high performance computing on graphics processing units: hgpu.org

Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of […]

Graphics processors are significantly faster than traditional processors, particularly for numerical code, and in recent years have become flexible enough to permit general-purpose use, rather than just graphics use. NVIDIA’s CUDA makes general-purpose graphics processor computing feasible, but it still requires significant programmer effort. My thesis is that array programming can be an effective way […]

In this article, we discuss how the fast multipole method (FMM) can be implemented on modern parallel computers, ranging from computer clusters to multicore processors and graphics cards (GPU). The FMM is a somewhat difficult application for parallel computing because of its tree structure and the fact that it requires many complex operations which are […]

The use of the GPU as a general purpose processor is becoming more popular and there are different approaches for this kind of programming. In this paper we present a comparison between different implementations of the OpenGL and CUDA approaches for solving our test case, a weighted Jacobi iteration with a structured matrix originating from […]

The paper compares three APIs for the implementation of cloth modelling on modern graphics processor units (GPU): OpenGL plus GLSL, NVIDIA CUDA and OpenCL. They are compared by programming features, platform and device portability, and performance for the purpose of dynamic cloth simulation. Results about performance are given and conclusions are drawn about use cases.

Performance of a treatment planning system is an essential factor in making sophisticated plans. The dose calculation is a major time-consuming process in planning operations. The standard algorithm for proton dose calculations is the pencil beam algorithm which produces relatively accurate results, but is time consuming. In order to shorten the computational time, we have […]

Algorithmic solutions can help reduce energy consumption in computing environs. Energy conservation is a major concern today. Federal programs provide incentives to save energy and promote the use of renewable energy resources. Individuals, companies, and organizations seek energyefficient products as the energy cost to run equipment has grown to be a major factor.

An indirect boundary element method (BEM) that uses the fast multipole method (FMM) was accelerated using graphics processing units (GPUs) to reduce the time required to calculate a three-dimensional electrostatic field. The BEM is designed to handle cubic voxel models and is specialized to consider square voxel walls as boundary surface elements. The FMM handles […]

We describe, implement and benchmark EigenCFA, an algorithm for accelerating higher-order control-flow analysis (specifically, 0CFA) with a GPU. Ultimately, our program transformations, reductions and optimizations achieve a factor of 72 speedup over an optimized CPU implementation. We began our investigation with the view that GPUs accelerate high-arithmetic, data-parallel computations with a poor tolerance for branching. […]

Scattering maps from strained or disordered nano-structures around a Bragg reflection can either be computed quickly using approximations and a (Fast) Fourier transform, or using individual atomic positions. In this article we show that it is possible to compute up to 4.10^10 $reflections.atoms/s using a single graphic card, and we evaluate how this speed depends […]

We describe the GPU implementation of shifted or multimass iterative solvers for sparse linear systems of the sort encountered in lattice gauge theory. We provide a generic tool that can be used by those without GPU programming experience to accelerate the simulation of a wide array of theories. We stress genericity, which is important to […]

OpenGL is the industry-leading, cross-platform graphics application programming interface (API), and the only major API with support for virtually all operating systems. Many languages, such as Fortran, Java, Tcl/Tk, and Python, have OpenGL bindings to take advantage of OpenGL visualization power. In this article, we present Ch OpenGL Toolkit, a truly platform-independent Ch binding to […]