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Buwalda, F.J.L. (author), de Goede, Erik (author), Knepflé, Maxim (author), Vuik, Cornelis (author)The accuracy, stability and computational efficiency of numerical methods on central processing units (CPUs) for the depth-averaged shallow water equations were well covered in the literature. A large number of these methods were already developed and compared. However, on graphics processing units (GPUs), such comparisons are relatively scarce....journal article 2023
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Wang, Y. (author), Voskov, D.V. (author), Daniilidis, Alexandros (author), Khait, M. (author), Saeid, S. (author), Bruhn, D.F. (author)The efficient operation and management of a geothermal project can be largely affected by geological, physical, operational and economic uncertainties. Systematic uncertainty quantification (UQ) involving these parameters helps to determine the probability of the focused outputs, e.g., energy production, Net Present Value (NPV), etc. However,...journal article 2023
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Bernardini, Matteo (author), Modesti, D. (author), Salvadore, Francesco (author), Sathyanarayana, Srikanth (author), Della Posta, Giacomo (author), Pirozzoli, Sergio (author)We present STREAmS-2.0, an updated version of the flow solver STREAmS, first introduced in Bernardini et al. (2021) [1]. STREAmS-2.0 has an object-oriented design which separates the physics equations from the specific back-end, making the code more suitable for future expansions, such as porting to novel computing architectures or...journal article 2023
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Koshakji, Anwar (author), Chomette, Grégoire (author), Turner, Jeffrey (author), Jablonski, Jonathan (author), Haynes, Aisha (author), Carlucci, Donald (author), Giovanardi, Bianca (author), Radovitzky, Raúl A. (author)The dynamic response of flexible filaments immersed in viscous fluids is important in cell mechanics, as well as other biological and industrial processes. In this paper, we propose a parallel computational framework to simulate the fluid-structure interactions in large assemblies of highly-flexible filaments immersed in a viscous fluid. We...journal article 2023
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Hogervorst, T.A. (author), Nane, R. (author), Marchiori, Giacomo (author), Qiu, Tong Dong (author), Blatt, Markus (author), Rustad, Alf Birger (author)Scientific computing is at the core of many High-Performance Computing applications, including computational flow dynamics. Because of the utmost importance to simulate increasingly larger computational models, hardware acceleration is receiving increased attention due to its potential to maximize the performance of scientific computing....journal article 2022
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Condia, Josie E.Rodriguez (author), Augusto da Silva, F. (author), Bagbaba, Ahmet Cagri (author), Guerrero-Balaguera, Juan-David (author), Hamdioui, S. (author), Sauer, Christian (author), Sonza Reorda, Matteo (author)Editor's notes: GPUs have seen an increased adoption in autonomous systems. This article assesses the fault coverage that can be attained through software self-test strategies for in-field test of GPUs. - Nicola Nicolici, McMaster Universityjournal article 2022
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Bernardini, Matteo (author), Modesti, D. (author), Salvadore, Francesco (author), Pirozzoli, Sergio (author)We present STREAmS, an in-house high-fidelity solver for direct numerical simulations (DNS) of canonical compressible wall-bounded flows, namely turbulent plane channel, zero-pressure gradient turbulent boundary layer and supersonic oblique shock-wave/boundary layer interaction. The solver incorporates state-of-the-art numerical algorithms,...journal article 2021
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Machidon, Alina L. (author), Machidon, Octavian M. (author), Ciobanu, C.B. (author), Ogrutan, Petre L. (author)Remote sensing data has known an explosive growth in the past decade. This has led to the need for efficient dimensionality reduction techniques, mathematical procedures that transform the high-dimensional data into a meaningful, reduced representation. Projection Pursuit (PP) based algorithms were shown to be efficient solutions for...journal article 2020
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Ahmed, N. (author), Qiu, T.D. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)BACKGROUND: In Overlap-Layout-Consensus (OLC) based de novo assembly, all reads must be compared with every other read to find overlaps. This makes the process rather slow and limits the practicality of using de novo assembly methods at a large scale in the field. Darwin is a fast and accurate read overlapper that can be used for de novo...journal article 2020
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van Kessel, L.C.P.M. (author), Hagen, C.W. (author)Monte Carlo simulations are frequently used to describe electron–matter interaction in the 0–50 keV energy range. It often takes hours to simulate electron microscope images using first-principle physical models. In an attempt to maintain a reasonable speed, empirical models are sometimes used. We present an open-source software package with...journal article 2020
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Ahmed, N. (author), Lévy, Jonathan (author), Ren, S. (author), Mushtaq, Hamid (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)BACKGROUND: Due the computational complexity of sequence alignment algorithms, various accelerated solutions have been proposed to speedup this analysis. NVBIO is the only available GPU library that accelerates sequence alignment of high-throughput NGS data, but has limited performance. In this article we present GASAL2, a GPU library for...journal article 2019
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Liu, S. (author), Oosterlee, C.W. (author), Bohte, Sander M. (author)This paper proposes a data-driven approach, by means of an Artificial Neural Network (ANN), to value financial options and to calculate implied volatilities with the aim of accelerating the corresponding numerical methods. With ANNs being universal function approximators, this method trains an optimized ANN on a data set generated by a...journal article 2019
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Ren, S. (author), Ahmed, N. (author), Bertels, K.L.M. (author), Al-Ars, Z. (author)Background: Pairwise sequence alignment is widely used in many biological tools and applications. Existing GPU accelerated implementations mainly focus on calculating optimal alignment score and omit identifying the optimal alignment itself. In GATK HaplotypeCaller (HC), the semi-global pairwise sequence alignment with traceback has so far<br/...journal article 2019
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Miri Rostami, Seyyed Reza (author), Mozaffarzadeh, M. (author), Ghaffari-Miab, Mohsen (author), Hariri, Ali (author), Jokerst, Jesse (author)Double-stage delay-multiply-and-sum (DS-DMAS) is an algorithm proposed for photoacoustic image reconstruction. The DS-DMAS algorithm offers a higher contrast than conventional delay-and-sum and delay-multiply and-sum but at the expense of higher computational complexity. Here, we utilized a compute unified device architecture (CUDA) graphics...journal article 2019
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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
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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
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Aissa, M.H. (author), Verstraete, Tom (author), Vuik, Cornelis (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, C. (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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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
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Knibbe, H.P. (author), Vuik, Cornelis (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
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