high performance computing on graphics processing units: hgpu.org

Using the new OpenCL (Open Computing Language) standard, you can write applications that access all available programming resources: CPUs, GPUs, and other processors such as DSPs and the Cell/B.E. processor. Already implemented by Apple, AMD, Intel, IBM, NVIDIA, and other leaders, OpenCL has outstanding potential for PCs, servers, handheld/embedded devices, high performance computing, and even […]

The assessment of chemical similarity between molecules is a basic operation in chemoinformatics, a computational area concerning with the manipulation of chemical structural information. Comparing molecules is the basis for a wide range of applications such as searching in chemical databases, training prediction models for virtual screening or aggregating clusters of similar compounds. However, currently […]

Real world data is likely to contain an inherent structure. Those structures may be represented with graphs which encode independence assumptions within the data. Performing inference in those models is nearly intractable on mobile devices or casual workstations. This work introduces and compares two approaches for accelerating the inference in graphical models by using GPUs […]

A new fault-tolerant message passing interface framework for a hybrid parallel com-puting in distributed volunteer-based networks is presented in this paper. It is a new programming core library being able to link together many CPUs and promis-ing General Purpose Graphic Processing Unit (GPGPU) devices over the Internet. We successfully developed a high-level programming interface on […]

In this short paper we describe simple approach to loosely compress the vertex data for ray tracing large triangular models on the GPU. The disadvantage of the GPU is limited memory capacity. The advantage of the GPU is high performance computation. Sometimes it is hard to load large models to the GPU and we suggest […]

Compiling Bayesian networks (BNs) to junction trees and performing belief propagation over them is among the most prominent approaches to computing posteriors in BNs. However, belief propagation over junction tree is known to be computationally intensive in the general case. Its complexity may increase dramatically with the connectivity and state space cardinality of Bayesian network […]

Secure end-to-end communication is becoming increasingly important as more private and sensitive data is transferred on the Internet. Unfortunately, today’s SSL deployment is largely limited to security or privacycritical domains. The low adoption rate is mainly attributed to the heavy cryptographic computation overhead on the server side, and the cost of good privacy on the […]

Advent of next generation gene sequencing machines has led to computationally intensive alignment problems that can take many hours on a modern computer. Considering the fast increasing rate of introduction of new short sequences that are sequenced, the large number of existing sequences and inaccuracies in the sequencing machines, short sequence alignment has become a […]

Solving large sparse linear systems is often the most computationally intensive component of many scientific computing applications. In the past, sparse multifrontal direct factorization has been shown to scale to thousands of processors on dedicated supercomputers resulting in a substantial reduction in computational time. In recent years, an alternative computing paradigm based on GPUs has […]

SUMMARY: OpenCL in Action is a thorough, hands-on presentation of OpenCL, with an eye toward showing developers how to build high-performance applications of their own. It begins by presenting the core concepts behind OpenCL, including vector computing, parallel programming, and multi-threaded operations, and then guides you step-by-step from simple data structures to complex functions. ABOUT […]

We present a new deformation pipeline that is independent of the integration solver used and allows fast rendering of deformable soft bodies on the GPU. The proposed method exploits the transform feedback mechanism of the modern GPU to bypass the CPU read-back, thus, reusing the modified positions and/or velocities of the deformable object in a […]

We developed the third version of SHADOW, a ray tracing software widely used to design optical system in the synchrotron world. SHADOW3 is written in Fortran 2003 and follows the new computer engineering standards. The users can always execute the program in the traditional file oriented approach. Moreover, advanced users can create personalized scripts, macros […]