Name
Abstract | ||
|---|---|---|
This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) algorithm for megabase DNA sequences in heterogeneous multi-GPU platforms. In our strategy, the computation of a single huge SW matrix is spread over multiple GPUs, which communicate border elements to the neighbour, using a circular buffer mechanism that hides the communication overhead. We compared 4 pairs of human-chimpanzee homologous chromosomes using 2 different GPU environments, obtaining a performance of up to 140.36 GCUPS (Billion of cells processed per second) with 3 heterogeneous GPUS. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1145/2555243.2555280 | PPOPP |
Keywords | Field | DocType |
parallel strategy,border element,different gpu environment,megabase dna sequence,circular buffer mechanism,communication overhead,single huge sw matrix,fine-grain parallel megabase sequence,heterogeneous multi-gpu platform,exact smith-waterman,multiple heterogeneous gpus,heterogeneous gpus,smith waterman | Computer science,Matrix (mathematics),Parallel computing,Circular buffer,Theoretical computer science,Smith–Waterman algorithm,Computation | Conference |
Volume | Issue | ISSN |
49 | 8 | 0362-1340 |
Citations | PageRank | References |
5 | 0.44 | 3 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| weigang | 1 | 22 | 2.61 |
| Guillermo Miranda | 2 | 26 | 1.62 |
| Alba Cristina Magalhaes Alves De Melo | 3 | 253 | 33.90 |
| Xavier Martorell | 4 | 1470 | 125.40 |
| Eduard Ayguade | 5 | 741 | 49.83 |