Communication-Efficient Cluster Scalable Genomics Data Processing Using Apache Arrow Flight

Current cluster scaled genomics data processing solutions rely on big data frameworks like Apache Spark, Hadoop and HDFS for data scheduling, processing and storage. These frameworks come with additional computation and memory overheads by default. It has been observed that scaling genomics dataset processing beyond 32 nodes is not efficient on...

Timing and Resource-aware Mapping of Quantum Circuits to Superconducting Processors

Quantum algorithms need to be compiled to respect the constraints imposed by quantum processors, which is known as the mapping problem. The mapping procedure will result in an increase of the number of gates and of the circuit latency, decreasing the algorithm's success rate. It is crucial to minimize mapping overhead, especially for noisy...

Time-Adaptive Grid Hydrological Solver Using PETSc

A high-resolution hydrological solver that solves on time-adaptive grids is created. The solver uses h-refinement strategies which adapts the resolution of the grid using a posteriori measure. It is based on an open-source scientific computing library named PETSc. With the use of highly scalable time-stepping solvers provided by PETSc, an...

ArrowSAM: In-Memory Genomics Data Processing Using Apache Arrow

The rapidly growing size of genomics data bases, driven by advances in sequencing technologies, demands fast and cost-effective processing. However, processing this data creates many challenges, particularly in selecting appropriate algorithms and computing platforms. Computing systems need data closer to the processor for fast processing....

Acceleration of Seed Extension for BWA-MEM DNA Alignment Using GPUs

DNA aligning is a compute-intensive and time-consuming task required for all further DNA processing. It consists in finding for each DNA string from a sample its location in a reference genome. Usual techniques for short reads (hundreds of bases) involve seed-extension, where a small matching seed is found with quick search through FM-index and...

VHDL Implementation of 4096-bit RNS Montgomery Modular Exponentiation for RSA Encryption

Modular exponentiation is the basis needed to perform RSA encryption and decryption. Execution of 4096-bit modular exponentiation using an embedded system requires many arithmetic operations. This work aims to improve the performance of modular exponentiation for an existing FPGA platform containing a soft core RISC-V processor. The solution is...

Time-division Multiplexing Automata Processor

Automata Processor (AP) is a special implementation of non-deterministic finite automata that performs pattern matching by exploring parallel state transitions. The implementation typically contains a hierarchical switching network, causing long latency. This paper proposes a methodology to split such a hierarchical switching network into...

A parallel N-dimensional Space-Filling Curve library and its application in massive point cloud management

Because of their locality preservation properties, Space-Filling Curves (SFC) have been widely used in massive point dataset management. However, the completeness, universality, and scalability of current SFC implementations are still not well resolved. To address this problem, a generic n-dimensional (nD) SFC library is proposed and...

Parallel creation of vario-scale data structures for large datasets

Processing massive datasets which are not fitting in the main memory of computer is challenging. This is especially true in the case of map generalization, where the relationships between (nearby) features in the map must be considered. In our case, an automated map generalization process runs offline to produce a dataset suitable for...

Efficient Execution of Video Applications on Heterogeneous Multi- and Many-Core Processors

In this dissertation we present methodologies and evaluations aiming at increasing the efficiency of video coding applications for heterogeneous many-core processors composed of SIMD-only, scratchpad memory based cores. Our contributions are spread in three different fronts: thread-level parallelism strategies for many-cores, identification of...

A filtered convolution method for the computation of acoustic wave fields in very large spatiotemporal domains

The full-wave computation of transient acoustic fields with sizes in the order of 100x100x100 wavelengths by 100 periods requires a numerical method that is extremely efficient in terms of storage and computation. Iterative integral equation methods offer a good performance on these points, provided that the recurring spatiotemporal convolutions...

Parallel Scalability of Video Decoders

An important question is whether emerging and future applications exhibit sufficient parallelism, in particular thread-level parallelism, to exploit the large numbers of cores future chip multiprocessors (CMPs) are expected to contain. As a case study we investigate the parallelism available in video decoders, an important application domain now...

Transport modelling in coastal waters using stochastic differential equations

In this thesis, the particle model that takes into account the short term correlation behaviour of pollutants dispersion has been developed. An efficient particle model for sediment transport has been developed. We have modified the existing particle model by adding extra equations for the suspension using a probabilistic concepts (the Poisson...

Structured parallelization of a multi-block Navier-Stokes solver targeting distributed memory platforms

SOLEQS is a sequential three-dimensional multi-block multi-zone compressible Navier-Stokes solver, produced by NLR. In this paper is described how this large-scale application code in the order of 120,000 lines can be parallelized towards different computing platforms in a structured and manageable way. This paralellization is done step-wise,...

On the feasibility of applying robot vision to proximity extraction based on one camera in space

Existing robot vision algorithms are evaluated for application in space for proximity extraction using one camera. Lighting conditions and image formation differ from earth conditions which have implications. An algorithm is derived which is based on the use of run coding, tracking and a least mean error method. Problems concerning hardware...

Preliminary design and analysis of procedures for the numerical generation of 3D block-structured grids

An analysis of various alternative approaches in grid generation is presented. A grid-generation procedure for complex aircraft configurations could be based on a combination of three subprocesses, . decomposition of the flow domain into about 100 hexahedronal blocks, . trilineair transfinite interpolation to generate initial grid point...

Design and Implementation of the Delft Image Processor DIP-1

This report describes the design and implementation of the Delft Image Processor DIP-1. In this pipelined image-processing computer, a number of storage and processing modules which operate concurrently and synchronously (hardware floating-point ALUs and multiplier, conversion table and cellularlogic table) may be interconnected in a...