Posts
Jul, 6
Tuning A Hybrid GPU-CPU V-cycle Multilevel Preconditioner for Solving Large Real and Complex Systems of FEM Equations
This paper presents techniques for tuning an accelerated preconditioned conjugate gradient solver with a multilevel preconditioner. The solver is optimized for a fast solution of sparse systems of equations arising in computational electromagnetics in a finite element method using higher order elements. The goal of the tuning is to increase the throughput while at the […]
Jul, 6
Flexible OpenCL accelerated disparity estimation for video communication applications
Due to widespread broadband connections in normal households, the use of video chats via Internet is no longer limited to business meetings. However, the camera configuration usually makes it impossible to achieve direct eye contact between the conversational partners. This effect can be compensated using virtual view synthesis methods based on disparity maps. The virtual […]
Jul, 6
Striped Smith-Waterman speeds database searches six times over other SIMD implementations
MOTIVATION: The only algorithm guaranteed to find the optimal local alignment is the Smith-Waterman. It is also one of the slowest due to the number of computations required for the search. To speed up the algorithm, Single-Instruction Multiple-Data (SIMD) instructions have been used to parallelize the algorithm at the instruction level. RESULTS: A faster implementation […]
Jul, 6
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
MOTIVATION: Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or […]
Jul, 6
Pseudo-random number generation for Brownian Dynamics and Dissipative Particle Dynamics simulations on GPU devices
Brownian Dynamics (BD), also known as Langevin Dynamics, and Dissipative Particle Dynamics (DPD) are implicit solvent methods commonly used in models of soft matter and biomolecular systems. The interaction of the numerous solvent particles with larger particles is coarse-grained as a Langevin thermostat is applied to individual particles or to particle pairs. The Langevin thermostat […]
Jul, 6
A Fast, GPU based, Dictionary Attack to OpenPGP Secret Keyrings
We describe the implementation, based on the Compute Unified Device Architecture (CUDA) for Graphics Processing Units (GPU), of a novel and very effective approach to quickly test passphrases used to protect private keyrings of OpenPGP cryptosystems. Our combination of algorithm and implementation, reduces the time required to test a set of possible passphrases by threeorders […]
Jul, 6
GPU Accelerated Chemical Similarity Calculation for Compound Library Comparison
Chemical similarity calculation plays an important role in compound library design, virtual screening, and "lead" optimization. In this manuscript, we present a novel GPU-accelerated algorithm for all-vs-all Tanimoto matrix calculation and nearest neighbor search. By taking advantage of multicore GPU architecture and CUDA parallel programming technology, the algorithm is up to 39 times superior to […]
Jul, 5
A straightforward CUDA implementation for interactive ray-tracing
In recent years, applying the powerful computational resources delivered by modern GPUs to ray tracing has resulted in a number of ray tracing implementations that allow rendering of moderately sized scenes at interactive speeds. In our poster, we present a fast implementation for ray tracing with CUDA. We describe an optimized GPU-based ray tracing approach […]
Jul, 5
High Performance Matrix Inversion on a Multi-core Platform with Several GPUs
Inversion of large-scale matrices appears in a few scientific applications like model reduction or optimal control. Matrix inversion requires an important computational effort and, therefore, the application of high performance computing techniques and architectures for matrices with dimension in the order of thousands. Following the recent uprise of graphics processors (GPUs), we present and evaluate […]
Jul, 5
Interactive visualization of streaming data with Kernel Density Estimation
In this paper, we discuss the extension and integration of the statistical concept of Kernel Density Estimation (KDE) in a scatterplot-like visualization for dynamic data at interactive rates. We present a line kernel for representing streaming data, we discuss how the concept of KDE can be adapted to enable a continuous representation of the distribution […]
Jul, 5
AES on GPU: a CUDA Implementation
Our research explores the possibility of efficiently implementing the Advanced Encryption Standard (AES) in the Graphic Processing Unit using the CUDA platform provided by Nvidia. GPUs present a considerable computational power that often is not used; their architecture seems particularly useful in the range of applications that use parallel processing. Because of its nature AES […]
Jul, 5
AES and DES Encryption with GPU
Graphics processing units (GPUs) are powerful computational devices tailored towards the needs of the 3-D gaming industry for high-performance, real-time graphics engines. As the processing power of such GPUs increases so does the possibilities for other, non-graphics related applications to be implemented on them. With the increase over the years of sensitive data that must […]
