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The Aho-Corasick algorithm is a multiple patterns searching algorithm running sequentially in various applications like network intrusion detection and bioinformatics for finding several input strings within a given large input string. The parallel version of the Aho-Corasick algorithm is called as Parallel Failure-less Aho-Corasick algorithm because it doesnt need failure links like in the original...
Modern graphics processing units (GPUs) offer very high computing power at relatively low cost. Nevertheless, designing efficient algorithms for the GPUs normally requires additional time and effort, even for experienced programmers. In this work we present a tuning methodology that allows the design for CUDA-enabled GPU architectures of index-digit algorithms, that is, algorithms where the data movement...
There exist large datasets containing the sequences of points that moving objects occupy in space as time goes by. Such sequences of moving objects are known as trajectories. Being able to issue queries that allow the extraction of patterns from the movements of these objects is important to many real world applications, such as urban planning in transportation and bird migration tracking in ecology...
We present JolokiaC++ a compiler framework to ease coding of irregular data applications on GPUs. The effectiveness of the compiler and runtime systems of JolokiaC++ is tested using three kernels IRREG, MOLDYN and NBF, executed on NVIDIA GPUs. We developed extensions for the generic parallel constructs that allow portable and efficient programming of codes with irregular accesses on the GPU. We present...
The volume of data has increased fast, particularly medical images, in big hospitals over the last years. This increase imposes a big challenge to medical specialists: the maintenance of high interpretation accuracy of image-based diagnosis. Computer-Aided Diagnosis software allied to the Content-Based Image Retrieval (CBIR) can provide decision support to specialists by allowing them to find images...
K-means clustering algorithm is a partition based clustering algorithm which has been widely used in data mining applications. This algorithm suffers from an issue, named initial centers selection. This problem significantly effects on the quality and running time of clustering. Several literatures discussed on this problem and try to select the best initial centers to prevent final results from getting...
Nowadays, with the explosive growth of the network technologies many new applications and services have been developed on Internet. World Wide Web can provide these services provided without the limitation of time and location. Obviously, the number of user is dramatically increasing from amount of the visitations of web pages. In our previous work, we proposed an algorithm to discover more significant...
Irregular algorithms are algorithms with complex main data structures such as directed and undirected graphs, trees, etc. A useful abstraction for many irregular algorithms is its operator formulation in which the algorithm is viewed as the iterated application of an operator to certain nodes, called active nodes, in the graph. Each operator application, called an activity, usually touches only a...
Since 1985, the IEEE 754 standard defines formats, rounding modes and basic operations for floating-point arithmetic. In 2008 the standard has been extended, and recommendations have been added about the rounding of some elementary functions such as trigonometric functions (cosine, sine, tangent and their inverses), exponentials, and logarithms. However to guarantee the exact rounding of these functions...
The advent of multicore and many-core architectures saw them being deployed to speed-up computations across several disciplines and application areas. Prominent examples include semi-numerical algorithms such as sorting, graph algorithms, image processing, scientific computations, and the like. In particular, using GPUs for general purpose computations has attracted a lot of attention given that GPUs...
Nowadays microscopic analysis of tissue samples is done more and more by using digital imagery and special immunodiagnostic software. These are typically specific applications developed for one distinct field, but some subroutines are commonly repeated, for example several applications contain steps that can detect cell nuclei in a sample image. The aim of our research is developing a new data parallel...
Map projection is a key task in cartography that transforms the geographical coordinates from one coordinate system to another. It has been widely used in the Geographic Information System application. However, map projection is a very time-consuming task, and fast processing speed is often required in interactive GIS scenarios. Parallel computation provides an opportunity to reduce run times. Nowadays,...
Fast Fourier Transform (FFT) is a useful tool for applications requiring signal analysis and processing. However, its high computational cost requires efficient implementations, specially if real time applications are used, where response time is a decisive factor. Thus, the computational cost and wide application range that requires FFT transforms has motivated the research of efficient implementations...
Graphics processing units provide a large computational power at a very low price which position them as an ubiquitous accelerator. General purpose programming on the graphics processing units (GPGPU) is best suited for regular data parallel algorithms. They are not directly amenable for algorithms which have irregular data access patterns such as list ranking, and finding the connected components...
Investigation of the cryptanalytic strength of RSA cryptography requires computing many GCDs of two long integers (e.g., of length 1024 bits). This paper presents a high throughput parallel algorithm to perform many GCD computations concurrently on a GPU based on the CUDA architecture. The experiments with an NVIDIA GeForce GTX285 GPU and a single core of 3.0 GHz Intel Core2 Duo E6850 CPU show that...
Suffix array is a simpler and compact alternative to the suffix tree, lexicographic name construction is the fundamental building block in suffix array construction process. This paper depicts the design issues of first data parallel implementation of the lexicographic name construction algorithm on a commodity multiprocessor GPU using the Compute Unified Device Architecture (CUDA) platform, both...
Counting sort is a simple, stable and efficient sort algorithm with linear running time, which is a fundamental building block for many applications. This paper depicts the design issues of a data parallel implementation of the count sort algorithm on a commodity multiprocessor GPU using the Compute Unified Device Architecture (CUDA) platform, both from NVIDIA Corporation. The full parallel version...
With the progress of high-density integration technology of the circuits, a variety of signal and power integrity problems have become serious and important for the electronic design. This paper describes the fast circuit simulation by GPGPU-LIM (GPGPU-based Latency Insertion Method). First, LIM is reviewed, which is a fast algorithm. Next, implementation of LIM on the general purpose computing on...
We present the design and performance analysis of a GPU-optimized implementation of a disk encryption application employing the XTS mode of operation applied together with the Twofish algorithm within the well-known TrueCrypt suite. We show how to correctly tune the design parameters, including data allocation, thread packing, and parallelization strategy. Overall, our implementation of TrueCrypt...
General purpose computing over graphical processing units (GPGPUs) is a huge shift of paradigm in parallel computing that promises a dramatic increase in performance. But GPGPUs also bring an unprecedented level of complexity in algorithmic design and software development. In this paper we describe the challenges and design choices involved in parallelization of Bayesian optimization algorithm (BOA)...
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