Offline Permutation on the CUDA-enabled GPU
نویسندگان
چکیده
منابع مشابه
Fast Sequence Alignment Method Using CUDA-enabled GPU
Sequence alignment is a task that calculates the degree of similarity between two sequences. Given a query sequence, finding a database sequence which is most similar to the query by sequence alignment is the first step in bioinformatics research. The first sequence alignment algorithm was proposed by Needleman and Wunsch. They got the optimal global alignment by using dynamic programming metho...
متن کاملOffline Permutation Algorithms on the Discrete Memory Machine with Performance Evaluation on the GPU
The Discrete Memory Machine (DMM) is a theoretical parallel computing model that captures the essence of the shared memory access of GPUs. The bank conflicts should be avoided for maximizing the bandwidth of the shared memory access. Offline permutation of an array is a task to copy all elements in array a into array b along a permutation given in advance. The main contribution of this paper is...
متن کاملCell Charge Approximation for Accelerating Molecular Simulation on CUDA-Enabled GPU
Methods for Molecular Dynamics(MD) simulations are investigated. MD simulation is the widely used computer simulation approach to study the properties of molecular system. Force calculation in MD is computationally intensive. Paral-lel programming techniques can be applied to improve those calculations. The major aim of this paper is to speed up the MD simulation calculations by/using General P...
متن کاملCUDAMPF++: A Proactive Resource Exhaustion Scheme for Accelerating Homologous Sequence Search on CUDA-enabled GPU
Genomic sequence alignment is an important research topic in bioinformatics and continues to attract significant efforts. As genomic data grow exponentially, however, most of alignment methods face challenges due to their huge computational costs. HMMER, a suite of bioinformatics tools, is widely used for the analysis of homologous protein and nucleotide sequences with high sensitivity, based o...
متن کاملA block-wise approximate parallel implementation for ART algorithm on CUDA-enabled GPU.
Computed tomography (CT) has been widely used to acquire volumetric anatomical information in the diagnosis and treatment of illnesses in many clinics. However, the ART algorithm for reconstruction from under-sampled and noisy projection is still time-consuming. It is the goal of our work to improve a block-wise approximate parallel implementation for the ART algorithm on CUDA-enabled GPU to ma...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: IEICE Transactions on Information and Systems
سال: 2014
ISSN: 0916-8532,1745-1361
DOI: 10.1587/transinf.2014pap0010