13088
Fahad Khalid, Frank Feinbube, Andreas Polze
The pipeline pattern for parallel programs is utilized in a wide array of scientific applications designed for execution on hybrid CPU-GPU architectures. However, there is a dearth of tools and libraries to support implementation of pipeline parallelism for hybrid architectures. We present the Hybrid Pipeline Framework (HyPi) that is intended to fill this gap. HyPi […]
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Di Zhao
High-accuracy optimizer is the essential part of accuracy-sensitive applications such as computational finance and computational biology, and we developed single-GPU based Iterative Discrete Approximation Monte Carlo Search (IDA-MCS) in our previous research. However, single-GPU IDA-MCS is in low performance or even functionless for optimization problems with large number of peaks because of the capability constrains […]
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David Markvica
The longest common subsequence (LCS) problem is one of the classic problems in string processing. It is commonly used in file comparison, pattern recognition, and computational biology as a measure of sequence similarity. Given a set of strings, the LCS is the longest string that is a subsequence of every string in the set. For […]
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Nikolay Pydiura, Pavel Karpov, Yaroslav Blume
The complexity and diversity of the computational biology tasks requires a deliberate approach to the computational resource management. We have analyzed the performance of the common CPU and hybrid CPU-GPU hardware configurations in molecular dynamics and homology modeling tasks. Our results show that on dual-processor nodes it is in overall more efficient to execute two […]
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Paolo Cazzaniga, Marco S. Nobile, Daniela Besozzi, Matteo Bellini, Giancarlo Mauri
The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing […]
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Sampath Kumar, P. K. Baruah
GPU parallelism for real applications can achieve enormous performance gain. CPU-GPU Communication is one of the major bottlenecks that limit this performance gain. Among several libraries developed so far to optimize this communication, DyManD (Dynamically Managed Data) provides better communication optimization strategies and achieves better performance on a single GPU. Smith-Waterman is a well known […]
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Da Li, Kittisak Sajjapongse, Huan Truong, Gavin Conant, Michela Becchi
Several problems in computational biology require the all-against-all pairwise comparisons of tens of thousands of individual biological sequences. Each such comparison can be performed with the well-known Needleman-Wunsch alignment algorithm. However, with the rapid growth of biological databases, performing all possible comparisons with this algorithm in serial becomes extremely time-consuming. The massive computational power of […]
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Lucas Beyer, Paolo Bientinesi
In the context of the genome-wide association studies (GWAS), one has to solve long sequences of generalized least-squares problems; such a task has two limiting factors: execution time often in the range of days or weeks and data management data sets in the order of Terabytes. We present an algorithm that obviates both issues. By […]
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Cheng Ling
Bioinformatics and Computational Biology (BCB) is a relatively new multidisciplinary field which brings together many aspects of the fields of biology, computer science, statistics, and engineering. Bioinformatics extracts useful information from biological data and makes these more intuitive and understandable by applying principles of information sciences, while computational biology harnesses computational approaches and technologies to […]
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Xiaoquan Su, Jian Xu, Kang Ning
BACKGROUND: Metagenomics method directly sequences and analyses genome information from microbial communities. There are usually more than hundreds of genomes from different microbial species in the same community, and the main computational tasks for metagenomic data analyses include taxonomical and functional component examination of all genomes in the microbial community. Metagenomic data analysis is both […]
Lin Ma, Roger D. Chamberlain
Graphics engines are excellent execution platforms for high-throughput computations that exploit a large degree of available parallelism. The achieved performance is, however, highly dependent on the access patterns that the application imposes on the memory subsystem. Here, we propose an analytic model that helps improve the understanding of the performance of memory-limited kernels that employ […]
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Themistoklis K. Pyrgiotis, Charalampos S. Kouzinopoulos, Konstantinos G. Margaritis
One of the most significant issues of the computational biology is the multiple pattern matching for locating nucleotides and amino acid sequence patterns into biological databases. Sequential implementations for these processes have become inadequate, due to an increasing demand for more computational power. Graphic cards offer a high parallelism computational power improving the performance of […]
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