Generating and auto-tuning parallel stencil codes

In this thesis, we present a software framework, Patus, which generates high performance stencil codes for different types of hardware platforms, including current multicore CPU and graphics processing unit architectures. The ultimate goals of the framework are productivity, portability (of both the code and performance), and achieving a high performance on the target platform. A stencil computation updates every grid point in a structured grid based on the values of its neighboring points. This class of computations occurs frequently in scientific and general purpose computing (e.g., in partial differential equation solvers or in image processing), justifying the focus on this kind of computation. The proposed key ingredients to achieve the goals of productivity, portability, and performance are domain specific languages (DSLs) and the auto-tuning methodology. The Patus stencil specification DSL allows the programmer to express a stencil computation in a concise way independently of hardware architecture-specific details. Thus, it increases the programmer productivity by disburdening her or him of low level programming model issues and of manually applying hardware platform-specific code optimization techniques. The use of domain specific languages also implies code reusability: once implemented, the same stencil specification can be reused on different hardware platforms, i.e., the specification code is portable across hardware architectures. Constructing the language to be geared towards a special purpose makes it amenable to more aggressive optimizations and therefore to potentially higher performance. Auto-tuning provides performance and performance portability by automated adaptation of implementation-specific parameters to the characteristics of the hardware on which the code will run. By automating the process of parameter tuning — which essentially amounts to solving an integer programming problem in which the objective function is the number representing the code's performance as a function of the parameter configuration, — the system can also be used more productively than if the programmer had to fine-tune the code manually. We show performance results for a variety of stencils, for which Patus was used to generate the corresponding implementations. The selection includes stencils taken from two real-world applications: a simulation of the temperature within the human body during hyperthermia cancer treatment and a seismic application. These examples demonstrate the framework's flexibility and ability to produce high performance code

The effect of magnification and contrast on reading performance in different types of simulated low vision

Low vision therapy, such as magnifiers or contrast enhancement, is widely used. Scientific evidence proving its efficacy is scarce however. The objective of this study was to investigate whether the benefits of magnification and contrast enhancement depended on the origin of low vision. For this purpose we measured reading speed with artificially induced low vision in 12 healthy subjects in conditions of a simulated central scotoma, blurred vision and oscillopsia. Texts were either blurred, set in motion or blanked at the gaze position by using eye tracking and gaze contingent display. The simulated visual impairment was calibrated such that all types of low vision caused equal reading impairment. We then tested the effect of magnification and contrast enhancement among the different types of low vision. We found that reading speed improved with increasing magnification and with higher contrast in all conditions. The effect of magnification was significantly different in the three low vision conditions: The gain from magnification was highest in simulated blur and least in central scotoma. Magnification eventually led to near normal reading speed in all conditions. High contrast was less effective than high magnification and the effect of contrast enhancement was similar in all low vision conditions. From these results we conclude that the type of low vision determines the benefit that can be expected from magnification. Contrast enhancement leads to similar improved reading speed in all low vision types. We provide evidence that supports the use of low vision aids

Semantic-driven Configuration of Internet of Things Middleware

We are currently observing emerging solutions to enable the Internet of Things (IoT). Efficient and feature rich IoT middeware platforms are key enablers for IoT. However, due to complexity, most of these middleware platforms are designed to be used by IT experts. In this paper, we propose a semantics-driven model that allows non-IT experts (e.g. plant scientist, city planner) to configure IoT middleware components easier and faster. Such tools allow them to retrieve the data they want without knowing the underlying technical details of the sensors and the data processing components. We propose a Context Aware Sensor Configuration Model (CASCoM) to address the challenge of automated context-aware configuration of filtering, fusion, and reasoning mechanisms in IoT middleware according to the problems at hand. We incorporate semantic technologies in solving the above challenges. We demonstrate the feasibility and the scalability of our approach through a prototype implementation based on an IoT middleware called Global Sensor Networks (GSN), though our model can be generalized into any other middleware platform. We evaluate CASCoM in agriculture domain and measure both performance in terms of usability and computational complexity.Comment: 9th International Conference on Semantics, Knowledge & Grids (SKG), Beijing, China, October, 201

Effect of epitaxial strain on ferroelectric polarization in multiferroic BiFeO3 films

Multiferroic BiFeO3 epitaxial films with thickness ranging from 40 nm to 960 nm were grown by pulsed laser deposition on SrTiO3 (001) substrates with SrRuO3 bottom electrodes. X-ray characterization shows that the structure evolves from angularly-distorted tetragonal with c/a ~ 1.04 to more bulk-like distorted rhombohedral (c/a ~ 1.01) as the strain relaxes with increasing thickness. Despite this significant structural evolution, the ferroelectric polarization along the body diagonal of the distorted pseudo-cubic unit cells, as calculated from measurements along the normal direction, barely changes.Comment: Legend in Fig.3 corrected and et

Sensor Search Techniques for Sensing as a Service Architecture for The Internet of Things

The Internet of Things (IoT) is part of the Internet of the future and will comprise billions of intelligent communicating "things" or Internet Connected Objects (ICO) which will have sensing, actuating, and data processing capabilities. Each ICO will have one or more embedded sensors that will capture potentially enormous amounts of data. The sensors and related data streams can be clustered physically or virtually, which raises the challenge of searching and selecting the right sensors for a query in an efficient and effective way. This paper proposes a context-aware sensor search, selection and ranking model, called CASSARAM, to address the challenge of efficiently selecting a subset of relevant sensors out of a large set of sensors with similar functionality and capabilities. CASSARAM takes into account user preferences and considers a broad range of sensor characteristics, such as reliability, accuracy, location, battery life, and many more. The paper highlights the importance of sensor search, selection and ranking for the IoT, identifies important characteristics of both sensors and data capture processes, and discusses how semantic and quantitative reasoning can be combined together. This work also addresses challenges such as efficient distributed sensor search and relational-expression based filtering. CASSARAM testing and performance evaluation results are presented and discussed.Comment: IEEE sensors Journal, 2013. arXiv admin note: text overlap with arXiv:1303.244

2-Factor authentication for mobile applications : introducing DoubleSec

With the increasing desire also of private individuals to access their confidential data even from their mobile devices, the need for strong security controls for such application arises – in the same way as it has years ago in the area of web applications. This paper covers one of the most important parts thereof: the login process that allows an application on a mobile device accessing data from a server using two-factor authentication

Temperature Driven Structural Phase Transition in Tetragonal-Like BiFeO3

Highly-strained BiFeO3 exhibits a "tetragonal-like, monoclinic" crystal structure found only in epitaxial films (with an out-of-plane lattice parameter exceeding the in-plane value by >20%). Previous work has shown that this phase is properly described as a M$_{C}$ monoclinic structure at room temperature [with a (010)$_{pc}$ symmetry plane, which contains the ferroelectric polarization]. Here we show detailed temperature-dependent x-ray diffraction data that evidence a structural phase transition at ~100C to a high-temperature M$_{A}$ phase ["tetragonal-like" but with a (1-10)$_{pc}$ symmetry plane]. These results indicate that the ferroelectric properties and domain structures of strained BiFeO$_3$ will be strongly temperature dependent.Comment: 10 pages, 3 figure

Identification of a CYP3A form (CYP3A126) in fathead minnow ( Pimephales promelas ) and characterisation of putative CYP3A enzyme activity

Cytochrome P450-dependent monooxygenases (CYPs) are involved in the metabolic defence against xenobiotics. Human CYP3A enzymes metabolise about 50% of all pharmaceuticals in use today. Induction of CYPs and associated xenobiotic metabolism occurs also in fish and may serve as a useful tool for biomonitoring of environmental contamination. In this study we report on the cloning of a CYP3A family gene from fathead minnows (Pimephales promelas), which has been designated as CYP3A126 by the P450 nomenclature committee (GenBank no. EU332792). The cDNA was isolated, identified and characterised by extended inverse polymerase chain reaction (PCR), an alternative to the commonly used method of rapid amplification of cDNA ends. In a fathead minnow cell line we identified a full-length cDNA sequence (1,863 base pairs (bp)) consisting of a 1,536bp open reading frame encoding a 512 amino acid protein. Genomic analysis of the identified CYP3A isoenzyme revealed a DNA sequence consisting of 13 exons and 12 introns. CYP3A126 is also expressed in fathead minnow liver as demonstrated by reverse transcription PCR. Exposure of fathead minnow (FHM) cells with the CYP3A inducer rifampicin leads to dose-dependent increase in putative CYP3A enzyme activity. In contrast, inhibitory effects of diazepam treatment were observed on putative CYP3A enzyme activity and additionally on CYP3A126 mRNA expression. This indicates that CYP3A is active in FHM cells and that CYP3A126 is at least in part responsible for this CYP3A activity. Further investigations will show whether CYP3A126 is involved in the metabolism of environmental chemicals. Figure Induction of CYP3A activity by rifampicin and inhibition by diazepam in FHM cell