13574
Dzmitry Razmyslovich, Guillermo Marcus, Markus Gipp, Marc Zapatka, Andreas Szillus
In this paper we present an implementation of the Smith-Waterman algorithm. The implementation is done in OpenCL and targets high-end GPUs. This implementation is capable of computing similarity indexes between reference and query sequences. The implementation is designed for the sequence alignment paths calculation. In addition, it is capable of handling very long reference sequences […]
Edgardo Mejia-Roa, Daniel Tabas-Madrid, Javier Setoain, Carlos Garcia, Francisco Tirado, Alberto Pascual-Montano
BACKGROUND: In the last few years, the Non-negative Matrix Factorization (NMF) technique has gained a great interest among the Bioinformatics community, since it is able to extract interpretable parts from high-dimensional datasets. However, the computing time required to process large data matrices may become impractical, even for a parallel application running on a multiprocessors cluster. […]
Jan Busa Jr., Jan Busa, Shura Hayryan, Chin-Kun Hu, Ming-Chya Wu
Here we present the revised and newly rewritten version of our earlier published CAVE package [J. Busa et al., Comput. Phys. Commun. 181 (2010) 2116] which was originally written in FORTRAN. The package has been rewritten in C language, the algorithm has been parallelized and implemented using OpenCL. This makes the program convenient to run […]
View View   Download Download (PDF)   
Benjamin J. Block
A system in a metastable state needs to overcome a certain free energy barrier to form a droplet of the stable phase. Standard treatments assume spherical droplets, but this is not appropriate in the presence of an anisotropy, such as for crystals. The anisotropy of the system has a strong effect on their surface free […]
View View   Download Download (PDF)   
Yun Tian, Bojian Xu
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by Ileri et al., using a total of the optimal O(n) time and space, where n is the string size. However, their solution can only find […]
View View   Download Download (PDF)   
Matija Korpar, Martin Sosic, Dino Blazeka, Mile Sikic
The deluge of next-generation sequencing (NGS) data and expanding database poses higher requirements for protein similarity search. State-of-the-art tools such as BLAST are not fast enough to cope with these requirements. Because of that it is necessary to create new algorithms that will be faster while keeping similar sensitivity levels. The majority of protein similarity […]
Andrew L Beam, Alison Motsinger-Reif, Jon Doyle
BACKGROUND: Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. RESULTS: A non-parametric Bayesian approach in the form of a Bayesian neural network is proposed for use in analyzing […]
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 […]
View View   Download Download (PDF)   
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 […]
View View   Download Download (PDF)   
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 […]
View View   Download Download (PDF)   
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 […]
View View   Download Download (PDF)   
Johannes Koster, Sven Rahmann
We present the q-group index, a novel data structure for read mapping tailored towards graphics processing units (GPUs) with a small memory footprint and efficient parallel algorithms for querying and building. On top of the q-group index we introduce PEANUT, a highly parallel GPU-based read mapper. PEANUT provides the possibility to output both the best […]
View View   Download Download (PDF)   
Page 1 of 3512345...102030...Last »

* * *

* * *

Like us on Facebook

HGPU group

218 people like HGPU on Facebook

Follow us on Twitter

HGPU group

1406 peoples are following HGPU @twitter

* * *

Free GPU computing nodes at hgpu.org

Registered users can now run their OpenCL application at hgpu.org. We provide 1 minute of computer time per each run on two nodes with two AMD and one nVidia graphics processing units, correspondingly. There are no restrictions on the number of starts.

The platforms are

Node 1
  • GPU device 0: nVidia GeForce GTX 560 Ti 2GB, 822MHz
  • GPU device 1: AMD/ATI Radeon HD 6970 2GB, 880MHz
  • CPU: AMD Phenom II X6 @ 2.8GHz 1055T
  • RAM: 12GB
  • OS: OpenSUSE 13.1
  • SDK: nVidia CUDA Toolkit 6.5.14, AMD APP SDK 3.0
Node 2
  • GPU device 0: AMD/ATI Radeon HD 7970 3GB, 1000MHz
  • GPU device 1: AMD/ATI Radeon HD 5870 2GB, 850MHz
  • CPU: Intel Core i7-2600 @ 3.4GHz
  • RAM: 16GB
  • OS: OpenSUSE 12.2
  • SDK: AMD APP SDK 2.9

Completed OpenCL project should be uploaded via User dashboard (see instructions and example there), compilation and execution terminal output logs will be provided to the user.

The information send to hgpu.org will be treated according to our Privacy Policy

HGPU group © 2010-2015 hgpu.org

All rights belong to the respective authors

Contact us: