The extraordinary growth of parallelism in high-performance computing requires efficient data communication for scaling compute performance. High-performance computing systems have been using photonic links for communication of large bandwidth-distance product during the last decade. Photonic interconnection networks, however, should not be a wire-for-wire replacement based on conventional electrical counterparts. Features of photonics beyond high bandwidth, such as transparent bandwidth steering, can implement important functionalities needed by applications. In another aspect, application characteristics can be exploited to design better photonic interconnects. Therefore, this thesis explores codesign opportunities at the intersection between photonic interconnect architectures and high-performance computing applications. The key accomplishments of this thesis, ranging from system level to node level, are as follows. Chapter 2 presents a system-level architecture that leverages photonic switching to enable a reconfigurable interconnect. The architecture, called Flexfly, reconfigures the inter-group level of the widely-used Dragonfly topology using information about the application’s communication pattern. It can steal additional direct bandwidth for communication-intensive group pairs. Simulations with applications such as GTC, Nekbone and LULESH show up to 1.8x speedup over Dragonfly paired with UGAL routing, along with halved hop count and latency for cross-group messages. To demonstrate the effectiveness of our approach, we built a 32-node Flexfly prototype using a silicon photonic switch connecting four groups and demonstrated 820 ns interconnect reconfiguration time. This is the first demonstration of silicon photonic switching and bandwidth steering in a high-performance computing cluster. Chapter 3 extends photonic switching to the node level and presents a reconfigurable silicon photonic memory interconnect for many-core architectures. The interconnect targets at important memory access issues, such as network-on-chip hot-spots and non-uniform memory access. Integrated with the processor through 2.5D/3D stacking, a fast-tunable silicon photonic memory tunnel can transparently direct traffic from any off-chip memory to any on-chip interface – thus alleviating the hot-spot and non-uniform access effects. We demonstrated the operation of our proposed architecture using a tunable laser, a 4-port silicon photonic switch (four wavelength-routed memory channels) and a 4x4 mesh network-on-chip synthesized by FPGA. The emulated system achieves a 15-ns channel switching time. Simulations based on a 12-core 4-memory model show that for such switching speeds the interconnect system can realize a 2x speedup for the STREAM benchmark in the hot-spot scenario and a reduction of execution time for data-intensive applications such as 3D stencil and K-means clustering by 23% and 17%, respectively. Chapters 4 explores application-level characteristics that can be exploited to hide photonic path setup delays. In view of the frequent reuse of optical circuits by many applications, we proposed a circuit-cached scheme that amortizes the setup overhead by maximizing circuit reuses. In order to improve circuit “hit” rates, we developed a reuse-distance based replacement policy called “Farthest Next Use”. We further investigated the tradeoffs between the realized hit rate and energy consumption. Finally, we experimentally demonstrated the feasibility of the proposed concept using silicon photonic devices in an FPGA-controlled network testbed. Chapter 5 proceeds to develop an application-guided circuit-prefetch scheme. By learning temporal locality and communication patterns from upper-layer applications, the scheme not only caches a set of circuits for reuses, but also proactively prefetches circuits based on predictions. We applied this technique to communication patterns from a spectrum of science and engineering applications. The results show that setup delays via circuit misses are significantly reduced, showing how the proposed technique can improve circuit switching in photonic interconnects.

Polymers are among the most important of various oilfield chemicals and are used for a variety of applications in the oil and gas industry (OGI) including water and gas shutoff, drilling mud viscosity modification, filtration loss control (FLC), swellable packers, loss circulation material (LCM) pills, enhanced oil recovery (EOR), fracture treatment and cleanup, chemical placement, etc. The deposition and retention of polymer molecules in porous media and their interactions with rock and fluids present complex phenomena that can induce formation damage. Formation damage due to polymer retention can occur via mobility reduction in three possible mechanisms of polymer-induced formation damage: 1) pore-throat blocking, 2) wettability alteration (which can alter permeability), and 3) increase in reservoir fluid viscosity. Physical adsorption can also cause permanent permeability impairment (formation damage). This polymer-induced formation damage (causing a reduction in net oil recovery) continues to be a fundamental problem in the industry owing to the rather shallow understanding of the mechanics of polymer-brine-rock interactions and the polymer-aided formation damage mechanisms. Most models available for polymer risk assessments appear to be utilised for all scenarios with unsatisfying results. For example, only very little, if any, is known on how polymer type, particularly in the presence of brine type impact on formation damage. In order words, one of current industry challenges is finding effective polymers for high salinity environments. Also, the effect of polymer charge, as well as charges at the brine-rock interface are issues that require a deeper understanding in order to address the role polymer play in formation damage. Furthermore, no much recognition has been given to polymer rheological behaviour in complex porous media, etc. The OGI therefore still faces the challenge of the inability to correctly predict hydrolysed polyacrylamide (HPAM) viscosity under shear degradation; and consequently have not been able to meet the need of production predictions. The effect of the above mentioned factors, etc have not been fully integrated into the polymer formation damage modelling. In this PhD research work, theoretical, numerical, laboratory experiments and analytical methods were used to further investigate the mechanics of polymer-brine-rock interactions and establish the mechanisms for formation damage related to polymer application. Three different hydrolysed polyacrylamide (HPAM) products (SNF FP3630 S, 3330 S and FloComb C3525) were used in the experiments; while Xanthan gum was used in the simulation work. The following variables were considered: 1) polymer type, 2) effect of concentration, 3) effect of salinity/hardness, 4) effect of permeability and pore size distributions, 5) effect of inaccessible pore volume (IAPV) on retention, 6) effect of flow rate (where a special method was established to quantify the effect of flow rate on polymer retention). Laboratory rheological and adsorption experiments were designed and conducted. Experimental results indicate that higher concentration of calcium divalent ions in brine help promote polymer retention on rock surface. On the basis of the experimental results, empirical models were developed and validated to: 1) predict HPAM rheological behaviour over a wide range of shear rates, 2) predict salinity-dependent polymer-induced formation damage, 3) in addition, a modified screening model that can aid polymer selection for field application design is proposed. Overall, these models can therefore serve as useful tools, and be used for quick look-ahead prediction and evaluation of polymer related formation damage in oil and gas-bearing formations.

從微藻提煉的生物燃料，是化石燃料和其他生物燃料的優良替代品。藻類生物燃料屬碳中性，因為微藻為光自養生物，能經光合作用吸收二氧化碳，並將之轉化成碳氫化合物和脂肪。碳氫化合物和脂肪可用以提煉生物燃料。此外，微藻可以吸收廢水中的污染物作生長的營養，同時作污水處理。 / 本研究項目的目的為透過下述方法，降低藻類生物燃料的生產成本，並提高藻株的脂肪含量： (1) 篩選可以在污水自養培育，並有高產油量的微藻菌株，(2) 以兩階段培養方法，用處理過的污水作培養，從而提高油脂產，(3) 透過微藻毒理測試，和水質化學分析，研究處理後的污水中影響微藻生長的污染物和有毒物質。 / 這個研究中使用從沙田污水處理廠收集的二級處理污水，其水質亦被研究。幾種微藻菌株分別為小球藻 (Chlorella pyrenoidosa)，叢粒藻 (Botryococcus braunii) 和微綠球藻 (Nannochloropsis oculata)，從鰂魚池水分離出的小球藻 (Chlorella sp.1)，及兩種從處理污水中分離出的小球藻(Chlorella sp. 2, Chlorella sp. 3)。微藻菌株分別在培養基和處理污水中培養，並比較在兩種情況下的脂肪，脂肪酸，碳水化合物，蛋白質含量，生物質量和總有機碳。結果發現，雖然經處理的污水中營養成分非常低 (<0.11 mg / L活性磷，<9.68 mg / L硝酸根，<0.5 mg / L鉀離子)，所有研究的微藻菌株都能存活。在兩階段培養法下，首先以「氮含量充足階段」(培養基)提高生物質量，然後以「氮含量不足階段」(經處理污水) 培養，培養成本可以降低，同時提高脂肪生產率。在兩階段培養法下，叢粒藻的脂肪生產率比在人工培養基和經處理污水高2.6倍和7.13倍。 / 沙田污水處理廠處理的污水水質良好，並無驗出有害重金屬，雙酚A(BPA)，四溴雙酚A(TBBPA)和2,3,7,8-四氯二苯並二噁英(TCDD)。從藻類產生的生物燃料將不含有重金屬。 / 在這個研究中的叢粒藻 (Botryococcus braunii)，微綠球藻 (Nannochloropsis oculata)和小球藻 (Chlorella sp.1)都可以容忍雙酚A(BPA)，四溴雙酚A(TBBPA)，二氯苯氧氯酚 (TCS)和2,3,7,8-四氯二苯並二噁英(TCDD)。他們可以培育在其他來源的經處理污水。 / 利用經處理污水於兩階段培養法，是一種新的、更經濟的增加微藻油脂產量方法，亦可以配合任何其他方法，以減低藻類生物燃料的製造成本。 / Biofuel from microalgae can be an excellent substitute of fossil fuel and other biofuels. Algal biofuel is carbon neutral as microalgae are photoautotrophic. Through photosynthesis, microalgae can capture and convert carbon dioxide to hydrocarbons or lipids which can be used for biofuel production. Besides, microalgae can use pollutants from wastewater as nutrients for growth, which can serve as a wastewater treatment process. / The aims of the project are to lower the cost of algal biofuel production and boost up lipid content of algal strains by (1) screen a microalgal strain that can be cultivated in treated sewage autotrophically and give high oil yield, (2) use two phase cultivation, with treated sewage as medium, to boost up lipid productivity, (3) investigate heavy metals and some organic pollutants that may exist in treated sewage and can affect algal growth by performing algal toxicity test and chemical analysis of treated sewage. / The secondarily treated sewage used in this project was collected from the Sha Tin Sewage Treatment Works. The quality of the secondarily treated sewage was monitored. Chlorella pyrenoidosa, Botryococcus braunii and Nannochloropsis oculata from commercial source, and Chlorella sp. 1 isolated from tilapia fish pond water, and two species of algae, Chlorella sp. 2 and Chlorella sp. 3, isolated from treated sewage were investigated. Microalgal strains are compared by investigating the content of lipid, fatty acid, carbohydrate, protein, biomass and total organic carbon when cultivated in culture medium and treated sewage. Results found that although nutrients in treated sewage were very low (<0.11 mg/L reactive phosphorus, <9.68 mg/L nitrate and <0.5 mg/L potassium ion), all the microalgae investigated could grow reasonably well. Using two phase cultivation, with an initial nitrogen sufficient phase (artificial media) for biomass production, followed by nitrogen limitation phase (treated sewage), cost of cultivation could be reduced and the overall lipid productivity could be increased. Under the two phase cultivation, the lipid productivity of Botryococcus braunii was 2.6 and 7.13 fold higher than cultivated in artificial medium and treated sewage respectively. / Treated sewage from the Sha Tin Sewage Treatment Works was in good quality without harmful concentrations of heavy metal and BPA, TBBPA and TCDD. The microalgae could not absorb or adsorb significant amount of the harmful substances and the algal biofuel produced would not contain heavy metals. All the microalgae investigated in this project could tolerate BPA, TBBPA, TCS and TCDD. They could be cultivated in treated sewage from other sources. / Two phase cultivation using treated sewage is a new way for increasing lipid productivity from microalgae economically and can be combined with any other means for producing algal biofuel with lowest cost. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Kwan, Ka Ki. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 104-113). / Abstracts also in Chinese. / Acknowledgements --- p.i / Abstract --- p.iii / 摘要 --- p.Vi / Table of Contents --- p.viii / List of Figures --- p.Xii / List of Plates --- p.Xvi / List of Tables --- p.xviii / Abbreviations --- p.xx / Chapter 1. --- General introduction / Chapter 1.1 --- Fossil fuel, the major energy source nowadays --- p.1 / Chapter 1.2 --- Disadvantages of using fossil fuel --- p.3 / Chapter 1.3 --- Biofuel --- p.5 / Chapter 1.4 --- Disadvantages of traditional biofuel production --- p.8 / Chapter 1.5 --- Characteristics of microalgae --- p.9 / Chapter 1.6 --- Biofuel from microalgae --- p.14 / Chapter 1.7 --- Nutrients for microalgae related to lipid production --- p.18 / Chapter 1.8 --- Current research on algal biofuel --- p.19 / Chapter 1.9 --- Two phase cultivation as a new way for lipid production --- p.24 / Chapter 1.10 --- Objectives --- p.24 / Chapter 2. --- Biofuel production under two phase cultivation with artificial medium and treated sewage / Chapter 2.1 --- Introduction --- p.26 / Chapter 2.2 --- Materials and Methods --- p.28 / Chapter 2.2.1 --- Algal strains collection and isolation --- p.28 / Chapter 2.2.2 --- Artificial culture media --- p.29 / Chapter 2.2.2.1 --- Bristol’s Medium (BM) --- p.29 / Chapter 2.2.2.2 --- Modified Bold 3N medium (MBM) --- p.31 / Chapter 2.2.3.3 --- F/2 medium (F/2) --- p.33 / Chapter 2.2.3 --- Water quality of treated sewage --- p.33 / Chapter 2.2.3.1 --- Chemical and biological condition --- p.34 / Chapter 2.2.3.2 --- Total organic carbon and total nitrogen (TOC/TN) --- p.35 / Chapter 2.2.3.3 --- Reactive phosphate --- p.35 / Chapter 2.2.3.4 --- Nitrate --- p.37 / Chapter 2.2.3.5 --- Ammonia --- p.39 / Chapter 2.2.3.6 --- Metal elements --- p.40 / Chapter 2.2.4 --- Cultivation conditions --- p.40 / Chapter 2.2.5 --- Growth monitor of microalgae in artificial medium and treated sewage --- p.41 / Chapter 2.2.6 --- Comparison of microalgae cultivated in artificial media and treated sewage --- p.42 / Chapter 2.2.6.1 --- Large scale cultivation --- p.42 / Chapter 2.2.6.2 --- Cell morphology --- p.43 / Chapter 2.2.6.3 --- Cell harvesting --- p.44 / Chapter 2.2.6.4 --- Dried biomass --- p.44 / Chapter 2.2.6.5 --- Lipid content --- p.45 / Chapter 2.2.6.6 --- Fatty acid profile --- p.46 / Chapter 2.2.6.7 --- Extraction of carbohydrates and protein --- p.48 / Chapter 2.2.6.8 --- Carbohydrate content --- p.48 / Chapter 2.2.6.9 --- Protein content --- p.49 / Chapter 2.2.7 --- Two phase cultivation --- p.50 / Chapter 2.2.8 --- Statistical analysis --- p.50 / Chapter 2.3 --- Results --- p.51 / Chapter 2.3.1 --- Water quality of treated sewage --- p.51 / Chapter 2.3.2 --- Nutrient contents in artificial medium --- p.54 / Chapter 2.3.3 --- Growth of microalgae in artificial medium and treated sewage --- p.54 / Chapter 2.3.3.1 --- Cell morphology and cell size --- p.57 / Chapter 2.3.3.2 --- Biomass --- p.59 / Chapter 2.3.3.3 --- Lipid content --- p.61 / Chapter 2.3.3.4 --- Fatty acid profile --- p.63 / Chapter 2.3.3.5 --- Carbohydrates content --- p.66 / Chapter 2.3.3.6 --- Protein content --- p.67 / Chapter 2.3.4 --- Two phase cultivation --- p.69 / Chapter 2.4 --- Discussion --- p.74 / Chapter 2.4.1 --- Water quality of treated sewage and nutrients in artificial medium --- p.74 / Chapter 2.4.2 --- Growth of microalgae in artificial medium and filtered treated sewage --- p.75 / Chapter 2.4.3 --- Microalgae cultivated in artificial media and treated sewage --- p.76 / Chapter 2.4.4 --- Two phase cultivation --- p.81 / Chapter 3. --- Possible toxic effect on algal growth from chemicals in sewage / Chapter 3.1 --- Introduction --- p.84 / Chapter 3.2 --- Materials and methods --- p.85 / Chapter 3.2.1 --- Analysis of dissolved metals by ICP --- p.85 / Chapter 3.2.2 --- Organic compounds --- p.86 / Chapter 3.2.3 --- Algal bioassay --- p.87 / Chapter 3.3 --- Results --- p.88 / Chapter 3.3.1 --- Dissolved metals and metalloids --- p.88 / Chapter 3.3.2 --- Organic compounds --- p.88 / Chapter 3.3.3 --- Algal bioassay --- p.91 / Chapter 3.4 --- Discussion --- p.97 / Chapter 4. --- Conclusion and future prospectives --- p.99 / Chapter 4.1 --- Summary --- p.99 / Chapter 4.2 --- Genetic engineering --- p.100 / Chapter 4.3 --- Further study --- p.102 / Chapter 4.4 --- Conclusion --- p.102 / Chapter 5. --- References --- p.104

Electronic patient records, containing data about the health and care of a patient, are a valuable source of information for longitudinal clinical studies. The General Practice Research Database (GPRD) has collected patient records from UK primary care practices since the late 1980s. These records contain both structured data (in the form of codes and numeric values) and free text notes. While the structured data have been used extensively in clinical studies, there are significant practical obstacles in extracting information from the free text notes. The main obstacles are data access restrictions, due to the presence of sensitive information, and the specific language of medical practitioners, which renders standard language processing tools ineffective. The aim of this research is to investigate approaches for computer analysis of free text notes. The research involved designing a primary care text corpus (the Harvey Corpus) annotated with syntactic chunks and clinically-relevant semantic entities, developing a statistical chunking model, and devising a novel method for applying machine learning for entity recognition based on chunk annotation. The tools produced would facilitate reliable information extraction from primary care patient records, needed for the development of clinically-related research. The three medical concept types targeted in this thesis could contribute to epidemiological studies by enhancing the detection of co-morbidities, and better analysing the descriptions of patient experiences and treatments. The main contributions of the research reported in this thesis are: guidelines for chunk and concept annotation of clinical text, an approach to maximising agreement between human annotators, the Harvey Corpus, a method for using a standard part-of-speech tagging model in clinical text chunking, and a novel approach to recognising clinically relevant medical concepts.

投影機相機(projector camera)系統近年相當流行，主要原因是它能夠靈活地展示影像，使用戶有更大的自由度作出操作。手提式投影機的技術在過往幾年急速發展、漸見成熟，知名的家用電子産品生産廠閱始推出内置迷你投影機的手機和攝影機。另一方面手機的運算能力正急劇地提升，它們多都配置不同種類且功能强大的周邊設備。 / 本論文提出並討論一種基於現場可编程邏輯閘陣列(Field Programmable Gate Array, FPGA),並適用於嵌入式系统的特殊處理器。該特殊處理器專門處理來自相機的資料串流，透過一系列的象素圖像處理運算如圖像梯度和高斯模糊，去找出相中物件的邊緣，藉此分擔微處器在運算上的負擔。實驗結果明這特殊處理器可實現於低端的FPGA上並和普遍的微處器一起運作。 / 本論文第二個探討的主題是一個利用多模卡爾曼濾波器(Multiple Model Kalman Filter)的直線追踪器，並利用多個直線追踪器去作投影面板的追踪。利用卡爾曼濾波器只需要很低的運算能力的優點,我們的直線追踪器在嵌入式系统實測時能達到每秒200幀的速度。多模卡爾曼濾波器在實驗中有滿意的成績並較單卡爾曼濾波器和擴展卡爾曼濾波器優異。 / Projector-camera (ProCam in short) systems are getting very popular since the user can change the display area dynamically and enjoy more freedom in handling the device. In recent years, the mobile projector technology is becoming mature and manufacturers are shipping mobile phones and digital cameras with projectors. On the other hand, the computation power of a cell phone had dramatically increased and the cell phones are accompanied with large number of powerful peripherals. / In this thesis, the possibility of making an embedded Projector-camera (ProCam) system is investigated. A ProCam system is developed by our research group previously and designed for desktop Personal Computers(PCs). The system uses computer vision techniques to detect a white cardboard as the projection screen and uses particle filter to trace the screen in subsequent frames. The system demands a large computation power, unfortunately the power of low cost embedded system is still not powerful enough to implement the ProCam system.Therefore, specially designed hardware and computationally efficient algorithm are required in order to implement the ProCam system on an embedded system. / An FPGA based special processor to share the workload of the microcontroller in the embedded system is proposed and tested. This special processor will take the data stream of the camera as the inputs and apply pixel-wise image operators such as image gradient and Gaussian blur in order to extract the edge pixels. As a result, the workload of the microcontroller in the embedded system is reduced. The experiments show that the design can be implement on a low-end FPGA with a simple microcontroller. / A line tracker using Multiple Model Kalman lter is also proposed in this thesis. The aim of this tracker is to reduce the time on tracking the board. Benet from the low computation requirement of Kalman filter, the proposed line tracker can run in 200 fps on our testing embedded system. The experiments also show that the robustness of the Multiple Model Kalman filter is satisfactory and it outperforms the line trackers using single Kalman filter or extended Kalman filter alone. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Fung, Hung Kwan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2012. / Includes bibliographical references (leaves 115-124). / Abstracts also in Chinese. / Abstract --- p.ii / Acknowledgement --- p.v / Chapter 1 --- Introduction --- p.1 / Chapter 1.1 --- Motivation and Objective --- p.1 / Chapter 1.2 --- Contributions --- p.3 / Chapter 1.3 --- Thesis Organization --- p.5 / Chapter 2 --- Background --- p.7 / Chapter 2.1 --- Introduction --- p.7 / Chapter 2.2 --- Projector-Camera System --- p.8 / Chapter 2.2.1 --- Static Projector-Screen --- p.9 / Chapter 2.2.2 --- Dynamic Projector-Screen --- p.13 / Chapter 2.3 --- Embedded Vision --- p.15 / Chapter 2.4 --- Summary --- p.25 / Chapter 3 --- System Overview --- p.26 / Chapter 3.1 --- System Design --- p.26 / Chapter 3.2 --- Our Approach --- p.28 / Chapter 3.2.1 --- Projector-camera system --- p.28 / Chapter 3.2.2 --- Smart Camera --- p.31 / Chapter 3.2.3 --- Quadrangle Detection and Tracking Module --- p.32 / Chapter 3.2.4 --- Projection Module --- p.32 / Chapter 3.3 --- Extension --- p.33 / Chapter 4 --- Smart Camera --- p.34 / Chapter 4.1 --- Introduction --- p.34 / Chapter 4.2 --- Hardware Overview --- p.35 / Chapter 4.3 --- Image Acquisition --- p.40 / Chapter 4.4 --- Image Processing --- p.42 / Chapter 4.4.1 --- RGB-to-Gray Conversion Module . --- p.44 / Chapter 4.4.2 --- Image Smoothing Module --- p.45 / Chapter 4.4.3 --- Image Gradient Module --- p.49 / Chapter 4.4.4 --- Non-maximum Suppression and Hysteresis Thresholding --- p.53 / Chapter 4.5 --- Summary --- p.55 / Chapter 5 --- Quadrangle Detection and Tracking --- p.57 / Chapter 5.1 --- Introduction --- p.57 / Chapter 5.2 --- Line Feature Extraction --- p.61 / Chapter 5.3 --- Automatic Quadrangle Detection --- p.62 / Chapter 5.4 --- Real-time Quadrangle Tracking --- p.68 / Chapter 5.4.1 --- Line Tracker --- p.69 / Chapter 5.5 --- Tracking Lose Strategy --- p.76 / Chapter 5.6 --- Recover from Tracking Failure --- p.77 / Chapter 5.7 --- Summary --- p.77 / Chapter 6 --- Implementation and Experiment Result --- p.79 / Chapter 6.1 --- Introduction --- p.79 / Chapter 6.2 --- Smart Camera --- p.79 / Chapter 6.3 --- Line Tracking --- p.87 / Chapter 7 --- Limitation and Discussion --- p.101 / Chapter 7.1 --- Introduction --- p.101 / Chapter 7.2 --- Limitation --- p.101 / Chapter 7.3 --- Summary --- p.105 / Chapter 8 --- Application --- p.107 / Chapter 8.1 --- Introduction --- p.107 / Chapter 8.2 --- Portable Projector-Camera System --- p.107 / Chapter 8.3 --- Summary --- p.110 / Chapter 9 --- Conclusion --- p.112 / Bibliography --- p.115

Application record and replay is the ability to record application execution and replay it at a later time. Record-replay has many use cases including diagnosing and debugging applications by capturing and reproducing hard to find bugs, providing transparent application fault tolerance by maintaining a live replica of a running program, and offline instrumentation that would be too costly to run in a production environment. Different record-replay systems may offer different levels of replay faithfulness, the strongest level being deterministic replay which guarantees an identical reenactment of the original execution. Such a guarantee requires capturing all sources of nondeterminism during the recording phase. In the general case, such record-replay systems can dramatically hinder application performance, rendering them unpractical in certain application domains. Furthermore, various use cases are incompatible with strictly replaying the original execution. For example, in a primary-secondary database scenario, the secondary database would be unable to serve additional traffic while being replicated. No record-replay system fit all use cases. This dissertation shows how to make deterministic record-replay fast and efficient, how broadening replay semantics can enable powerful new use cases, and how choosing the right level of abstraction for record-replay can support distributed and heterogeneous database replication with little effort. We explore four record-replay systems with different semantics enabling different use cases. We first present Scribe, an OS-level deterministic record-replay mechanism that support multi-process applications on multi-core systems. One of the main challenge is to record the interaction of threads running on different CPU cores in an efficient manner. Scribe introduces two new lightweight OS mechanisms, rendezvous point and sync points, to efficiently record nondeterministic interactions such as related system calls, signals, and shared memory accesses. Scribe allows the capture and replication of hard to find bugs to facilitate debugging and serves as a solid foundation for our two following systems. We then present RacePro, a process race detection system to improve software correctness. Process races occur when multiple processes access shared operating system resources, such as files, without proper synchronization. Detecting process races is difficult due to the elusive nature of these bugs, and the heterogeneity of frameworks involved in such bugs. RacePro is the first tool to detect such process races. RacePro records application executions in deployed systems, allowing offline race detection by analyzing the previously recorded log. RacePro then replays the application execution and forces the manifestation of detected races to check their effect on the application. Upon failure, RacePro reports potentially harmful races to developers. Third, we present Dora, a mutable record-replay system which allows a recorded execution of an application to be replayed with a modified version of the application. Mutable record-replay provides a number of benefits for reproducing, diagnosing, and fixing software bugs. Given a recording and a modified application, finding a mutable replay is challenging, and undecidable in the general case. Despite the difficulty of the problem, we show a very simple but effective algorithm to search for suitable replays. Lastly, we present Synapse, a heterogeneous database replication system designed for Web applications. Web applications are increasingly built using a service-oriented architecture that integrates services powered by a variety of databases. Often, the same data, needed by multiple services, must be replicated across different databases and kept in sync. Unfortunately, these databases use vendor specific data replication engines which are not compatible with each other. To solve this challenge, Synapse operates at the application level to access a unified data representation through object relational mappers. Additionally, Synapse leverages application semantics to replicate data with good consistency semantics using mechanisms similar to Scribe.

Sinais caóticos são determinísticos, aperiódicos e apresentam dependência sensível às condições iniciais. Esta dependência significa que o estado de dois sistemas caóticos idênticos, iniciados com condições cuja diferença seja arbitrariamente pequena estarão distantes no espaço de fase depois de um tempo finito. Estes sinais podem ser interessantes para algumas áreas da Engenharia de Telecomunicações por apresentarem espectro de Fourier plano, dificuldade de previsão e serem facilmente confundíveis com ruído. Devido à sensibilidade às condições iniciais pode parecer que o sincronismo de dois sistemas caóticos seja impossível. Porém, Pecora e Carroll mostraram que este sincronismo é possível desde que os sistemas obedeçam a certas condições necessárias e suficientes. Este resultado deu um grande impulso para a geração de muitos trabalhos sobre sistemas de comunicação com detecção coerente utilizando sinais caóticos. Regra geral, eles apresentam um subsistema transmissor que gera um sinal caótico a partir do sinal de informação a ser transmitido e um subsistema receptor que consegue produzir um sinal sincronizado com o do transmissor e recuperar o sinal de informação. A literatura mostra que estes sistemas funcionam perfeitamente em condições ideais. O objetivo principal deste trabalho é estudar de forma teórica e numerica o critério de sincronismo de Pecora e Carroll e alguns dos sistemas de comunicação utilizando sinais caóticos propostos na literatura, sobretudo o seu desempenho quando há introdução de ruído branco gaussiano na transmissão e o canal é limitado em freqüência, casos pouco estudados. Mais especificamente, são analisados com certo detalhe os sistemas de comunicação analógica propostos por Cuomo e Oppenheim, por Wu e Chua e o sistema digital Chaotic Phase Shift Keying (CPSK) proposto por Ushio. Mostra-se que nas condições não-ideais citadas, esses sistemas têm desempenho muito pobre no que diz respeito à relação sinal-ruído na saída do receptor. Neste trabalho é apresentada uma solução para este problema no caso de transmissão em canal limitado em banda e é analisada uma proposta de melhoria para o caso de ruído no canal. Conclui-se que, apesar de todas as propriedades interessantes do ponto de vista de comunicações que os sinais caóticos possuem, ainda é necessária muita pesquisa e desenvolvimento para que os sistemas com detecção coerente baseados neles possam concorrer, em situações práticas, com os sistemas em uso atualmente. / Chaotic signals are deterministic, nonperiodic and exhibit sensitive dependence on initial conditions. This dependence means that the states of two identical chaotic systems started with two conditions whose difference is arbitrarily small will be distant in the phase space after a finite time. These signals may be interesting in some Telecommunication Engineering fields because their Fourier spectrum is plane, they are difficult to predict and they are noise-like. Due to the sensitive dependence on initial conditions, it may seem that the synchronism of two chaotic systems is impossible. However, as Pecora and Carroll have shown, this synchronism is possible if the systems satisfy some necessary and sufficient conditions. This result has inspired the development of many communication systems based on coherent detection of chaotic signals. In general, they are composed of a transmitter subsystem that generates a chaotic signal depending on the information to be transmitted and a receptor subsystem that can generate a chaotic signal synchronized with the one on the transmitter and can recover the information signal. These systems are known to work well under ideal conditions. The main objective of this work is to study, theoretically and numerically, Pecora and Carroll's criterion and some of the communication systems using chaotic signals proposed in the literature, specially their behavior when additive white gaussian noise is added to the transmitted signal and the channel is band-limited. Specifically, the analog communication systems proposed by Cuomo and Oppenheim, by Wu and Chua and the Chaotic Phase Shift Keying (CPSK) system proposed by Ushio are analyzed in some detail. We show that when the mentioned non-ideal conditions are present the above systems have poor performance when considering the signal-to-noise ratio at the output of the receiver. In this work a solution is presented for the case of transmission over a bandlimited channel and a method for improving the results in the case of noisy channels is analyzed. We conclude that, regardless all the potential properties chaotic signals may have for communication applications, research and development are still necessary so that systems based on them can surpass in practical situations the usual systems used nowadays.

O MPS é um método lagrangeano sem malha para simulação de fluidos, que teve origem para estudos de fluxo incompressíveis com superfície livre. Ele possui diversas vantagens se comparado a métodos convencionais baseados no uso de malha, podendo-se citar como principais a facilidade de representação de interfaces e geometrias complexas, assim como a ausência do termo de convecção nas equações algébricas. Este trabalho foca na aplicação de métodos de computação paralela para simulações de escoamento utilizando a variante explícita do método MPS, denominado E-MPS. O objetivo é a diminuição do tempo de processamento das simulações, e o aumento da quantidade de partículas, que possibilita a simulação de casos cada vez mais complexos, e o real emprego do método para solução de problemas de engenharia. O método proposto consiste de dois níveis de paralelismo: um através de uma decomposição de domínio espacial sobre uma arquitetura de memória distribuída, e outra pelo uso de processamento paralelo em uma arquitetura com memória compartilhada, podendo ser pelo uso de dispositivos Graphics Processing Unit (GPU), ou pelo uso de processadores multicore. Os métodos de decomposição de domínio espacial tratados neste trabalho são o estático, ou não adaptativo, o Orthogonal Recursive Bisection (ORB), o ortogonal e uma nova proposta chamada cell transfer. Dentre os métodos já existentes, o ortogonal se mostrou mais atrativo devido à sua simplicidade, conseguindo manter um melhor nível de balanceamento do que o estático no caso estudado. O novo método cell transfer tenta superar as limitações geométricas dos outros métodos citados, ao levar em consideração a natureza do fluxo. Uma das grandes contribuições deste trabalho é um novo método genérico de comunicação entre subdomínios, que evita a reordenação das partículas, e serve para todos os métodos de decomposição investigadas neste trabalho. / MPS is a meshless lagrangian method for computational fluid dynamics that was created to study incompressible free surface flows and has many advantages compared to traditional mesh based methods, such as the ability to represent complex geometries, interface problems, and the absence of the advection term in the algebraic equations. This work focus on the use of parallel computing methods for fluid dynamic simulation, and more specifically, on the explicit variant of the MPS method, namely E-MPS, to decrease the amount of processing needed to perform a simulation and increase the number of particles, which enables the simulation of real and complex engineering problems. The proposed method is composed of two levels of parallelism: a distributed memory parallelism based on spatial domain decomposition, and a shared memory parallelism, using either GPU or multicore CPUs, for fast computation of each subdomain. Static non-adaptive, ORB, orthogonal, and cell transfer spatial decomposition methods are subject of investigations in this work, the latter being originally proposed by this work to overcome the drawbacks found in most of the methods found in the literature. Among the already proposed methods the more attractive was the orthogonal, due to its simplicity, and capability of maintaining a good load balance in the test case. The new cell transfer method was proposed to overcome the geometrical limitations found in all the above methods, by considering the flux while balancing the load among subdomains. One of the main contributions of this work is a new method for the communication of subdomains, which avoids additional sorting steps, and proved to be generic for all the decomposition methods investigated.

O MPS é um método lagrangeano sem malha para simulação de fluidos, que teve origem para estudos de fluxo incompressíveis com superfície livre. Ele possui diversas vantagens se comparado a métodos convencionais baseados no uso de malha, podendo-se citar como principais a facilidade de representação de interfaces e geometrias complexas, assim como a ausência do termo de convecção nas equações algébricas. Este trabalho foca na aplicação de métodos de computação paralela para simulações de escoamento utilizando a variante explícita do método MPS, denominado E-MPS. O objetivo é a diminuição do tempo de processamento das simulações, e o aumento da quantidade de partículas, que possibilita a simulação de casos cada vez mais complexos, e o real emprego do método para solução de problemas de engenharia. O método proposto consiste de dois níveis de paralelismo: um através de uma decomposição de domínio espacial sobre uma arquitetura de memória distribuída, e outra pelo uso de processamento paralelo em uma arquitetura com memória compartilhada, podendo ser pelo uso de dispositivos Graphics Processing Unit (GPU), ou pelo uso de processadores multicore. Os métodos de decomposição de domínio espacial tratados neste trabalho são o estático, ou não adaptativo, o Orthogonal Recursive Bisection (ORB), o ortogonal e uma nova proposta chamada cell transfer. Dentre os métodos já existentes, o ortogonal se mostrou mais atrativo devido à sua simplicidade, conseguindo manter um melhor nível de balanceamento do que o estático no caso estudado. O novo método cell transfer tenta superar as limitações geométricas dos outros métodos citados, ao levar em consideração a natureza do fluxo. Uma das grandes contribuições deste trabalho é um novo método genérico de comunicação entre subdomínios, que evita a reordenação das partículas, e serve para todos os métodos de decomposição investigadas neste trabalho. / MPS is a meshless lagrangian method for computational fluid dynamics that was created to study incompressible free surface flows and has many advantages compared to traditional mesh based methods, such as the ability to represent complex geometries, interface problems, and the absence of the advection term in the algebraic equations. This work focus on the use of parallel computing methods for fluid dynamic simulation, and more specifically, on the explicit variant of the MPS method, namely E-MPS, to decrease the amount of processing needed to perform a simulation and increase the number of particles, which enables the simulation of real and complex engineering problems. The proposed method is composed of two levels of parallelism: a distributed memory parallelism based on spatial domain decomposition, and a shared memory parallelism, using either GPU or multicore CPUs, for fast computation of each subdomain. Static non-adaptive, ORB, orthogonal, and cell transfer spatial decomposition methods are subject of investigations in this work, the latter being originally proposed by this work to overcome the drawbacks found in most of the methods found in the literature. Among the already proposed methods the more attractive was the orthogonal, due to its simplicity, and capability of maintaining a good load balance in the test case. The new cell transfer method was proposed to overcome the geometrical limitations found in all the above methods, by considering the flux while balancing the load among subdomains. One of the main contributions of this work is a new method for the communication of subdomains, which avoids additional sorting steps, and proved to be generic for all the decomposition methods investigated.

A recent dramatic increase in the availability of early literacy applications (apps) for mobile devices has led teachers to incorporate them into their educational programs. This study explored teachers' perceptions and opinions regarding three early literacy apps: Endless Reader, Preschool Matching Game: Rhyming Words, and Hideout: Early Reading. The study consisted of 15 preschool teachers who interacted with each app and answered questions regarding their opinions about the apps and the use of digital devices in the classroom in general. Teacher responses were analyzed and categorized based on common topics that emerged from the data set. The results of the study imply that teachers prefer apps that include sound pedagogical principles as well as game-like features to keep students engaged in learning. Future research should explore the processes and guidelines teachers use when selecting apps for classroom use as well as investigating what students actually understand from early literacy apps and other apps used in the classroom.