Optimal Mixing Evolutionary Algorithms for Large-Scale Real-Valued Optimization: Including Real-World Medical Applications

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...

Delft Advanced Research Terra Simulator: General Purpose Reservoir Simulator with Operator-Based Linearization

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...

On Hardware-Accelerated Maximally-Efficient Systolic Arrays: Acceleration and Optimization of Genomics Pipelines Through Hardware/Software Co-Design

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...

Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems

Next generation sequencing (NGS) technologies have transformed the landscape of genomic research. With the significant advances in NGS technologies, DNA sequencing is more affordable and accessible than ever before. Meanwhile, many DNA sequence analysis tools have been developed to derive useful information from the raw sequencing data produced...

GPU-accelerated CFD Simulations for Turbomachinery Design Optimization

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.<br/>High...

Efficient High Performance Computing on Heterogeneous Platforms

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...

GPU acceleration of preconditioned solvers for ill-conditioned linear systems

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...

Toward Turbulence-Resolving Weather and Climate Simulation

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....

Reduction of computing time for seismic applications based on the Helmholtz equation by Graphics Processing Units

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...

Power Grid Simulation with GPU-Accelerated Iterative Solvers and Preconditioners

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...

Hardware Acceleration of Bioinformatics Sequence Alignment Applications

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...