high performance computing on graphics processing units: hgpu.org

With the amount of sequence data deluge as a result of next generation sequencing, there comes a need to leverage the large-scale biological sequence data. Therefore, the role of high performance computational methods to mining interesting information solely from these sequence data becomes increasingly important. Almost everything in bioinformatics counts on the inter-relationship between sequences, […]

MOTIVATION: Quantification of the contribution of genetic variation to phenotypic variation for complex traits becomes increasingly computationally demanding with increasing numbers of SNPs and individuals. To meet the challenges in making feasible large scale studies, we present the REACTA software. Adapted from ACTA (and, in turn, GCTA), it is tailored to exploit the parallelism present […]

The interaction of flows and solid objects is a recurring problem in several engineering disciplines. The objective of this work is to present a fully coupled model, based on the fundamental conservation laws of hydrodynamics, namely the continuity and Navier-Stokes equations, and the equation of conservation of momentum of solid bodies. The coupled numerical solution, […]

Tools that aim to automatically map parallel computations to heterogeneous and hierarchical systems try to divide the whole computation in parts with computational loads adjusted to the capabilities of the target devices. Some parts are executed in node cores, while others are executed in accelerator devices. Each part requires one or more data-structure pieces that […]

Computer systems increasingly rely on heterogeneity to achieve greater performance, scalability and energy efficiency. Because heterogeneous systems typically comprise multiple execution contexts with different programming abstractions and runtimes, programming them remains extremely challenging. Dandelion is a system designed to address this programmability challenge for data-parallel applications. Dandelion provides a unified programming model for heterogeneous systems […]

This thesis presents a parallel intermediate representation for embedded languages called PIRE, and its incorporation into the Feldspar language. The original Feldspar backend translates the parallel loops of Feldspar to ordinary for loops, meaning that they are not actually parallel in the generated code. We create an alternate backend for the Feldspar project, where the […]

We present an implementation of Overdetermined Laplacian Partial Differentiation Equations (ODETLAP) that uses CUDA directly. This lossy compression technique approximates a solution to an overdetermined system of equations in order to reconstruct gridded, correlated data. ODETLAP can be used to compress a dataset or to reconstruct missing data. Parallelism in CUDA provides speed performance improvements […]

A new molecular simulation toolkit composed of some lately developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at mesoscopic scale by utilizing the computational power of GPUs. In addition, the hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can […]

We introduce an algorithm for the deconvolution of radio synthesis images that accounts for the non-coplanar-baseline effect, allows multiscale reconstruction onto arbitrarily positioned pixel grids, and allows the antenna elements to have directional dependent gains. Using numerical L1-minimisation techniques established in the application of compressive sensing to radio astronomy, we directly solve the deconvolution equation […]

Aggregate Risk Analysis is a computationally intensive and a data intensive problem, thereby making the application of high-performance computing techniques interesting. In this paper, the design and implementation of a parallel Aggregate Risk Analysis algorithm on multi-core CPU and many-core GPU platforms are explored. The efficient computation of key risk measures, including Probable Maximum Loss […]

The N-body problem appears in many computational physics simulations. At each time step the computation involves an all-pairs sum whose complexity is quadratic, followed by an update of particle positions. This cost means that it is not practical to solve such dynamic N-body problems on large scale. To improve this situation, we use both algorithmic […]

Gaspi (Global Address Space Programming Interface) is an API specification for Partitioned Global Address Spaces. The Gaspi API is focused on three key objectives: scalability, exibility and failure tolerance. Gaspi uses one-sided RDMA driven communication in combination with remote completion in a PGAS environment. As such, Gaspi aims to initiate a paradigm shift from bulk-synchronous […]