high performance computing on graphics processing units: hgpu.org

General purpose computing on graphics processing units (GPGPU) is dramatically changing the landscape of high performance computing in astronomy. In this paper, we identify and investigate several key decision areas, with a goal of simplyfing the early adoption of GPGPU in astronomy. We consider the merits of OpenCL as an open standard in order to […]

Four-dimensional computed tomography (4DCT) has been widely used in cancer radiotherapy for accurate target delineation and motion measurement for tumors in thorax and upper abdomen areas. However, 4DCT simulation is associated with much higher imaging dose than conventional CT simulation, which is a major concern in its clinical application. Conventionally, each phase of 4DCT is […]

When x-rays penetrate soft matter, their phase changes more rapidly than their amplitude. Interference effects visible with high brightness sources creates higher contrast, edge enhanced images. When the object is piecewise smooth (made of big blocks of a few components), such higher contrast datasets have a sparse solution. We apply basis pursuit solvers to improve […]

Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a (C)alpha-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics […]

High radiation dose in CT scans increases a lifetime risk of cancer and has become a major clinical concern. Recently, iterative reconstruction algorithms with Total Variation (TV) regularization have been developed to reconstruct CT images from highly undersampled data acquired at low mAs levels in order to reduce the imaging dose. Nonetheless, TV regularization may […]

Computing on graphics processors is maybe one of the most important developments in computational science to happen in decades. Not since the arrival of the Beowulf cluster, which combined open source software with commodity hardware to truly democratize high-performance computing, has the community been so electrified. Like then, the opportunity comes with challenges. The formulation […]

We present an implementation of a general purpose GPU-Molecular Dynamics code named LAMMPScuda which is based on LAMMPS. It exhibits excellent scaling behavior, allowing for the efficient usage of hundreds of GPUs for a single simulation. At the same time each GPU provides the equivalent performance of approximately 5 modern Quad Core CPUs. By supporting […]

We accelerate many-flavor lattice QCD simulations using multiple GPUs. Multiple pseudo-fermion fields are introduced additively and independently for each flavor in the many-flavor HMC algorithm. Using the independence of each pseudo-fermion field and the blocking technique for the quark solver, we can assign the solver task to each GPU card. In this report we present […]

We present the first ever direct $N$-body computations of an old Milky Way globular cluster over its entire life time on a star-by-star basis. Using recent GPU hardware at Bonn University, we have performed a comprehensive set of $N$-body calculations to model the distant outer halo globular cluster Palomar 14 (Pal 14). By varying the […]

Nowadays, several industrial applications are being ported to parallel architectures. In fact, these platforms allow acquire more performance for system modelling and simulation. In the electric machines area, there are many problems which need speed-up on their solution. This paper examines the parallelism of sparse matrix solver on the graphics processors. More specifically, we implement […]

Currently there is considerable interest in making use of many-core processor architectures, such as Nvidia and AMD graphics processing units (GPUs) for scientific computing. In this work we explore the use of the Open Computing Language (OpenCL) for a typical Numerical Relativity application: a time-domain Teukolsky equation solver (a linear, hyperbolic, partial differential equation solver […]

We report results of the performance test of GPUs obtained using the conjugate gradient (CG) algorithm for staggered fermions on the MILC fine lattice ($28^3 times 96$). We use GPUs of nVIDIA GTX 295 model for the test. When we turn off the MPI communication and use only a single GPU, the performance is 35 […]