high performance computing on graphics processing units: hgpu.org

Quantum.Ligand.Dock (protein-ligand docking with graphic processing unit (GPU) quantum entanglement refinement on a GPU system) is an original modern method for in silico prediction of protein-ligand interactions via high-performance docking code. The main flavour of our approach is a combination of fast search with a special account for overlooked physical interactions. On the one hand, […]

For many-core architectures like the GPUs, efficient off-chip memory access is crucial to high performance; the applications are often limited by off-chip memory bandwidth. Transforming data layout is an effective way to reshape the access patterns to improve off-chip memory access behavior, but several challenges had limited the use of automated data layout transformation systems […]

The efficient solution of the Frank-Kamenetskii partial differential equation through the implementation of parallelized numerical algorithms or GPUs (Graphics Processing Units) in MATLAB is a natural progression of the work which has been conducted in an area of practical import. There is an on-going interest in the mathematics describing thermal explosions due to the significance […]

This paper introduces a library which supports programmers to write parallel programs on GPU architecture, especially with a system consisting of multi-GPUs. The library is designed from the idea of skeletons, which helps us to make parallel programs easily and quickly as if writing sequential programs. Skeletons usually are described by functional language which supports […]

In this paper we introduce a method for computing fitness in evolutionary learning systems based on NVIDIA’s massive parallel technology using the CUDA library. Both the match process of a population of classifiers against a training set and the computation of the fitness of each classifier from its matches have been parallelized. This method has […]

Time series shapelet discovery algorithm finds subsequences from a set of time series for use as primitives for time series classification. This algorithm has drawn a lot of interest because of the interpretability of its results. However, computation requirements restrict the algorithm from dealing with large data sets and may limit its application in many […]

In program inference, the evaluation of how well a candidate solution solves a certain task is usually a computationally intensive procedure. Most of the time, the evaluation involves either submitting the program to a simulation process or testing its behavior on many input arguments; both situations may turn out to be very time-consuming. Things get […]

In adaptive radiotherapy, a deformable image registration is often conducted between the planning CT and the treatment CT (or cone beam CT) to generate a deformation vector field (DVF) for dose accumulation and contour propagation. The auto-propagated contours on the treatment CT may contain relatively large errors especially in low-contrast regions. Clinician’s inspection and editing […]

We discuss how the steepest descent method with Fourier acceleration for Laudau gauge fixing in lattice SU(3) simulations can be implemented using CUDA. The scaling of the gauge fixing code was investigated using a Tesla C2070 Fermi architecture, and compared with a parallel CPU gauge fixing code.

The use of graphics processing units for scientific computations is an emerging strategy that can significantly speed up various different algorithms. In this review, we discuss advances made in the field of computational physics, focusing on classical molecular dynamics, and on quantum simulations for electronic structure calculations using the density functional theory, wave function techniques, […]

Distance-to-Default(DTD), which is used to describe the default risk of a rm, acts an important role in credit research. Nowadays, since we can access a large amount of historical data, we can get a more accurate DTD result. However, this directly increases the computation time as well as the computation power. Meanwhile, Graphic Processing Unit(GPU), […]

PATRIC is a particle tracking code used at GSI to study collective effects in the FAIR synchrotrons. Due to the need for calculation-intense simulations, parallel programming methods are being explored to optimize calculation performance. Presently the tracking part of the code is parallelized using MPI, where each node represents one slice of the particles that […]