excepcions o situacions de competició. StreamIt to OmpSs és unaeina per convertir un programa de streams codificat en el llenguatge StreamIt aun programa de tasques en StarSs planificat de forma dinàmica.Postprint (published version

Profile-driven parallelisation of sequential programs

Traditional parallelism detection in compilers is performed by means of static analysis and more specifically data and control dependence analysis. The information that is available at compile time, however, is inherently limited and therefore restricts the parallelisation opportunities. Furthermore, applications written in C – which represent the majority of today’s scientific, embedded and system software – utilise many lowlevel features and an intricate programming style that forces the compiler to even more conservative assumptions. Despite the numerous proposals to handle this uncertainty at compile time using speculative optimisation and parallelisation, the software industry still lacks any pragmatic approaches that extracts coarse-grain parallelism to exploit the multiple processing units of modern commodity hardware. This thesis introduces a novel approach for extracting and exploiting multiple forms of coarse-grain parallelism from sequential applications written in C. We utilise profiling information to overcome the limitations of static data and control-flow analysis enabling more aggressive parallelisation. Profiling is performed using an instrumentation scheme operating at the Intermediate Representation (Ir) level of the compiler. In contrast to existing approaches that depend on low-level binary tools and debugging information, Ir-profiling provides precise and direct correlation of profiling information back to the Ir structures of the compiler. Additionally, our approach is orthogonal to existing automatic parallelisation approaches and additional fine-grain parallelism may be exploited. We demonstrate the applicability and versatility of the proposed methodology using two studies that target different forms of parallelism. First, we focus on the exploitation of loop-level parallelism that is abundant in many scientific and embedded applications. We evaluate our parallelisation strategy against the Nas and Spec Fp benchmarks and two different multi-core platforms (a shared-memory Intel Xeon Smp and a heterogeneous distributed-memory Ibm Cell blade). Empirical evaluation shows that our approach not only yields significant improvements when compared with state-of- the-art parallelising compilers, but comes close to and sometimes exceeds the performance of manually parallelised codes. On average, our methodology achieves 96% of the performance of the hand-tuned parallel benchmarks on the Intel Xeon platform, and a significant speedup for the Cell platform. The second study, addresses the problem of partially sequential loops, typically found in implementations of multimedia codecs. We develop a more powerful whole-program representation based on the Program Dependence Graph (Pdg) that supports profiling, partitioning and codegeneration for pipeline parallelism. In addition we demonstrate how this enhances conventional pipeline parallelisation by incorporating support for multi-level loops and pipeline stage replication in a uniform and automatic way. Experimental results using a set of complex multimedia and stream processing benchmarks confirm the effectiveness of the proposed methodology that yields speedups up to 4.7 on a eight-core Intel Xeon machine

Dependable Computing on Inexact Hardware through Anomaly Detection.

Reliability of transistors is on the decline as transistors continue to shrink in size. Aggressive voltage scaling is making the problem even worse. Scaled-down transistors are more susceptible to transient faults as well as permanent in-field hardware failures. In order to continue to reap the benefits of technology scaling, it has become imperative to tackle the challenges risen due to the decreasing reliability of devices for the mainstream commodity market. Along with the worsening reliability, achieving energy efficiency and performance improvement by scaling is increasingly providing diminishing marginal returns. More than any other time in history, the semiconductor industry faces the crossroad of unreliability and the need to improve energy efficiency. These challenges of technology scaling can be tackled by categorizing the target applications in the following two categories: traditional applications that have relatively strict correctness requirement on outputs and emerging class of soft applications, from various domains such as multimedia, machine learning, and computer vision, that are inherently inaccuracy tolerant to a certain degree. Traditional applications can be protected against hardware failures by low-cost detection and protection methods while soft applications can trade off quality of outputs to achieve better performance or energy efficiency. For traditional applications, I propose an efficient, software-only application analysis and transformation solution to detect data and control flow transient faults. The intelligence of the data flow solution lies in the use of dynamic application information such as control flow, memory and value profiling. The control flow protection technique achieves its efficiency by simplifying signature calculations in each basic block and by performing checking at a coarse-grain level. For soft applications, I develop a quality control technique. The quality control technique employs continuous, light-weight checkers to ensure that the approximation is controlled and application output is acceptable. Overall, I show that the use of low-cost checkers to produce dependable results on commodity systems---constructed from inexact hardware components---is efficient and practical.PhDComputer Science and EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/113341/1/dskhudia_1.pd

Event extraction from biomedical texts using trimmed dependency graphs

This thesis explores the automatic extraction of information from biomedical publications. Such techniques are urgently needed because the biosciences are publishing continually increasing numbers of texts. The focus of this work is on events. Information about events is currently manually curated from the literature by biocurators. Biocuration, however, is time-consuming and costly so automatic methods are needed for information extraction from the literature. This thesis is dedicated to modeling, implementing and evaluating an advanced event extraction approach based on the analysis of syntactic dependency graphs. This work presents the event extraction approach proposed and its implementation, the JReX (Jena Relation eXtraction) system. This system was used by the University of Jena (JULIE Lab) team in the "BioNLP 2009 Shared Task on Event Extraction" competition and was ranked second among 24 competing teams. Thereafter JReX was the highest scorer on the worldwide shared U-Compare event extraction server, outperforming the competing systems from the challenge. This success was made possible, among other things, by extensive research on event extraction solutions carried out during this thesis, e.g., exploring the effects of syntactic and semantic processing procedures on solving the event extraction task. The evaluations executed on standard and community-wide accepted competition data were complemented by real-life evaluation of large-scale biomedical database reconstruction. This work showed that considerable parts of manually curated databases can be automatically re-created with the help of the event extraction approach developed. Successful re-creation was possible for parts of RegulonDB, the world's largest database for E. coli. In summary, the event extraction approach justified, developed and implemented in this thesis meets the needs of a large community of human curators and thus helps in the acquisition of new knowledge in the biosciences

Low-Power Design of Digital VLSI Circuits around the Point of First Failure

As an increase of intelligent and self-powered devices is forecasted for our future everyday life, the implementation of energy-autonomous devices that can wirelessly communicate data from sensors is crucial. Even though techniques such as voltage scaling proved to effectively reduce the energy consumption of digital circuits, additional energy savings are still required for a longer battery life. One of the main limitations of essentially any low-energy technique is the potential degradation of the quality of service (QoS). Thus, a thorough understanding of how circuits behave when operated around the point of first failure (PoFF) is key for the effective application of conventional energy-efficient methods as well as for the development of future low-energy techniques. In this thesis, a variety of circuits, techniques, and tools is described to reduce the energy consumption in digital systems when operated either in the safe and conservative exact region, close to the PoFF, or even inside the inexact region. A straightforward approach to reduce the power consumed by clock distribution while safely operating in the exact region is dual-edge-triggered (DET) clocking. However, the DET approach is rarely taken, primarily due to the perceived complexity of its integration. In this thesis, a fully automated design flow is introduced for applying DET clocking to a conventional single-edge-triggered (SET) design. In addition, the first static true-single-phase-clock DET flip-flop (DET-FF) that completely avoids clock-overlap hazards of DET registers is proposed. Even though the correct timing of synchronous circuits is ensured in worst-case conditions, the critical path might not always be excited. Thus, dynamic clock adjustment (DCA) has been proposed to trim any available dynamic timing margin by changing the operating clock frequency at runtime. This thesis describes a dynamically-adjustable clock generator (DCG) capable of modifying the period of the produced clock signal on a cycle-by-cycle basis that enables the DCA technique. In addition, a timing-monitoring sequential (TMS) that detects input transitions on either one of the clock phases to enable the selection of the best timing-monitoring strategy at runtime is proposed. Energy-quality scaling techniques aimat trading lower energy consumption for a small degradation on the QoS whenever approximations can be tolerated. In this thesis, a low-power methodology for the perturbation of baseline coefficients in reconfigurable finite impulse response (FIR) filters is proposed. The baseline coefficients are optimized to reduce the switching activity of the multipliers in the FIR filter, enabling the possibility of scaling the power consumption of the filter at runtime. The area as well as the leakage power of many system-on-chips is often dominated by embedded memories. Gain-cell embedded DRAM (GC-eDRAM) is a compact, low-power and CMOS-compatible alternative to the conventional static random-access memory (SRAM) when a higher memory density is desired. However, due to GC-eDRAMs relying on many interdependent variables, the adaptation of existing memories and the design of future GCeDRAMs prove to be highly complex tasks. Thus, the first modeling tool that estimates timing, memory availability, bandwidth, and area of GC-eDRAMs for a fast exploration of their design space is proposed in this thesis

Proceedings of the Conference on Natural Language Processing 2010

This book contains state-of-the-art contributions to the 10th conference on Natural Language Processing, KONVENS 2010 (Konferenz zur Verarbeitung natürlicher Sprache), with a focus on semantic processing. The KONVENS in general aims at offering a broad perspective on current research and developments within the interdisciplinary field of natural language processing. The central theme draws specific attention towards addressing linguistic aspects ofmeaning, covering deep as well as shallow approaches to semantic processing. The contributions address both knowledgebased and data-driven methods for modelling and acquiring semantic information, and discuss the role of semantic information in applications of language technology. The articles demonstrate the importance of semantic processing, and present novel and creative approaches to natural language processing in general. Some contributions put their focus on developing and improving NLP systems for tasks like Named Entity Recognition or Word Sense Disambiguation, or focus on semantic knowledge acquisition and exploitation with respect to collaboratively built ressources, or harvesting semantic information in virtual games. Others are set within the context of real-world applications, such as Authoring Aids, Text Summarisation and Information Retrieval. The collection highlights the importance of semantic processing for different areas and applications in Natural Language Processing, and provides the reader with an overview of current research in this field

Deep learning methods for knowledge base population

Knowledge bases store structured information about entities or concepts of the world and can be used in various applications, such as information retrieval or question answering. A major drawback of existing knowledge bases is their incompleteness. In this thesis, we explore deep learning methods for automatically populating them from text, addressing the following tasks: slot filling, uncertainty detection and type-aware relation extraction. Slot filling aims at extracting information about entities from a large text corpus. The Text Analysis Conference yearly provides new evaluation data in the context of an international shared task. We develop a modular system to address this challenge. It was one of the top-ranked systems in the shared task evaluations in 2015. For its slot filler classification module, we propose contextCNN, a convolutional neural network based on context splitting. It improves the performance of the slot filling system by 5.0% micro and 2.9% macro F1. To train our binary and multiclass classification models, we create a dataset using distant supervision and reduce the number of noisy labels with a self-training strategy. For model optimization and evaluation, we automatically extract a labeled benchmark for slot filler classification from the manual shared task assessments from 2012-2014. We show that results on this benchmark are correlated with slot filling pipeline results with a Pearson's correlation coefficient of 0.89 (0.82) on data from 2013 (2014). The combination of patterns, support vector machines and contextCNN achieves the best results on the benchmark with a micro (macro) F1 of 51% (53%) on test. Finally, we analyze the results of the slot filling pipeline and the impact of its components. For knowledge base population, it is essential to assess the factuality of the statements extracted from text. From the sentence "Obama was rumored to be born in Kenya", a system should not conclude that Kenya is the place of birth of Obama. Therefore, we address uncertainty detection in the second part of this thesis. We investigate attention-based models and make a first attempt to systematize the attention design space. Moreover, we propose novel attention variants: External attention, which incorporates an external knowledge source, k-max average attention, which only considers the vectors with the k maximum attention weights, and sequence-preserving attention, which allows to maintain order information. Our convolutional neural network with external k-max average attention sets the new state of the art on a Wikipedia benchmark dataset with an F1 score of 68%. To the best of our knowledge, we are the first to integrate an uncertainty detection component into a slot filling pipeline. It improves precision by 1.4% and micro F1 by 0.4%. In the last part of the thesis, we investigate type-aware relation extraction with neural networks. We compare different models for joint entity and relation classification: pipeline models, jointly trained models and globally normalized models based on structured prediction. First, we show that using entity class prediction scores instead of binary decisions helps relation classification. Second, joint training clearly outperforms pipeline models on a large-scale distantly supervised dataset with fine-grained entity classes. It improves the area under the precision-recall curve from 0.53 to 0.66. Third, we propose a model with a structured prediction output layer, which globally normalizes the score of a triple consisting of the classes of two entities and the relation between them. It improves relation extraction results by 4.4% F1 on a manually labeled benchmark dataset. Our analysis shows that the model learns correct correlations between entity and relation classes. Finally, we are the first to use neural networks for joint entity and relation classification in a slot filling pipeline. The jointly trained model achieves the best micro F1 score with a score of 22% while the neural structured prediction model performs best in terms of macro F1 with a score of 25%

Abstracts from the 25th Fungal Genetics Conference

Abstracts from the 25th Fungal Genetics Conferenc