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Rahul Sharma, Michael Bauer, Alex Aiken
Previous efforts to formally verify code written for GPUs have focused solely on kernels written within the traditional data-parallel GPU programming model. No previous work has considered the higher performance, but more complex, warp-specialized kernels based on producer-consumer named barriers available on current hardware. In this work we present the first formal operational semantics for […]
Scott Zimmerman
This whitepaper is intended for Microsoft Windows developers who are considering writing high-performance parallel code in Amazon Web Services (AWS) using the Microsoft C++ Accelerated Massive Parallelism (C++ AMP) library. This paper describes an ASP.NET Model-View-Controller (MVC) web application written in C# that invokes C++ functions running on the graphics processing unit (GPU) for matrix […]
Long Wang, Rainer Spurzem, Sverre Aarseth, Keigo Nitadori, Peter Berczik, M.B.N. Kouwenhoven, Thorsten Naab
Accurate direct N-body simulations help to obtain detailed information about the dynamical evolution of star clusters. They also enable comparisons with analytical models and Fokker-Planck or Monte-Carlo methods. NBODY6 is a well-known direct N-body code for star clusters, and NBODY6++ is the extended version designed for large particle number simulations by supercomputers. We present NBODY6++GPU, […]
Wim Vanderbauwhede
In this report we present a novel approach to model coupling for shared-memory multicore systems hosting OpenCL-compliant accelerators, which we call The Glasgow Model Coupling Framework (GMCF). We discuss the implementation of a prototype of GMCF and its application to coupling the Weather Research and Forecasting Model and an OpenCL-accelerated version of the Large Eddy […]
Anton Wijs
Bisimilarity checking is an important operation to perform explicit-state model checking when the state space of a model under verification has already been generated. It can be applied in various ways: reduction of a state space w.r.t. a particular flavour of bisimilarity, or checking that two given state spaces are bisimilar. Bisimilarity checking is a […]
Sven Warris, Feyruz Yalcin, Katherine J. L. Jackson, Jan Peter Nap
MOTIVATION: To obtain large-scale sequence alignments in a fast and flexible way is an important step in the analyses of next generation sequencing data. Applications based on the Smith-Waterman (SW) algorithm are often either not fast enough, limited to dedicated tasks or not sufficiently accurate due to statistical issues. Current SW implementations that run on […]
Adam Betts, Nathan Chong, Alastair F. Donaldson, Jeroen Ketema, Shaz Qadeer, Paul Thomson, John Wickerson
We present a technique for the formal verification of GPU kernels, addressing two classes of correctness properties: data races and barrier divergence. Our approach is founded on a novel formal operational semantics for GPU kernels termed synchronous, delayed visibility (SDV) semantics, which captures the execution of a GPU kernel by multiple groups of threads. The […]
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 […]
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