21 papers · ranked by Valyu relevance
Pekka Jääskeläinen, Carlos S. de La Lama, Erik Schnetter, Kalle Raiskila + 2 more
'Kalle Raiskila' 'Jarmo Takala' 'Heikki Berg'] don'tAbstract OpenCL is a standard for parallel programming of heterogeneous systems. The benefits of a common programming standard are clear; multiple vendors can provide support for application descriptions written according to the standard, thus reducing the program…
Simon McIntosh-Smith, James Price, Richard B Sessions, Amaurys A Ibarra
'Amaurys A Ibarra'] Drug screening is an important part of the drug development pipeline for the pharmaceutical industry. Traditional, lab-based methods are increasingly being augmented with computational methods, ranging from simple molecular similarity searches through more complex pharmacophore matching to more…
Raphael Hiesgen, Dominik Charousset, Thomas C. Schmidt
The actor model of computation has been designed for a seamless support of concurrency and distribution. However, it remains unspecific about data parallel program flows, while available processing power of modern many core hardware such as graphics processing units (GPUs) or coprocessors increases the relevance of…
Yupu Song, Cailin Li, Shiyang Xiao, Han Xiao + 1 more
In view of the low computational efficiency and the limitations of the platform of the unsharp masking image enhancement algorithm, an unsharp masking image enhancement parallel algorithm based on Open Computing Language (OpenCL) is proposed. Based on the analysis of the parallel characteristics of the algorithm, the…
Yupu Song, Cailin Li, Shiyang Xiao, Qinglei Zhou + 2 more
'Ayesha Maqbool'] In the process of Canny edge detection, a large number of high complexity calculations such as Gaussian filtering, gradient calculation, non-maximum suppression, and double threshold judgment need to be performed on the image, which takes up a lot of operation time, which is a great challenge to the…
Cathal Ó Broin, L. A. A. Nikolopoulos
Open Computing Language (OpenCL) is a parallel processing language that is ideally suited for running parallel algorithms on Graphical Processing Units (GPUs). In the present work we report on the development of a generic parallel single-GPU code for the numerical solution of a system of first-order ordinary…
David A. Richie, James A. Ross
> Abstract. There is interest in exploring hybrid OpenSHMEM + X programming models to extend the applicability of the OpenSHMEM interface to more hardware architectures. We present a hybrid OpenCL + OpenSHMEM programming model for device-level programming for architectures like the Adapteva Epiphany many-core RISC…
Nikolaos Alachiotis, Simon A Berger, Alexandros Stamatakis
Background Aligning short DNA reads to a reference sequence alignment is a prerequisite for detecting their biological origin and analyzing them in a phylogenetic context. With the PaPaRa tool we introduced a dedicated dynamic programming algorithm for simultaneously aligning short reads to reference alignments and…
Manuel de Castro, Roberto R. Osorio, David L. Vilariño, Arturo Gonzalez-Escribano + 1 more
'Arturo Gonzalez-Escribano' 'Diego R. Llanos'] Motion Estimation is one of the main tasks behind any video encoder. It is a computationally costly task; therefore, it is usually delegated to specific or reconfigurable hardware, such as FPGAs. Over the years, multiple FPGA implementations have been developed, mainly…
Federico Simmross‐Wattenberg, Manuel Rodríguez-Cayetano, Javier Royuela‐del‐Val, Elena Martín-González + 3 more
'Javier Royuela‐del‐Val' 'Elena Martín-González' 'Elisa Moya‐Sáez' 'Marcos Martín‐Fernández' 'Carlos Alberola‐López'] Abstract— Medical image processing is often limited by the computational cost of the involved algorithms. Whereas dedicated computing devices (GPUs in particular) exist and do provide significant…
Ricardo Tapiador, Antonio Ríos-Navarro, A. Linares-Barranco, Minkyu Kim + 2 more
'Minkyu Kim' 'Deepak Kadetotad' 'Jae-sun Seo'] Abstract—Deep learning has significantly advanced the state of the art in artificial intelligence, gaining wide popularity from both industry and academia. Special interest is around Convolutional Neural Networks (CNN), which take inspiration from the hierarchical…
Bogdan Oancea, Tudorel Andrei, Raluca Mariana Drăgoescu
Since the first idea of using GPU to general purpose computing, things have evolved over the years and now there are several approaches to GPU programming. GPU computing practically began with the introduction of CUDA (Compute Unified Device Architecture) by NVIDIA and Stream by AMD. These are APIs designed by the GPU…
Vahid Tavakkoli, Kabeh Mohsenzadegan, Jean Chamberlain Chedjou, Kyandoghere Kyamakya
'Kyandoghere Kyamakya'] Solving ordinary differential equations (ODE) on heterogenous or multi-core/parallel embedded systems does significantly increase the operational capacity of many sensing systems in view of processing tasks such as self-calibration, model-based measurement and self-diagnostics. The main…
Nuno Fachada, Vítor V. Lopes, Rui C. Martins, Agostinho Rosa
OpenCL is an open standard for parallel programming of heterogeneous compute devices, such as GPUs, CPUs, DSPs or FPGAs. However, the verbosity of its C host API can hinder application development. In this paper we present cf4ocl, a software library for rapid development of OpenCL programs in pure C. It aims to reduce…
Zhikun Wu, Honghui Shang, Yangjun Wu, Zhongcheng Zhang + 5 more
'Yuyang Zhang' 'Yucheng Ouyang' 'Huimin Cui' 'Xiaobing Feng'] We have proposed, for the first time, an OpenCL implementation for the all-electron density-functional perturbation theory (DFPT) calculations in FHI-aims, which can effectively compute all its time-consuming simulation stages, i.e., the real-space…
Authors not listed
The era of exascale computing presents both exciting opportunities and unique challenges for quantum mechanical simulations. While the transition from petaflops to exascale computing has been marked by a steady increase in computational power, the shift towards heterogeneous architectures, particularly the dominant…
Qianqian Fang, Shijie Yan
The mesh-based Monte Carlo (MMC) algorithm is increasingly used as the gold-standard for developing new biophotonics modeling techniques in 3-D complex tissues, including both diffusion-based and various Monte Carlo (MC) based methods. Compared to multi-layered and voxel-based MCs, MMC can utilize tetrahedral meshes to…
James C. Pino, Martina Prugger, Alexander L. R. Lubbock, Leonard A. Harris + 1 more
Stochasticity due to fluctuations in chemical reactions can play important roles in cellular network-driven processes. Although the Stochastic Simulation Algorithm (SSA, aka Gillespie Algorithm) has long been accepted as a suitable method to solve the time-dependent chemical master equation, its computational cost is…
Hadrien Caron, Pierre Pouget
To elicit complex and rich graphical displays, and record neuronal phenomena ofinterest while all simultaneously being capable to interact in a closed-loop with external devises is a challenging task to all neurophysiologists. To facilitate this process, we have developed an Open-Source software system using a single…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Andrew Stokely, Lane Votapka, Marcus Hock, Abigail Teitgen + 3 more
We present the Netsci program - an open-source scientific software package that leverages GPU acceleration and a k-nearest-neighbor algorithm in order to estimate the mutual information (MI) between data in a set. The GPU acceleration presented here, as an improvement upon existing estimators, enables calculation…