Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm
نویسندگان
چکیده
منابع مشابه
Communication Optimization for Multi GPU Implementation of Smith-Waterman Algorithm
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. SmithWaterman is a wel...
متن کاملGPU Accelerated Smith-Waterman
We present a novel hardware implementation of the double affine Smith-Waterman (DASW) algorithm, which uses dynamic programming to compare and align genomic sequences such as DNA and proteins. We implement DASW on a commodity graphics card, taking advantage of the general purpose programmability of the graphics processing unit to leverage its cheap parallel processing power. The results demonst...
متن کاملParallel Smith-Waterman Algorithm for Gene Sequencing
Smith-Waterman Algorithm represents a highly robust and efficient parallel computing system development for biological gene sequence. The research work here gives a deep understanding and knowledge transfer about exiting approach for gene sequencing and alignment using Smith-waterman their strength and weaknesses. Smith-Waterman algorithm calculates the local alignment of two given sequences us...
متن کاملAccelerating the Smith-Waterman Algorithm for Bio-sequence Matching on GPU
Nowadays, GPU has emerged as one promising computing platform to accelerate bio-sequence analysis applications by exploiting all kinds of parallel optimization strategies. In this paper, we take a well-known algorithm in the field of pair-wise sequence alignment and database searching, the Smith-Waterman (S-W) algorithm as an example, and demonstrate approaches that fully exploit its performanc...
متن کاملPerformance Improvement of the Smith-Waterman Algorithm
Efficient sequence alignment is one of the most important and challenging activities in bioinformatics. Many algorithms have been proposed to perform and accelerate sequence alignment activities. Among them SmithWaterman (S-W) is the most sensitive (accurate) algorithm, however, the fact that it is the most computationally intensive algorithm makes it necessary to implement hardware acceleratio...
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: International Journal of Computer Applications
سال: 2013
ISSN: 0975-8887
DOI: 10.5120/13910-1121