high performance computing on graphics processing units: hgpu.org

Graphics processors (GPUs) provide a vast number of simple, data-parallel, deeply multithreaded cores and high memory bandwidths. GPU architectures are becoming increasingly programmable, offering the potential for dramatic speedups for a variety of general-purpose applications compared to contemporary general-purpose processors (CPUs). This paper uses NVIDIA’s C-like CUDA language and an engineering sample of their recently […]

We describe a complete implementation of all-atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it […]

The modern graphics processing unit (GPU) is the result of 40 years of evolution of hardware to accelerate graphics processing operations. It represents the convergence of support for multiple market segments: computer-aided design, medical imaging, digital content creation, document and presentation applications, and entertainment applications. The exceptional performance characteristics of the GPU make it an […]

This paper describes designing a parallel GA with GPU computation to solve the quadratic assignment problem (QAP) which is one of the hardest optimization problems in permutation domains. For the parallel method, a multiple-population, coarse-grained GA model was used. Each subpopulation is evolved by a multiprocessor in a GPU (NVIDIA GeForce GTX285). At predetermined intervals […]

GPUs for numerical computations are becoming an attractive alternative in research. In this paper, we propose a new parallel processing environment for matrix multiplications by using both CPUs and GPUs. The execution time of matrix multiplications can be decreased to 40.1% by our method, compared with using the fastest of either CPU only case or […]

Despite the increasing adoption of other imaging modalities, ultrasound guidance is widely used for surgical procedures and clinical imaging due to its low cost, non-invasiveness, and real-time visual feedback. Many ultrasound-guided procedures require extensive training and where possible training on simulations should be preferred over patients. Computational resources for existing approaches to ultrasound simulation are […]

We implement a high-order finite-element application, which performs the numerical simulation of seismic wave propagation resulting for instance from earthquakes at the scale of a continent or from active seismic acquisition experiments in the oil industry, on a large cluster of NVIDIA Tesla graphics cards using the CUDA programming environment and non-blocking message passing based […]

We are interested in the intensive use of Factorial Correspondence Analysis (FCA) for large-scale content-based image retrieval. Factorial Correspondence Analysis, is a useful method for analyzing textual data, and we adapt it to images using the SIFT local descriptors. FCA is used to reduce dimensions and to limit the number of images to be considered […]

This paper presents a single-instruction-multiple-data (SIMD) based implementation of the transient stability simulation on the Graphics Processing Unit (GPU). Two programming models to implement the standard method of the transient stability simulation are proposed and implemented on a single GPU. In the first model the CPU is responsible for part of the simulation, while the […]

It is well-established that a linear correlation exists between accessible surface areas and experimentally measured solvation energies. Combining this knowledge with an analytic formula for calculation of solvent accessible surfaces, we derive a simple model of desolvation energy as a differentiable function of atomic positions. Additionally, we find that this algorithm is particularly well suited […]

In the last years, the performance and capabilities of Graphics Processing Units (GPUs) improved drastically, mostly due to the demands of the entertainment market, with consumers and companies alike pushing for improvements in the level of visual fidelity, which is only achieved with high performing GPU solutions. Beside the entertainment market, there is an ongoing […]

Scientific applications do frequently suffer from limited compute performance. In this article, we investigate the suitability of specialized computer chips to overcome this limitation. An enhanced Poisson Boltzmann program is ported to the graphics processing unit and the application specific integrated circuit MDGRAPE-3 and resulting execution times are compared to the conventional performance obtained on […]