high performance computing on graphics processing units: hgpu.org

Parallelism is becoming the leading paradigm in today’s computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating […]

MOTIVATION: Bayesian phylogenetic inference can be used to propose a “tree of life” for a collection of species whose DNA sequences are known. While there are many packages available that implement Bayesian phylogenetic inference, such as the popular MrBayes, running these programs poses significant computational challenges. Parallelized versions of the Metropolis coupled Markov chain Monte […]

Locating object boundaries, modeling shapes is still an interesting and important task in many applications such as computer vision, object detection, image segmentation and tracking. In this paper we show the implementation of 2D and 3D algorithms based on the level sets using the advantages residing in today’s common GPUs. One main goal of this […]

We present the implementation and performance of a class of directionally unsplit Riemann-solver-based hydrodynamic schemes on Graphic Processing Units (GPU). These schemes, including the MUSCL-Hancock method, a variant of the MUSCL-Hancock method, and the corner-transport-upwind method, are embedded into the adaptive-mesh-refinement (AMR) code GAMER. Furthermore, a hybrid MPI/OpenMP model is investigated, which enables the full […]

PURPOSE: The graphical processing unit (GPU) on modern graphics cards offers the possibility of accelerating arithmetically intensive tasks. By splitting the work into a large number of independent jobs, order-of-magnitude speedups are reported. In this article, the possible speedup of PLATO’s ray tracing algorithm for dose calculations using a GPU is investigated. METHODS: A GPU […]

With the rapid development of GPU (Graphics Processor Unit) in recent years, GPGPU (General-Purpose computation on GPU) has become an important technique in scientific research. However GPU might well be seen more as a cooperator than a rival to CPU. Therefore, we focus on exploiting the power of CPU and GPU in solving generic problems […]

As heterogeneous parallel systems become dominant, application developers are being forced to turn to an incompatiblemix of low level programming models (e.g. OpenMP, MPI, CUDA, OpenCL). However, these models do little to shield developers from the difficult problems of parallelization, data decomposition and machine-specific details. Most programmersare having a difficult time using these programming models […]

The efficiency of implementations of algorithms with a fine-grained parallelism on GPUs that support the CUDA architecture is studied. Cellular automata and difference schemes are used for testing. Several versions of implementations are proposed and their efficiency is analyzed. An example of GPU application for modeling the process of carbon dioxide oxidation on the catalyst […]

Coordinated checkpoint and recovery is a common approach to achieve fault tolerance on large-scale systems. The traditional mechanism dumps the process image to a local disk or a central storage area of all the processes involved in the parallel job. When a failure occurs, the processes are restarted and restored to the latest checkpoint image. […]

Structured illumination fluorescence microscopy is a powerful super-resolution method that is capable of achieving a resolution below 100 nm. Each super-resolution image is computationally constructed from a set of differentially illuminated images. However, real-time application of structured illumination microscopy (SIM) has generally been limited due to the computational overhead needed to generate super-resolution images. Here, […]

The lattice-Boltzmann method is well suited for implementation in single-instruction multiple-data (SIMD) environments provided by general purpose graphics processing units (GPGPUs). This paper discusses the integration of these GPGPU programs with OpenMP to create lattice-Boltzmann applications for multi-GPU clusters. In addition to the standard single-phase single-component lattice-Boltzmann method, the performances of more complex multiphase, multicomponent […]

Recent GPU algorithms for constructing spatial hierarchies achieve promising performance for moderately complex models by using the BFS (breadth-first search) construction order. While being able to exploit the massive parallelism on the GPU, the BFS order consumes excessive GPU memory, which becomes a serious issue. In this paper, we propose to use the PBFS (partial […]