Gloria Ortega Lopez
This thesis, entitled "High Performance Computing for solving large sparse systems. Optical Diffraction Tomography as a case of study" investigates the computational issues related to the resolution of linear systems of equations which come from the discretization of physical models described by means of Partial Differential Equations (PDEs). These physical models are conceived for the […]
Benjamin Schmid, Jan Huisken
In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution employs the point spread functions (PSF) of the different views to simultaneously fuse and deconvolve the images in 3D, but processing takes a multiple of the acquisition time and […]
Andreas Klockner
A large amount of numerically-oriented code is written and is being written in legacy languages. Much of this code could, in principle, make good use of data-parallel throughput-oriented computer architectures. Loo.py, a transformation-based programming system targeted at GPUs and general data-parallel architectures, provides a mechanism for user-controlled transformation of array programs. This transformation capability is […]
Richard Wilton, Tamas Budavari, Ben Langmead, Sarah J. Wheelan, Steven L. Salzberg, Alexander S. Szalay
When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach […]
Vadim Demchik
General principles of pseudorandom numbers production for Monte Carlo simulations on GPUs are discussed by creating an OpenCL open-source library of pseudorandom number generators PRNGCL. The library contains implementation of a number of the most popular uniform generators. The most popular pseudorandom number generators for Monte Carlo simulations and libraries for GPUs are reviewed. Some […]
Johannes Koster
The analysis of next-generation sequencing (NGS) data is a major topic in bioinformatics: short reads obtained from DNA, the molecule encoding the genome of living organisms, are processed to provide insight into biological or medical questions. This thesis provides novel solutions to major topics within the analysis of NGS data, focusing on parallelization, scalability and […]
Peter Klages, Kevin Bandura, Nolan Denman, Andre Recnik, Jonathan Sievers, Keith Vanderlinde
Interferometric radio telescopes often rely on computationally expensive O(N^2) correlation calculations; fortunately these computations map well to massively parallel accelerators such as low-cost GPUs. This paper describes the OpenCL kernels developed for the GPU based X-engine of a new hybrid FX correlator. Channelized data from the F-engine is supplied to the GPUs as 4-bit, offset-encoded […]
Weifeng Liu, Brian Vinter
Sparse matrix-vector multiplication (SpMV) is a fundamental building block for numerous applications. In this paper, we propose CSR5 (Compressed Sparse Row 5), a new storage format, which offers high-throughput SpMV on various platforms including CPUs, GPUs and Xeon Phi. First, the CSR5 format is insensitive to the sparsity structure of the input matrix. Thus the […]
Ken Miura, Tatsuya Harada
Deep learning can achieve outstanding results in various fields. However, it requires so significant computational power that graphics processing units (GPUs) and/or numerous computers are often required for the practical application. We have developed a new distributed calculation framework called "Sashimi" that allows any computer to be used as a distribution node only by accessing […]
Lukas Polok, Viorela Ila, Pavel Smrz
Sparse matrix multiplication is an important algorithm in a wide variety of problems, including graph algorithms, simulations and linear solving to name a few. Yet, there are but a few works related to acceleration of sparse matrix multiplication on a GPU. We present a fast, novel algorithm for sparse matrix multiplication, outperforming the previous algorithm […]
Simon L. Grimm, Kevin Heng
We present an ultrafast opacity calculator for application to exoplanetary atmospheres, which we name HELIOS-K. It takes a line list as an input, computes the shape of each spectral line (e.g., a Voigt profile) and provides an option for grouping an enormous number of lines into a manageable number of bins. We implement a combination […]
Adam Polak
The clustering coefficient and the transitivity ratio are concepts often used in network analysis, which creates a need for fast practical algorithms for counting triangles in large graphs. Previous research in this area focused on sequential algorithms, MapReduce parallelization, and fast approximations. In this paper we propose a parallel triangle counting algorithm for CUDA GPU. […]
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