high performance computing on graphics processing units: hgpu.org

BACKGROUND: The prediction of sites and products of metabolism in xenobiotic compounds is key to the development of new chemical entities, where screening potential metabolites for toxicity or unwanted side-effects is of crucial importance. In this work 2D topological fingerprints are used to encode atomic sites and three probabilistic machine learning methods are applied: Parzen-Rosenblatt […]

The Unified Memory Machine (UMM) is a theoretical parallel computing model that captures the essence of the global memory access of GPUs. A sequential algorithm is oblivious if an address accessed at each time does not depend on input data. Many important tasks including matrix computation, signal processing, sorting, dynamic programming, and encryption/decryption can be […]

This paper addresses adjustments, implementation and performance comparison of the Moving Average with Local Difference (MALD) method for ceramic tile surface defects detection. Ceramic tile production process is completely autonomous, except the final stage where human eye is required for defects detection. Recent computational platform development and advances in machine vision provides us with several […]

We present a unified dynamics framework for real-time visual effects. Using particles connected by constraints as our fundamental building block allows us to treat contact and collisions in a unified manner, and we show how this representation is flexible enough to model gases, liquids, deformable solids, rigid bodies and clothing with two-way interactions. We address […]

Scientific data is mostly multi-valued, e.g., coordinates, velocities, moments or feature components, and it comes in large quantities. The data layout of such containers has an enormous impact on the achieved performance, however, layout optimization is very time-consuming and error-prone because container access syntax in standard programming languages is not sufficiently abstract. This means that […]

Processing moving object trajectories arises in many application domains and has been addressed by practitioners in the spatiotemporal database and Geographical Information System communities. In this work, we focus on a trajectory similarity search, the distance threshold query, which finds all trajectories within a given distance d of a search trajectory over a time interval. […]

The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing […]

The main purpose of the work is optimization of the solver for rarefied gas flow modeling based on the Boltzmann equation. Optimization method is based on SIMD extensions for x86 processors. Computational code is profiled and manually optimized with SSE instructions. Heat flow, shock waves and Knudsen pump are modeled with optimized solver. Dependencies of […]

The modern manycore coprocessors and GPUs demonstrate very high performance on certain problems. Recent research has shown that these coprocessors can be used to accelerate database operations. But, to the best of our knowledge, there is only a little prior work on using coprocessors in multiprocessor database systems. This paper focuses on evaluation of database […]

High-density oligonucleotide microarrays allow several millions of genetic markers in a single experiment to be observed. Current bioinformatics tools for gene-expression quantile data normalization are unable to process such huge data sets. In parallel with this reality, the huge volume of molecular data produced by current high-throughput technologies in modern molecular biology has increased at […]

The main purpose of this work is to show the advantages of using various approaches of heterogeneous programming. The results were received on the example of solving the system of the linear equations by the conjugate gradient method. High-level and low-level technologies (OpenACC and CUDA respectively) were used to accelerate computations on the GPU. The […]

The Sequential Monte Carlo (SMC) method is a simulation-based approach to compute posterior distributions. SMC methods often work well on applications considered intractable by other methods due to high dimensionality, but they are computationally demanding. While SMC has been implemented efficiently on FPGAs, design productivity remains a challenge. This paper introduces a design flow for […]