high performance computing on graphics processing units: hgpu.org

SCELib is a computer program which implements the Single Center Expansion (SCE) method to describe molecular electronic densities and the interaction potentials between a charged projectile (electron or positron) and a target molecular system. The first version (CPC Catalog identifier ADMG_v1_0) was submitted to the CPC Program Library in 2000, and version 2.0 (ADMG_v2_0) was […]

This paper presents iNFAnt, a parallel engine for regular expression pattern matching. In contrast with traditional approaches, iNFAnt adopts non-deterministic automata, allowing the compilation of very large and complex rule sets that are otherwise hard to treat. iNFAnt is explicitly designed and developed to run on graphical processing units that provide large amounts of concurrent […]

This paper describes the use of CUDA to accelerate the Linpack benchmark on heterogenous clusters, where both CPUs and GPUs are used in synergy with minor or no modifications to the original source code. A host library intercepts the calls to DGEMM and DTRSM and executes them simultaneously on both GPUs and CPU cores. An […]

As growing power dissipation and thermal effects disrupted the rising clock frequency trend and threatened to annul Moore’s law, the computing industry has switched its route to higher performance through parallel processing. The rise of multi-core systems in all domains of computing has opened the door to heterogeneous multi-processors, where processors of different compute characteristics […]

In this paper we present a general software platform that enables real time surgery simulation on the newly available compute unified device architecture (CUDA)from NVIDIA. CUDA-enabled GPUs harness the power of 128 processors which allow data parallel computations. Compared to the previous GPGPU, it is significantly more flexible with a C language interface. We report […]

Binding site mapping refers to the computational prediction of the regions on a protein surface that are likely to bind a small molecule with high affinity. The process involves flexibly docking a variety of small molecule probes and finding a consensus site that binds most of those probes. Due to the computational complexity of flexible […]

In this work, we propose a new FPGA design flow that combines the CUDA programming model from Nvidia with the state of the art high-level synthesis tool AutoPilot from AutoESL, to efficiently map the exposed parallelism in CUDA kernels onto reconfigurable devices. The use of the CUDA programming model offers the advantage of a common […]

Recently introduced new sequencing technologies can produce massive amounts of short-read data. Detection and correction of sequencing errors in this data is an important but time-consuming pre-processing step for de-novo genome assembly. In this paper, we demonstrate how the quality-score value associated with each base-call can be integrated in a CUDA-based parallel error correction algorithm. […]

Volume ray casting experiences a renewed interest in the last decade. Largely due to the graphics hardware, which enabled real-time implementations competitive in speed with slicing. However these implementations need specialized shader languages and are forced to use graphics APIs. It makes implementation of advanced methods difficult and hinders performance, bending the programming and execution […]

Drainage networks determination from Digital Elevation Models (DEM) has been a widely studied problem in the last three decades. During this time, satellite technology has been improving and optimizing digitalized images, and computers have been increasing their capabilities to manage such a huge quantity of information. The rapid growth of CPU power and memory size […]

The Canny edge detector is a very popular and effective edge feature detector that is used as a pre-processing step in many computer vision algorithms. It is a multi-step detector which performs smoothing and filtering, non-maxima suppression, followed by a connected-component analysis stage to detect ldquotruerdquo edges, while suppressing ldquofalserdquo non edge filter responses. While […]

Molecular dynamics simulations are a common and often repeated task in molecular biology. The need for speeding up this treatment comes from the requirement for large system simulations with many atoms and numerous time steps. In this paper we present a new approach to high performance molecular dynamics simulations on graphics processing units. Using modern […]