The ability to timely process significant amounts of continuously updated spatial data is mandatory for an increasing number of applications. In this paper we focus on a specific data-intensive problem concerning the repeated processing of huge amounts of k nearest neighbours (k-NN) queries over massive sets of moving objects, where the spatial extents of queries […]

December 22, 2014 by hgpu

This thesis studies the scalability of the similarity search problem in large-scale multidimensional data. Similarity search, translating into the neighbour search problem, finds many applications for information retrieval, visualization, machine learning and data mining. The current exponential growth of data motivates the need for approximate and scalable algorithms. In most of existing algorithms and data-structures, […]

October 13, 2014 by hgpu

The problem of computing the Betweenness Centrality (BC) is important in analyzing graphs in many practical applications like social networks, biological networks, transportation networks, electrical circuits, etc. Since this problem is computation intensive, researchers have been developing algorithms using high performance computing resources like supercomputers, clusters, and Graphics Processing Units (GPUs). Current GPU algorithms for […]

September 30, 2014 by hgpu

Graphics Processing Units (GPUs) have been used to enhance the speed and efficiency of both data structures and algorithms alike. A common data structure used in Computer Science is the Bloom Filter, which is used in many types of applications including databases and security logging. The Bloom Filter is a lossy data structure that uses […]

August 13, 2014 by hgpu

We present PEANUT (ParallEl AligNment UTility), a highly parallel GPU-based read mapper with several distinguishing features, including a novel q-gram index (called the q-group index) with small memory footprint built on-the-fly over the reads and the possibility to output both the best hits or all hits of a read. Designing the algorithm particularly for the […]

March 10, 2014 by hgpu

The availability and utility of large numbers of Graphical Processing Units (GPUs) have enabled parallel computations using extensive multi-threading. Sequential access to global memory and contention at the size-limited shared memory have been main impediments to fully exploiting potential performance in architectures having a massive number of GPUs. After performing extensive study of data structures […]

July 16, 2013 by hgpu

As Graphics Processing Units (GPUs) have gained in capability and GPU development environments have matured, developers are increasingly turning to the GPU to off-load the main host CPU of numerically-intensive, parallelizable computations. Modern GPUs feature hundreds of cores, and offer programming niceties such as double-precision floating point, and even limited recursion. This shift from CPU […]

May 1, 2013 by hgpu

Simulation and visualization of particles in real-time can be a computationally intensive task. This intensity comes from diverse factories, being one of them is the O(n^2) complexity of the traversal algorithm, necessary for the proximity queries of all pair of particles that decide the need to compute collisions. Previous works reduced this complexity by considerably […]

March 23, 2013 by hgpu

In this paper, a contrastive evaluation of massive parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU(kepler architecture). Due to the more regular execution flow of the indexed binary search algorithm, the more efficient use of the […]

March 18, 2013 by hgpu

The analysis of several algorithms and data structures can be framed as a peeling process on a random hypergraph: vertices with degree less than k are removed until there are no vertices of degree less than k left. The remaining hypergraph is known as the k-core. In this paper, we analyze parallel peeling processes, where […]

March 2, 2013 by hgpu

We show that a simple algorithm for computing a matching on a graph runs in a logarithmic number of phases incurring work linear in the input size. The algorithm can be adapted to provide efficient algorithms in several models of computation, such as PRAM, External Memory, MapReduce and distributed memory models. Our CREW PRAM algorithm […]

February 23, 2013 by hgpu

We describe efficient algorithms to analyze the cycle structure of the graph induced by the state transition function of the A5/1 stream cipher used in GSM mobile phones and report on the results of the implementation. The analysis is performed in five steps utilizing HPC clusters, GPGPU and external memory computation. A great reduction of […]

October 25, 2012 by hgpu