Analysis and performance of a UPC implementation of a parallel longest common subsequence algorithm


Autoria(s): Franklin, Bryan M.
Data(s)

01/01/2009

Resumo

An important problem in computational biology is finding the longest common subsequence (LCS) of two nucleotide sequences. This paper examines the correctness and performance of a recently proposed parallel LCS algorithm that uses successor tables and pruning rules to construct a list of sets from which an LCS can be easily reconstructed. Counterexamples are given for two pruning rules that were given with the original algorithm. Because of these errors, performance measurements originally reported cannot be validated. The work presented here shows that speedup can be reliably achieved by an implementation in Unified Parallel C that runs on an Infiniband cluster. This performance is partly facilitated by exploiting the software cache of the MuPC runtime system. In addition, this implementation achieved speedup without bulk memory copy operations and the associated programming complexity of message passing.

Formato

application/pdf

Identificador

http://digitalcommons.mtu.edu/etds/184

http://digitalcommons.mtu.edu/cgi/viewcontent.cgi?article=1183&context=etds

Publicador

Digital Commons @ Michigan Tech

Fonte

Dissertations, Master's Theses and Master's Reports - Open

Tipo

text