high performance computing on graphics processing units: hgpu.org

Power constraints are forcing HPC systems to continue to increase hardware concurrency. Efficiently scaling applications on future machines will be essential for improved science and it is recognised that the "flat" MPI model will start to reach its scalability limits. The optimal approach is unknown, necessitating the use of mini-applications to rapidly evaluate new approaches. […]

Past researches on multicore scheduling assume that a computational unit has already been parallelized into a prefixed number of threads. However, with recent technologies such as OpenCL, a computational unit can be parallelized in many different ways with runtime selectable numbers of threads. This paper proposes an optimal algorithm for parallelizing and scheduling a set […]

Dictionary training for sparse representations involves dealing with large chunks of data and complex algorithms that determine time consuming implementations. SBO is an iterative dictionary learning algorithm based on constructing unions of orthonormal bases via singular value decomposition, that represents each data item through a single best fit orthobase. In this paper we present a […]

GPU-based beamforming is a relatively unexplored area in radio astronomy, possibly due to the assumption that any such system will be severely limited by the PCIe bandwidth required to transfer data to the GPU. We have developed a CUDA-based GPU implementation of a coherent beamformer, specifically designed and optimised for deployment at the BEST-2 array […]

We present a state-of-the-art speech recognition system developed using end-to-end deep learning. Our architecture is significantly simpler than traditional speech systems, which rely on laboriously engineered processing pipelines; these traditional systems also tend to perform poorly when used in noisy environments. In contrast, our system does not need hand-designed components to model background noise, reverberation, […]

We present highly efficient algorithms for performing forward and backward propagation of Convolutional Neural Network (CNN) for pixelwise classification on images. For pixelwise classification tasks, such as image segmentation and object detection, surrounding image patches are fed into CNN for predicting the classes of centered pixels via forward propagation and for updating CNN parameters via […]

Training classifiers can be seen as an optimization problem. With this view, we have developed a method to train a type of nearest centroid classifier with PSO. Results showed an improvement on most of the datasets tested. Additionally, we have developed a method to utilize the developed classifier with datasets containing both numeric and categorical […]

With the advent of multi and many-core processors, communication has replaced computation as the performance bottleneck. Most current approaches to the problem try to tolerate memory access latency through a high amount of Thread-Level Parallelism. However, not all applications benefit from such techniques and there is a need to address the weakness of the underlying […]

Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing $3_1$, $5_1$ knots and catenanes made up of two unknotted rings scale like $N^{1/3}$ in the limit of large ring sizes $N$. This is […]

MatConvNet is an implementation of Convolutional Neural Networks (CNNs) for MATLAB. The toolbox is designed with an emphasis on simplicity and flexibility. It exposes the building blocks of CNNs as easy-to-use MATLAB functions, providing routines for computing linear convolutions with filter banks, feature pooling, and many more. In this manner, MatConvNet allows fast prototyping of […]

The tooling landscape of deep learning is fragmented by a growing gap between the generic and productivity-oriented tools that optimize for algorithm development and the task-specific ones that optimize for speed and scale. This creates an artificial barrier to bring new innovations into real-world applications. Minerva addresses this issue with a layered design that provides […]

BACKGROUND: Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS: A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing […]