high performance computing on graphics processing units: hgpu.org

GPUs are seeing increasingly widespread use for general purpose computation due to their excellent performance for highly-parallel, throughput-oriented applications. For many workloads, however, the performance benefits of offloading are hindered by the large and unpredictable overheads of launching GPU kernels and of transferring data between CPU and GPU. This paper proposes and evaluates hardware and […]

This paper introduces a reaction-diffusion-chemotaxis model for bacterial aggregation patterns on the surface of thin agar plates. It is based on the non-linear degenerate cross diffusion model proposed by Kawasaki et al. (J. of Theor. Biol. 188(2) 1997) and it includes a suitable nutrient chemotactic term compatible with such type of diffusion. High resolution numerical […]

As we are in the development phase of our own super computer, we have identified several applications which are highly computationally intensive applications for a normal desktop computer to achieve the solution. These identified applications are related to multidisciplinary like bio-medical, mathematics, fluid dynamics, genetic algorithms. We are actually identifying the parallel computations involved in […]

Graphics processing units (GPUs) are the state of the art embracing the concept of many-core technology. Their significant advantage in performance and performanceper-watt compared to traditional microprocessors has facilitated development of GPUs in many compute applications. However, GPUs are often treated as "black-box" devices due to proprietary strategies of hardware vendors. One of the greatest […]

We propose a model that uses a small set of quite simple parameters to devise a proper partitioning{between CPU and GPU cores{of the tasks deriving from structured data parallel patterns/algorithmic skeletons. The model takes into account both hardware related and application dependent parameters. It eventually computes the percentage of tasks to be executed on CPU […]

In recent years, researchers have employed a wide array of multi-physics computational tools, of varying sophistication, to simulate brownout conditions [1-3]. Among these tools, compressible high-fidelity Reynolds-Averaged Navier Stokes (RANS) solvers [3] depend the least on empirical assumptions. However, the high computational expense involved in RANS simulations of viscous, rotary environments, makes it less attractive […]

There has been considerable research into improving Fast Fourier Transform (FFT) performance through parallelization and optimization for specialized hardware. However, even with those advancements, processing of very large files, over 1TB in size, still remains prohibitively slow. Analysts performing signal processing are forced to wait hours or days for results, which results in a disruption […]

The PEPPHER component model defines an environment for annotation of native C/C++ based components for homogeneous and heterogeneous multicore and manycore systems, including GPU and multi-GPU based systems. For the same computational functionality, captured as a component, different sequential and explicitly parallel implementation variants using various types of execution units might be provided, together with […]

In this thesis, we examine the optical properties of metallic nanostructures with typical feature sizes of the order of visible light. The interaction of light with such structures can be accurately described by classical electrodynamics. Thus, for the analysis of metallic nanostructures within this thesis, we will employ Maxwell’s equations [1] to model the physical […]

Positron emission tomography (PET) is an important imaging modality in both clinical usage and research studies. We have developed a compact high-sensitivity PET system that consisted of two large-area panel PET detector heads, which produce more than 224 million lines of response and thus request dramatic computational demands. In this work, we employed a state-of-the-art […]

This paper presents the first deployment of the Fast Multipole Method on the Cell processor (PowerXCell 8i). We rely on the matrix formulation with BLAS routines of the FMB code (Fast Multipole with BLAS) in order to directly and efficiently offload the most time consuming operators of both far field and near field computations on […]

This paper presents a fast GPU-based solution to compensate positron range effects in heterogeneous media for iterative PET reconstruction. We assume a factorized approach, where projections are decomposed to phases according to the main physical effects. Positron range is the first effect in this chain, which causes a spatially varying blurring according to local material […]