high performance computing on graphics processing units: hgpu.org

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

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 […]

Web servers often need to manage encrypted transfers of data. The encryption activity is computationally intensive, and exposes a significant degree of parallelism. At the same time, cheap multicore processors are readily available on graphics hardware, and toolchains for development of general purpose programs are being released by the vendors. In this paper, we propose […]

Encryption and decryption are increasingly important. In order to protect the security of individuals, corporations and even governments, information needs to be secured against potential threats. The basis of encryption’s security is its robustness under a brute force attack as the key space of AES-128 is 3.4×10^38 keys in size. Even at a sustained rate […]

Development of Central Processing Unit (CPU) is approaching its physical limits, struggling at the same time with problems like high temperature and increasing need of extra power. There are mainly two alternatives to relieve those problems – Grid computing and Multi Core processors. Both of those approaches are able to give us more computing power […]