Name
Abstract | ||
|---|---|---|
Elementary Flux Modes (EFMs) can be used to characterize functional cellular networks and have gained importance in systems biology. Enumeration of EFMs is a compute-intensive problem due to the combinatorial explosion in candidate generation. While there exist parallel implementations for shared-memory SMP and distributed memory architectures, tools supporting heterogeneous platforms have not yet been developed. Here we propose and evaluate a heterogeneous implementation of combinatorial candidate generation that employs GPUs as accelerators. It uses a 3-stage pipeline based method to manage arithmetic intensity. Our implementation results in a 6x speedup over the serial implementation, and a 1.8x speedup over a multithreaded implementation for CPU-only SMP architectures. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1007/978-3-642-40047-6_75 | international conference on parallel processing |
Keywords | DocType | Volume |
heterogeneous combinatorial candidate generation,multithreaded implementation,candidate generation,heterogeneous implementation,parallel implementation,combinatorial candidate generation,implementation result,cpu-only smp architecture,heterogeneous platform,combinatorial explosion,serial implementation | Conference | 8097 |
ISSN | Citations | PageRank |
0302-9743 | 3 | 0.41 |
References | Authors | |
15 | 4 | |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Fahad Khalid | 1 | 3 | 1.08 |
| Zoran Nikoloski | 2 | 314 | 27.59 |
| Peter Tröger | 3 | 69 | 10.52 |
| Andreas Polze | 4 | 268 | 51.57 |