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Bouter, P.A. (author)In recent years, the use of Artificial Intelligence (AI) has become prevalent in a large number of societally relevant, real-world problems, e.g., in the domains of engineering and health care. The field of Evolutionary Computation (EC) can be considered to be a sub-field of AI, concerning optimization using Evolutionary Algorithms (EAs), which...doctoral thesis 2023
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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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Sun, W. (author), Katsifodimos, A (author), Hai, R. (author)Recent advances in Graphic Processing Units (GPUs) have facilitated a significant performance boost for database operators, in particular, joins. It has been intensively studied how conventional join implementations, such as hash joins, benefit from the massive parallelism of GPUs. With the proliferation of machine learning, more databases...conference paper 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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Park, Seongyeon (author), Kim, Hajin (author), Ahmad, T. (author), Ahmed, N. (author), Al-Ars, Z. (author), Hofstee, H.P. (author), Kim, Youngsok (author), Lee, Jinho (author)Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...conference paper 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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Bulavintsev, V. (author), Zhdanov, Dmitry D. (author)We propose a generalized method for adapting and optimizing algorithms for efficient execution on modern graphics processing units (GPU). The method consists of several steps. First, build a control flow graph (CFG) of the algorithm. Next, transform the CFG into a tree of loops and merge non-parallelizable loops into parallelizable ones....conference paper 2021
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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), Bertels, K.L.M. (author), Al-Ars, Z. (author)The seeding heuristic is widely used in many DNA analysis applications to speed up the analysis time. In many applications, seeding takes a substantial amount of the total execution time. In this paper, we present an efficient GPU implementation for computing maximal exact matching (MEM) seeds in long DNA reads. We applied various...conference paper 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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Khait, M. (author)Numerical simulation is based on space and time discretization providing a trade-off between accuracy and computational performance. The operator-based Linearization (OBL) approach introduces an additional discretization domain for the physical description of fluid and rock. Delft Advanced Research Terra Simulator (DARTS) is a general-purpose...doctoral thesis 2019
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Houtgast, E.J. (author)Developments in sequencing technology have drastically reduced the cost of DNA sequencing. The raw sequencing data being generated requires processing through computationally demanding suites of bioinformatics algorithms called genomics pipelines. The greatly decreased cost of sequencing has resulted in its widespread adoption, and the amount of...doctoral thesis 2019
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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