high performance computing on graphics processing units: hgpu.org

With the commissioning of the Insertable B-Layer (IBL) in 2013 at the ATLAS experiment 12~million additional pixels will be added to the current Pixel Detector. While the idea of employing pairs of VME based Read-Out Driver (ROD) and Back of Crate (BOC) cards in the read-out chain remains unchanged, modifications regarding the IBL calibration procedure […]

Emerging GPGPU architectures, along with programming models like CUDA and OpenCL, offer a cost-effective platform for many applications by providing high thread level parallelism at lower energy budgets. Unfortunately, for many general-purpose applications, available hardware resources of a GPGPU are not efficiently utilized, leading to lost opportunity in improving performance. A major cause of this […]

As part of a 3-wk intersession workshop funded by a National Science Foundation Expeditions in Computing award, 15 undergraduate students from the City University of New York1 collaborated on a study aimed at characterizing the voltage dynamics and arrhythmogenic behavior of cardiac cells for a broad range of physiologically relevant conditions using an in silico […]

Dislocations play an important role in the deformation behaviors of metals. They not only interact via long-range elastic stress, but also interact with shortrange interactions; they annihilate, tangle, get stuck, and unstuck. These interaction between dislocations lead to interesting dislocation wall formation at the mesoscales. A recently developed continuum dislocation dynamics model that shows dislocation […]

The SIMD (Single Instruction-Multiple Data) execution model of Graphics Processing Units (GPUs) allows for many concurrent threads to simultaneously request data from the memory subsystem. This imposes a large bandwidth demand on the memory interfaces at each level. Each level of the memory hierarchy needs to provide enough bandwidth in order to ensure good response […]

The paper introduces an algorithm which improves the value of the real giga floating point operations per second (GFLOPS) for matrix multiplication algorithm on Graphical Process Unit-GPU by overlapping the data transfers between (CPU) and the device (GPU) with the kernel execution. The input matrices are divided into n sections and the output matrix into […]

In this article we present a graphics processing unit (GPU) implementation of a particle method for transport equations. More precisely the numerical method under consideration is a remeshed particle method. Not only remeshing particles makes simulations more accurate in flows with strong strain, but it leads to algorithms more regular in term of data structures. […]

Inference of protein structure from experimental data is of crucial interest in science, medicine and biotechnology. Low-resolution methods, such as small angle X-ray scattering (SAXS), play a major role in investigating important biological questions regarding the structure of proteins in solution. To infer protein structure from SAXS data, it is necessary to calculate the expected […]

The secondary structure that maximizes the number of non-crossing matchings between complimentary bases of an RNA sequence of length n can be computed in O(n^3) time using dynamic programming. Four-Russians is a technique that will reduce the running time for certain dynamic programming algorithms by a factor after a preprocessing step where solutions to all […]

Differential evolution (DE) is an efficient populational meta-heuristic optimization algorithm that has been applied to many difficult real world problems. Due to the relative simplicity of its operations and real encoded data structures, it is very suitable for a parallel implementation on multicore systems and on the GPUs that nowadays reach peak performance of hundreds […]

Current computational platforms have become continuously more and more heterogeneous and parallel over the last years, as a consequence of incorporating accelerators whose architectures are parallel and different from the CPU. As a result, several frameworks were developed to aid to program these platforms mainly targeting better productivity ratios. In this context, GAMA framework is […]

Nondeterminism is a key challenge in developing multithreaded applications. Even with the same input, each execution of a multithreaded program may produce a different output. This behavior complicates debugging and limits one’s ability to test for correctness. This non-reproducibility situation is aggravated on massively parallel architectures like graphics processing units (GPUs) with thousands of concurrent […]