Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets.

Analysis of Parallel Algorithms on SMP Node and Cluster of Workstations Using Parallel Programming Models with New Tile-based Method for Large Biological Datasets. Bioinform Biol Insights. 2016;10:255-265 Authors: Shrimankar DD, Sathe SR Abstract Sequence alignment is an important tool for describing the relationships between DNA sequences. Many sequence alignment algorithms exist, differing in efficiency, in their models of the sequences, and in the relationship between sequences. The focus of this study is to obtain an optimal alignment between two sequences of biological data, particularly DNA sequences. The algorithm is discussed with particular emphasis on time, speedup, and efficiency optimizations. Parallel programming presents a number of critical challenges to application developers. Today's supercomputer often consists of clusters of SMP nodes. Programming paradigms such as OpenMP and MPI are used to write parallel codes for such architectures. However, the OpenMP programs cannot be scaled for more than a single SMP node. However, programs written in MPI can have more than single SMP nodes. But such a programming paradigm has an overhead of internode communication. In this work, we explore the tradeoffs between using OpenMP and MPI. We demonstrate that the communication overhead incurs significantly even in OpenMP loop execution and increases with the number of cores participating. We also demonstrate a communication model ...
Source: Bioinformatics and Biology Insights - Category: Bioinformatics Authors: Tags: Bioinform Biol Insights Source Type: research