high performance computing on graphics processing units: hgpu.org

Geometry images resample meshes to represent them as texture for efficient GPU processing by forcing a regular parameterization that often incurs a large amount of distortion. Previous approaches broke the geometry image into multiple rectangular or irregular charts to reduce distortion, but complicated the automatic level of detail one gets from MIP-maps of the geometry […]

Computer-generated holography is a computationally intensive process particularly well suited to the architecture of graphics processing units (GPUs). This work investigates the performance improvements achievable through utilization of a GPU for optimization of holograms via simulated annealing. Two examples are given; accelerated training of an optical correlator to accept or reject inputs over sets of […]

We describe the porting of the Lattice Boltzmann component of MUPHY, a multi-physics/scale simulation software, to multiple graphics processing units using the Compute Unified Device Architecture. The novelty of this work is the development of ad hoc techniques for optimizing the indirect addressing that MUPHY uses for efficient simulations of irregular domains.

Among all the factors that determine the resolution of a 3D reconstruction by single particle electron cryo-microscopy (cryoEM), the number of particle images used in the dataset plays a major role. More images generally yield better resolution, assuming the imaged protein complex is conformationally and compositionally homogeneous. To facilitate processing of very large datasets, we […]

Recent advancements in cryo-electron microscopy (cryoEM) have made it technically possible to determine the three-dimensional (3D) structures of macromolecular complexes at atomic resolution. However, processing the large amount of data needed for atomic resolution reconstructions requires either accessing to very expensive computer clusters or waiting for weeks of continuous computation in a personal computer (PC). […]

Maximum-likelihood (ML) estimation has very desirable properties for reconstructing 3D volumes from noisy cryo-EM images of single macromolecular particles. Current implementations of ML estimation make use of the Expectation-Maximization (EM) algorithm or its variants. However, the EM algorithm is notoriously computation-intensive, as it involves integrals over all orientations and positions for each particle image. We […]

Functional magnetic resonance imaging allows non-invasive measurements of brain dynamics and has already been used for neurofeedback experiments, which relies on real time data processing. The limited computational resources that are typically available for this have hindered the use of connectivity analysis in this context. A basic, but already computationally demanding analysis method of neural […]

In this article, we look at early, recent, and state-of-the-art methods for registration of medical images using a range of high-performance computing (HPC) architectures including symmetric multiprocessing (SMP), massively multiprocessing (MMP), and architectures with distributed memory (DM), and nonuniform memory access (NUMA). The article is designed to be self-sufficient. We will take the time to […]

A very efficient implementation of a lattice Boltzmann (LB) kernel in 3D on a graphical processing unit using the compute unified device architecture interface developed by nVIDIA is presented. By exploiting the explicit parallelism offered by the graphics hardware, we obtain an efficiency gain of up to two orders of magnitude with respect to the […]

In-memory tree structured index search is a fundamental database operation. Modern processors provide tremendous computing power by integrating multiple cores, each with wide vector units. There has been much work to exploit modern processor architectures for database primitives like scan, sort, join and aggregation. However, unlike other primitives, tree search presents significant challenges due to […]

Is CUDA the parallel programming model that application developers have been waiting for?

A large number of algorithms have been developed to perform non-rigid registration and it is a tool commonly used in medical image analysis. The free-form deformation algorithm is a well-established technique, but is extremely time consuming. In this paper we present a parallel-friendly formulation of the algorithm suitable for graphics processing unit execution. Using our […]