high performance computing on graphics processing units: hgpu.org

General purpose application development for GPUs (GPGPU) has recently gained momentum as a cost-effective approach for accelerating data- and compute-intensive applications. It has been driven by the introduction of C-based programming environments such as NVIDIA’s CUDA, OpenCL, and Intel’s Ct. While significant effort has been focused on developing and evaluating applications and software tools, comparatively […]

Summary form only given. NVIDIA’s CUDA architecture provides a powerful platform for writing highly parallel programs. By providing simple abstractions for hierarchical thread organization, memories, and synchronization, the CUDA programming model allows programmers to write scalable programs without the burden of learning a multitude of new programming constructs. The CUDA architecture can support many languages […]

New high performance computing (HPC) applications recently have to face scalability over an increasing number of nodes and the programming of special accelerator hardware. Hybrid composition of large computing systems leads to a new dimension in complexity of software development. This paper presents a novel approach to gain insight into accelerator interaction and utilization without […]

Parallel processor architectures are a promising solution to provide the required computing performance for current and future high performance applications. Certainly, the impact on the computational power of such a parallel computer system is related to the inherent parallelism of the algorithm to be implemented. The implementation of an algorithm onto a parallel computer architecture, […]

As the amount of data and the complexity of the processing rise, the demand for processing power in remote sensing applications is increasing. The processing speed is a critical aspect to enable a productive interaction between the human operator and the machine in order to achieve ever more complex tasks satisfactorily. Graphic processing units (GPU) […]

Three initial fits of 1ubi in a 6.6A resolution synthesized density map had backbone RMSDs to the correct placement of 2.7, 2.9 and 6.6A. They have been refined with a Powell optimizer [5] in 10 iterations using 6 directions, 3 rotations a, beta with 0.15 radians and gamma with 0.075 radians starting direction to cover […]

We present a framework, OpenCLosE, for dynamic resource management and scheduling of applications written in open compute language (OpenCL) for heterogeneous multimedia and graphics platforms, such as those found in multimedia smartphones and automotive infotainment clusters. We describe the design of a resource manager and master scheduler for the OpenCLosE environment, that allows efficient realization […]

Here, we present a GPU-accelerated OpenCL implementation of a back-propagation artificial neural network for the creation of QSAR models for drug discovery and virtual high-throughput screening. A QSAR model for HSD achieved an enrichment of 5.9 and area under the curve of 0.83 on an independent data set which signifies sufficient predictive ability for virtual […]

Google’s famous PageRank algorithm is widely used to determine the importance of web pages in search engines. Given the large number of web pages on the World Wide Web, efficient computation of PageRank becomes a challenging problem. We accelerated the power method for computing PageRank on AMD GPUs. The core component of the power method […]

Local Sequence alignment is an important task for bioinformatics. The most widely used algorithm is Smith-Waterman has a quadratic time complexity which is time consuming especially in large biological database search. Many attempts were made to accelerate Smith-Waterman using parallel architecture. In this paper a parallel implementation of Smith Waterman algorithm will be presented. This […]

Paper presents results obtained when porting FEM 2D linear elastostatic local stiffness matrix calculations to Tesla architecture with OpenCL framework. Comparison with native NVIDIA CUDA implementations has been provided.

The current trend towards multi-core/manycore and accelerated architectures presents challenges, both in portability, and also in the choices that developers must make on how to use the resources that these architectures provide. This paper explores some of the possibilities that are enabled by the Open Computing Language (OpenCL), and proposes a programming model that will […]