Design and implementation of a hybrid MPI-CUDA model for the Smith-Waterman algorithm.
Int J Data Min Bioinform
; 12(3): 313-27, 2015.
Article
em En
| MEDLINE
| ID: mdl-26510289
ABSTRACT
This paper provides a novel hybrid model for solving the multiple pair-wise sequence alignment problem combining message passing interface and CUDA, the parallel computing platform and programming model invented by NVIDIA. The proposed model targets homogeneous cluster nodes equipped with similar Graphical Processing Unit (GPU) cards. The model consists of the Master Node Dispatcher (MND) and the Worker GPU Nodes (WGN). The MND distributes the workload among the cluster working nodes and then aggregates the results. The WGN performs the multiple pair-wise sequence alignments using the Smith-Waterman algorithm. We also propose a modified implementation to the Smith-Waterman algorithm based on computing the alignment matrices row-wise. The experimental results demonstrate a considerable reduction in the running time by increasing the number of the working GPU nodes. The proposed model achieved a performance of about 12 Giga cell updates per second when we tested against the SWISS-PROT protein knowledge base running on four nodes.
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Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
/
Linguagens de Programação
/
Computadores
/
Modelos Teóricos
Tipo de estudo:
Prognostic_studies
Idioma:
En
Revista:
Int J Data Min Bioinform
Ano de publicação:
2015
Tipo de documento:
Article