high performance computing on graphics processing units: hgpu.org

It is compute-intensive to evaluate the probability of an observation sequence on a hidden Markov model. Some fast algorithms exit, the forward-backward procedure is the most popular one among them. The forward-backward procedure can save much computation, but its time complexity is N^2T, in other words, there is a high computational complexity in the algorithm. […]

Many system-level design tasks (e.g. timing analysis, hardware/software partitioning and design space exploration) involve computational kernels that are intractable (usually NP-hard). As a result, they involve high running times even for mid-sized problems. In this paper we explore the possibility of using commodity graphics processing units (GPUs) to accelerate such tasks that commonly arise in […]

We present in this paper our work regarding simulating a type of P system known as a spiking neural P system (SNP system) using graphics processing units (GPUs). GPUs, because of their architectural optimization for parallel computations, are well-suited for highly parallelizable problems. Due to the advent of general purpose GPU computing in recent years, […]

We present a method to couple particle-based fluid simulation methods such as Smoothed Particle Hydrodynamics (SPH) and volume rendering in order to visualize the fluid. A volume is generated from the fluid’s implicit density field so volume raycasting can be performed to render the surface on the GPU. The volume generation algorithm is also implemented […]

Scale invariant feature transform (SIFT) and stereo vision are applied together to recognize objects in real time. This work reports the performance of a GPU (graphic processing unit) based real-time feature detector in capturing the features of 3D objects when the objects undergo rotational and translational motions in cluttered backgrounds. We have compared the performance […]

Future mainstream microprocessors will likely integrate specialized accelerators, such as GPUs, onto a single die to achieve better performance and power efficiency. However, it remains a keen challenge to program such a heterogeneous multicore platform, since these specialized accelerators feature ISAs and functionality that are significantly different from the general purpose CPU cores. In this […]

The modern graphics processing unit (GPU) found in many standard personal computers is a highly parallel math processor capable of nearly 1 TFLOPS peak throughput at a cost similar to a high-end CPU and an excellent FLOPS/watt ratio. High-level linear algebra operations are computationally intense, often requiring O(N3) operations and would seem a natural fit […]

The Clustering Coefficient (CC) is a fundamental measure in social network analysis assessing the degree to which nodes tend to cluster together. While CC computation on static graphs is well studied, emerging applications have new requirements for online query of the “global” CC of a given subset of a graph. As social networks are widely […]

The analysis of medical image, in particular Magnetic Resonance Imaging (MRI), is a very useful tool to help the neurologists on the diagnosis. One of the stages on the analysis of MRI is given by a classification based on the Markov Random Fields (MRF) method. It is possible to find in the literature several packages […]

A recent trend in computer science and related fields is general purpose computing on graphics processing units (GPUs), which can yield impressive performance. With multiple cores connected by high memory bandwidth, today’s GPUs offer resources for non-graphics parallel processing. This article provides a brief introduction into the field of GPU computing and includes examples. In […]

MOTIVATION: The introduction of next generation sequencing techniques and especially the high-throughput systems Solexa (Illumina Inc.) and SOLiD (ABI) made the mapping of short reads to reference sequences a standard application in modern bioinformatics. Short read alignment is needed for reference based re-sequencing of complete genomes as well as for gene expression analysis based on […]

BACKGROUND: Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter and more error-prone than conventional Sanger shotgun reads. This poses a challenge for the de novo assembly in terms of assembly quality and scalability for large-scale short read datasets. RESULTS: We present […]