high performance computing on graphics processing units: hgpu.org

The Global Array toolkit (GA) [1] is a powerful framework for implementing algorithms with irregular communication patterns, such as those of quantum chemistry. On the other hand, accelerators such as GPUs have shown great potential for important kernels in quantum chemistry, for example, atomic integral generation [2] and dense linear algebra in correlated methods [3]. […]

Shape analysis based on images and implicit surfaces has been an active area of research for the past several years. Particle systems have emerged as a viable solution to represent shapes for statistical analysis. One of the most widely used representations of shapes in computer graphics and visualization is the triangular mesh. It is desirable […]

The map is a higher-order function that applies a given function to the list or lists of elements producing the list of results. The mapped function is applied to each element of the list independently, thus can be performed for all elements in parallel, making the GPU an interesting platform to be implemented on. Although […]

In this short paper we present a GPU code for MD simulations of large membrane regions in the NVT and NVE ensembles with explicit solvent. We give an overview of the code and present preliminary performance results.

Although the hardware has dramatically changed in the last few years, nodes of multicore chips augmented by Graphics Processing Units (GPUs) seem to be a trend of major importance. Previous approaches for scheduling dense linear operations on such a complex node led to high performance but at the double cost of not using the potential […]

Recent microprocessor designs concentrate upon adding cores rather than increasing clock speeds in order to achieve enhanced performance. As a result, in the last few years computational accelerators featuring many cores per chip have begun to appear in high performance scientific computing systems. The IBM Cell processor, with its 9 heterogeneous cores, was the first […]

The goal of this research is to integrate graphics processing units (GPUs) into SCIRun, a biomedical problem solving environment, in a way that is transparent to the scientist. We have developed a portable mechanism that allows seamless coexistence of CPU and accelerated GPU computations to provide the best performance while also providing ease of use. […]

Takagi factorization or symmetric singular value decomposition is a special form of SVD applicable to symmetric complex matrices. The computation takes advantage of symmetry to reduce computation and storage requirements. The Jacobi method with chess tournament ordering was used to perform the computation in parallel on a GPU using the CUDA programming model. We were […]

The Multicore+GPU architecture has been adopted in some of the fastest supercomputers listed on the TOP500. The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures processors like Multicore+GPU. However, to provide portable performance, manual parameter tuning is required. This paper presents automatically tuned LU factorization. The […]

In recent years, Graphics Processing Units (GPUs) have emerged as a powerful accelerator for general-purpose computations. Current approaches to program GPUs are still relatively low-level programming models such as Compute Unified Device Architecture (CUDA), a programming model from NVIDIA, and Open Compute Language (OpenCL), created by Apple in cooperation with others. These two programming models […]

GPUs constitute nowadays a solid alternative for high performance computing, and the advent of CUDA/OpenCL allow programmers a friendly model to accelerate a broad range of applications. The way GPUs exploit parallelism differ from multi-core CPUs, which raises new challenges to take advantage of its tremendous computing power. In this respect, P systems or Membrane […]

In order for scientists to learn more about molecular biology, it is imperative that they have the ability to construct and evaluate models. Model statistics consistent with the chemical master equation can be obtained using Gillespie’s stochastic simulation algorithm (SSA). Due to the stochastic nature of the Monte Carlo simulations, large numbers of simulations must […]