high performance computing on graphics processing units: hgpu.org

Efficiently studying Sodium Dodecyl Sulfate (SDS) molecules’ formations in the presence of different molar concentrations on high-end GPU clusters whose nodes share accelerators exposes us to several challenges, including the need to dynamically adapt the job lengths. Neither virtualization nor lightweight OS solutions can easily support generality, portability, and maintainability in concert. Our solution complements […]

Parallel algorithms for modern high performance computing systems are required for fast modelling of high dimensional convection-diffusion processes in air. Such algorithms, designed for alternate-triangular finite difference splitting schemes applied to convection-diffusion equation, have been considered. An algorithm for single GPU systems and an algorithm for clusters with graphical processors has been described, algorithms’ performance […]

A flexible and extensible simulation tool architecture, called gpusim, is proposed for heterogeneous grid systems with graphics accelerators. The tool is based on open source Java framework GridSim. Checking for models adequacy and their initial investigation has been performed using known examples of parallel computation problems. The tool allows choosing the most optimal setting parameters […]

IceCube is a one-gigaton neutrino detector designed to detect high-energy cosmic neutrinos. It is located at the geographic South Pole and was completed at the end of 2010. Simulation and data processing for IceCube requires a significant amount of computational power. We describe the design and functionality of IceProd, a management system based on Python, […]

This paper presents an approach to create what we have called a Unified Sentiment Lexicon (USL). This approach aims at aligning, unifying and expanding the set of sentiment lexicons which are available on the web in order to increase their robustness of coverage. A sentiment lexicon is a critical and essential resource for tagging subjective […]

Constituency parsing with rich grammars remains a computational challenge. Graphics Processing Units (GPUs) have previously been used to accelerate CKY chart evaluation, but gains over CPU parsers were modest. In this paper, we describe a collection of new techniques that enable chart evaluation at close to the GPU’s practical maximum speed (a Teraflop), or around […]

BACKGROUND: Picking images of particles in cryo-electron micrographs is an important step in solving the 3D structures of large macromolecular assemblies. However, in order to achieve sub-nanometre resolution it is often necessary to capture and process many thousands or even several millions of 2D particle images. Thus, a computational bottleneck in reaching high resolution is […]

DNA microarrays are used to simultaneously analyze the expression level of thousands of genes under multiple conditions; however, massive amount of data is generated making its analysis a challenge and an ideal candidate for massive parallel processing. Among the available technologies, the use of General Purpose computation on Graphics Processing Units (GPGPU) is an efficient […]

In this paper, a research about the usability, advantages and disadvantages of using Compute Unified Device Architecture (CUDA) is presented, implementing an algorithm based on populations called Particle Swarm Optimization (PSO) [5]. In order to test the performance of the proposed algorithm, a hide watermark image application is put into practice. The PSO is used […]

We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up to 256k (2^18) processors. We present error analysis and scientific application results from a series of more than ten 69 […]

Multiphase flows are widely used in many practical applications in industry, such as oil industry, chemical and thermal engineering, bioengineering and medicine. Especially flows in tubes with granular layer. Multiphase flows in inclined tubes are poorly studied. Numerical study of multiphase flows in inclined tubes was performed. Cases of clear tube and tube with granular […]

We present a single-chain parallelization strategy for Gibbs sampling of probabilistic Directed Acyclic Graphs, where contributions from child nodes to the conditional posterior distribution of a given node are calculated concurrently. For statistical models with many independent observations, such parallelism takes a Single-Instruction-Multiple-Data form, and can be efficiently implemented using multicore parallelization and vector instructions […]