high performance computing on graphics processing units: hgpu.org

The applicability and effectiveness of adaptive design optimization (ADO) in selecting optimal stimuli or designs for experimental trials has been well demonstrated in several content areas of cognitive psychology (Myung & Pitt, 2009; Cavagnaro et al, 2010). On the other hand, when applying ADO to real-time, online experiments such as psychophysical experiments with human subjects, […]

Linear SVMs are a popular choice of binary classifier. It is often necessary to train many different classifiers on a multiclass dataset in a one-versus-rest fashion, and this for several values of the regularization constant. We propose to harness GPU parallelism by training as many classifiers as possible at the same time. We optimize the […]

High quality global illumination can enhance the visual perception of depth cue and local thickness of volumetric data but it is seldom used in scientific visualization because of its high computational cost. This paper presents a novel grid-based illumination technique which is specially designed and optimized for volume visualization purpose. It supports common light sources […]

Molecular dynamics (MD) simulations now play a key role in many areas of theoretical chemistry, biology, physics, and materials science. In many cases, such calculations are significantly limited by the massive amount of computer time needed to perform calculations of interest. Herein, we present Long Timestep Molecular Dynamics (LTMD), a method to significantly speed MD […]

The development of parallel architectures is now nearly ubiquitous in not only the high-performance computing field, but also the commodity electronics market. Even embedded processors found in cell phones and tablet computers are starting to incorporate parallel architectures. These architectures are exploiting both SIMD (Single-Instruction Multiple-Data) and SIMT (Simple- Instruction Multiple-Thread) parallelism to achieve higher […]

Two block cyclic reduction linear system solvers are considered and implemented using the OpenCL framework. The topics of interest include a simplified scalar cyclic reduction tridiagonal system solver and the impact of increasing the radix-number of the algorithm. Both implementations are tested for the Poisson problem in two and three dimensions, using a Nvidia GTX […]

Nowadays, there is a lack of performance models for the execution of programs implemented using the CUDA model for GPU (Graphics Processing Units) devices. We have designed and implemented a suite of micro-benchmarks, called uBench. The purpose of uBench is to identify the effects on performance derived from the combination of: (1) the hardware details […]

Bioinformatics and Computational Biology (BCB) is a relatively new multidisciplinary field which brings together many aspects of the fields of biology, computer science, statistics, and engineering. Bioinformatics extracts useful information from biological data and makes these more intuitive and understandable by applying principles of information sciences, while computational biology harnesses computational approaches and technologies to […]

We present a comparison of several modern C++ libraries providing high-level interfaces for programming multi- and many-core architectures on top of CUDA or OpenCL. The comparison focuses on the solution of ordinary differential equations and is based on odeint, a framework for the solution of systems of ordinary differential equations. Odeint is designed in a […]

Simulators are limited by the available resources on the GPU as well as the CPU. Simulation of P systems with active membrane using GPUs is a new concept in the development of applications for membrane computing. P systems are an alternative approach to extract all performance available on GPUs due to its parallel nature. In […]

From the beginning the Geant4 Visualisation System was designed to support several simultaneous graphics systems written to common abstract interfaces. Today it has matured into a powerful diagnostic and presentational tool. It comes with a library of models that may be added to the current scene and which include the representation of the Geant4 geometry […]

We develop an inertial coupling method for modeling the dynamics of point-like "blob" particles immersed in an incompressible fluid, generalizing previous work for compressible fluids [F. Balboa Usabiaga, I. Pagonabarraga, and R. Delgado-Buscalioni, J. Comp. Phys., 235:701-722, 2013]. The coupling consistently includes excess (positive or negative) inertia of the particles relative to the displaced fluid, […]