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Unnikrishnan C, Y N Srikant, Rupesh Nasre
Graph algorithms are used in several domains such as social networking, biological sciences, computational geometry, and compilers, to name a few. It has been shown that they possess enough parallelism to keep several computing resources busy – even hundreds of cores on a GPU. Unfortunately, tuning their implementation for efficient execution on a particular hardware […]
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Christopher D. Cooper, Lorena A. Barba
Interactions between surfaces and proteins occur in many vital processes and are crucial in biotechnology: the ability to control specific interactions is essential in fields like biomaterials, biomedical implants and biosensors. In the latter case, biosensor sensitivity hinges on ligand proteins adsorbing on bioactive surfaces with a favorable orientation, exposing reaction sites to target molecules. […]
Avadhesh Pratap Singh, Dhirendra Pratap Singh
K-shortest path algorithm is generalization of the shortest path algorithm. K-shortest path is used in various fields like sequence alignment problem in molecular bioinformatics, robot motion planning, path finding in gene network where speed to calculate paths plays a vital role. Parallel implementation is one of the best ways to fulfill the requirement of these […]
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Dominik Charousset, Raphael Hiesgen, Thomas C. Schmidt
The actor model of computation has gained significant popularity over the last decade. Its high level of abstraction makes it appealing for concurrent applications in parallel and distributed systems. However, designing a real-world actor framework that subsumes full scalability, strong reliability, and high resource efficiency requires many conceptual and algorithmic additives to the original model. […]
H.A. Du Nguyen, Zaid Al-Ars, Georgios Smaragdos, Christos Strydis
The Inferior Olive (IO) in the brain, in conjunction with the cerebellum, is responsible for crucial sensorimotor-integration functions in humans. In this paper, we simulate a computationally challenging IO neuron model consisting of three compartments per neuron in a network arrangement on GPU platforms. Several GPU platforms of the two latest NVIDIA GPU architectures (Fermi, […]
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Chok Meng Yip
Both size and computational activities of Vehicular Area Network (VANET) are growing. Simulation of VANETs not only requires the simulation of network standards, but also the mobility of nodes. Such dynamic system involves computation of node distance, routing protocols, application layer, data send, data receive, etc. The simulation model of VANET requires both hardware and […]
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Bo Joel Svensson, Michael Vollmer, Eric Holk, Trevor L. McDonell, Ryan R. Newton
High-level domain-specific languages for array processing on the GPU are increasingly common, but they typically only run on a single GPU. As computational power is distributed across more devices, languages must target multiple devices simultaneously. To this end, we present a compositional translation that fissions data-parallel programs in the Accelerate language, allowing subsequent compiler and […]
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Paul Harvey, Saji Hameed, Wim Vanderbauwhede
FLEXPART is a popular simulator that models the transport and diffusion of air pollutants, based on the Lagrangian approach. It is capable of regional and global simulation and supports both forward and backward runs. A complex model like this contains many calculations suitable for parallelisation. Recently, a GPU-accelerated version of the simulator (FLEXCPP) has been […]
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Blesson Varghese
The risk of reinsurance portfolios covering globally occurring natural catastrophes, such as earthquakes and hurricanes, is quantified by employing simulations. These simulations are computationally intensive and require large amounts of data to be processed. The use of many-core hardware accelerators, such as the Intel Xeon Phi and the NVIDIA Graphics Processing Unit (GPU), are desirable […]
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Jade Alglave, Mark Batty, Alastair F. Donaldson, Ganesh Gopalakrishnan, Jeroen Ketema, Daniel Poetzl, Tyler Sorensen, John Wickerson
Concurrency is pervasive and perplexing, particularly on graphics processing units (GPUs). Current specifications of languages and hardware are inconclusive; thus programmers often rely on folklore assumptions when writing software. To remedy this state of affairs, we conducted a large empirical study of the concurrent behaviour of deployed GPUs. Armed with litmus tests (i.e. short concurrent […]
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Tianren Wang, Yun Jing
This paper presents a numerical study on a fast marching method based back projection reconstruction algorithm for photoacoustic tomography in heterogeneous media. Transcranial imaging is used here as a case study. To correct for the phase aberration from the heterogeneity (i.e., skull), the fast marching method is adopted to compute the phase delay based on […]
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Michael Gowanlock, Henri Casanova
Applications in many domains search moving object trajectory databases. The distance threshold search finds all trajectories within a given distance of a query trajectory. We develop three GPU distance threshold search implementations that use indexing techniques significantly different from those used in CPU implementations. We determine experimentally under which conditions each approach performs well using […]
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