high performance computing on graphics processing units: hgpu.org

Today’s general purpose computers lack in meeting the requirements on computing performance for standard applications in bioinformatics like DNA sequence alignment, error correction for assembly, or TFBS finding. The size of DNA sequence databases doubles twice a year. On the other hand the advance in computing performance per unit cost only doubles every 2 years. […]

Abstract We introduce a novel, automatic streamline seeding algorithm for vector fields defined on surfaces in 3D space. The algorithm generates evenly spaced streamlines fast, simply and efficiently for any general surface-based vector field. It is general because it handles large, complex, unstructured, adaptive resolution grids with holes and discontinuities, does not require a parametrization, […]

Emerging DNA sequencing technologies open up exciting new opportunities for genome sequencing by generating read data with a massive throughput. However, produced reads are significantly shorter and more error-prone compared to the traditional Sanger shotgun sequencing method. This poses challenges for de-novo DNA fragment assembly algorithms in terms of both accuracy (to deal with short, […]

Computing large multiple protein sequence alignments using progressive alignment tools such as ClustalW requires several hours on state-of-the-art workstations. ClustalW uses a three-stage processing pipeline: (i) pairwise distance computation; (ii) phylogenetic tree reconstruction; and (iii) progressive multiple alignment computation. Previous work on accelerating ClustalW was mainly focused on parallelizing the first stage and achieved good […]

Main objective of this paper is to outline possibleways how to achieve a substantial acceleration in caseof advection-diffusion equation (A-DE) calculation,which is commonly used for a description of thepollutant behavior in atmosphere. A-DE is a kind ofpartial differential equation (PDE) and in general caseit is usually solved by numerical integration due to itshigh complexity. These […]

Behavioral models have been used in the entertainment industry to increase the realism in the simulation of large groups of individuals. Unfortunately, the classical models can be very compute-intensive when very large groups are considered, reducing its applicability in games and other interactive systems. In this article we explore both search space reduction and parallelism […]

Many methodologies dealing with prediction or simulation of soft tissue deformations on medical image data require preprocessing of the data in order to produce a different shape representation that complies with standard methodologies, such as mass-spring networks, finite element method s (FEM). On the other hand, methodologies working directly on the image space normally do […]

Pathfinding is one of the tasks, apart from graphics rendering, requiring most CPU resources. Although there are many approaches to effectively solve pathfinding problems, they are becoming less suitable as more and more games have larger game worlds that dynamically change during the game play. These new games have more visually realistic graphics that increase […]

The limiting factor for efficiency of sparse linear solvers is the memory bandwidth. In this work, we describe a fast Conjugate Gradient solver for unstructured problems, which runs on multiple GPUs installed on a single mainboard. The solver achieves double precision accuracy with single precision GPUs, using a mixed precision iterative refinement algorithm. To achieve […]

In this paper, we describe an improved particle-based volume rendering (PBVR) technique for previewing a large irregular volume dataset using the CUDA architecture. This technique allows for opaque and emissive particles to render translucent volumes without visibility sorting. Our GPU acceleration of PBVR provides the multi-volume rendering feature while remaining compatible with both regular and […]

The development of high performance dense linear algebra (DLA) critically depends on highly optimized BLAS, and especially on the matrix multiplication routine (GEMM). This is especially true for Graphics Processing Units (GPUs), as evidenced by recently published results on DLA for GPUs that rely on highly optimized GEMM. However, the current best GEMM performance, e.g. […]

The small number of some reactant molecules in biological systems formed by living cells can result in dynamical behavior which cannot be captured by traditional deterministic models. In such a problem, a more accurate simulation can be obtained with discrete stochastic simulation (Gillespie’s stochastic simulation algorithm – SSA). Many stochastic realizations are required to capture […]