Searched for: subject:"GPU"
(1 - 17 of 17)
document
Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)

We present our work on hardware accelerated genomics pipelines, using either FPGAs or GPUs to accelerate execution of BWA-MEM, a widely-used algorithm for genomic short read mapping. The mapping stage can take up to 40% of overall processing time for genomics pipelines. Our implementation offloads the Seed Extension function, one of the main...

journal article 2018
document
Ren, S. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
GATK HaplotypeCaller (HC) is a popular variant caller, which is widely used to identify variants in complex genomes. However, due to its high variants detection accuracy, it suffers from long execution time. In GATK HC, the pair-HMMs forward algorithm accounts for a large percentage of the total execution time. This article proposes to...
journal article 2018
document
Aissa, M.H. (author)
Design optimization relies heavily on time-consuming simulations, especially when using gradient-free optimization methods. These methods require a large number of simulations in order to get a remarkable improvement over reference designs, which are nowadays based on the accumulated engineering knowledge already quite optimal.
High...
doctoral thesis 2017
document
Aissa, M.H. (author), Verstraete, Tom (author), Vuik, C. (author)
A computational Fluid Dynamics (CFD) code for steady simulations solves a set of non-linear partial differential equations using an iterative time stepping process, which could follow an explicit or an implicit scheme. On the CPU, the difference between both time stepping methods with respect to stability and performance has been well covered in...
journal article 2017
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Smaragdos, Georgios (author), Chatzikonstantis, Georgios (author), Kukreja, Rahul (author), Sidiropoulos, Harry (author), Rodopoulos, Dimitrios (author), Sourdis, Ioannis (author), Al-Ars, Z. (author), Kachris, Christoforos (author), Soudris, Dimitrios (author), De Zeeuw, Chris I. (author), Strydis, Christos (author)

Objective. The advent of high-performance computing (HPC) in recent years has led to its increasing use in brain studies through computational models. The scale and complexity of such models are constantly increasing, leading to challenging computational requirements. Even though modern HPC platforms can often deal with such challenges, the...

journal article 2017
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Houtgast, E.J. (author), Sima, V.M. (author), Marchiori, G. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
Next Generation Sequencing techniques have dramatically reduced the cost of sequencing genetic material, resulting in huge amounts of data being sequenced. The processing of this data poses huge challenges, both from a performance perspective, as well as from a power-efficiency perspective. Heterogeneous computing can help on both fronts, by...
conference paper 2016
document
Houtgast, E.J. (author), Sima, V.M. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)
We are rapidly entering the era of genomics. The dramatic cost reduction of DNA sequencing due to the introduction of Next Generation Sequencing (NGS) techniques has resulted in an exponential growth of genetics data. The amount of data generated, and its associated processing into useful information, poses serious computational challenges. Here...
abstract 2016
document
Knibbe, H. (author), Vuik, C. (author), Oosterlee, C.W. (author)
In geophysical applications, the interest in least-squares migration (LSM) as an imaging algorithm is increasing due to the demand for more accurate solutions and the development of high-performance computing. The computational engine of LSM in this work is the numerical solution of the 3D Helmholtz equation in the frequency domain. The...
journal article 2015
document
Knibbe, H.P. (author), Vuik, C. (author), Oosterlee, C.W. (author)
In geophysical applications, the interest in least-squares migration (LSM) as an imaging algorithm is increasing due to the demand for more accurate solutions and the development of high-performance computing. The computational engine of LSM in this work is the numerical solution of the 3D Helmholtz equation in the frequency domain. The...
journal article 2015
document
Shen, J. (author)
Heterogeneous platforms are mixes of different processing units in a compute node (e.g., CPUs+GPUs, CPU+MICs) or a chip package (e.g., APUs). This type of platforms keeps gaining popularity in various computer systems ranging from supercomputers to mobile devices. In this context, improving their efficiency and usability has become increasingly...
doctoral thesis 2015
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Gupta, R. (author)
In this work we study the implementations of deflation and preconditioning techniques for solving ill-conditioned linear systems using iterative methods. Solving such systems can be a time-consuming process because of the jumps in the coefficients due to large difference in material properties. We have developed implementations of the iterative...
doctoral thesis 2015
document
Schalkwijk, J. (author)
De vorige eeuw was getuige van de opkomst van numerieke weer- en klimaatmodellen. Weersvoorspelling, voorheen een empirische procedure gebaseerd op de persoonlijke ervaring van de meteoroloog, ontwikkelde zich tot een wetenschappelijke methode om de toekomstige toestand van de atmosfeer te voorspellen op basis van de huidige toestand en tendens....
doctoral thesis 2015
document
Knibbe, H.P. (author)
The oil and gas industry makes use of computational intensive algorithms to provide an image of the subsurface. The image is obtained by sending wave energy into the subsurface and recording the signal required for a seismic wave to reflect back to the surface from the Earth interfaces that may have different physical properties. A seismic wave...
doctoral thesis 2015
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Zhang, B. (author), Van der Weide, J.A.M. (author), Oosterlee, C.W. (author)
In this article, we propose an efficient pricing method for Asian options with early–exercise features. It is based on a two–dimensional integration and a backward recursion of the Fourier coefficients, in which several numerical techniques, like Fourier cosine expansions, Clenshaw–Curtis quadrature and the Fast Fourier transform (FFT) are...
report 2012
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Xu, S. (author)
This thesis deals with two research problems. The first research problem is motivated by the numerical computation involved in the Time Domain Simulation (TDS) of Power Grids. Due to the ever growing size and complexity of Power Grids such as the China National Grid, accelerating TDS has become a stringent need for the online analysis of these...
doctoral thesis 2011
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Xu, S. (author), Xue, W. (author), Lin, H.X. (author)
In this article, we discuss the performance modeling and optimization of Sparse Matrix-Vector Multiplication (SpMV) on NVIDIA GPUs using CUDA. SpMV has a very low computation-data ratio and its performance is mainly bound by the memory bandwidth. We propose optimization of SpMV based on ELLPACK from two aspects: (1) enhanced performance for the...
journal article 2011
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Hasan, L. (author)
Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of protein or DNA sequences. An accurate alignment...
doctoral thesis 2011
Searched for: subject:"GPU"
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