Table 1.
Performance comparison among different software approaches.
| Acceleration strategies | Supporting software/package | Accelerated programs | Datasets | Hardware environment | Achieved speedup |
|---|---|---|---|---|---|
| Instruction-level parallelism | SSE2 Instructions | hmmpfam, hmmsearch | Pfam and nr databases | 2.66 GHz Intel Xeon processor with 2.5 GB of memory | 1.2x~1.3x [9] |
|
| |||||
| Shared memory parallelism | OpenMP | hmmpfam | 600 HMM profiles and 250 sequences | 16 x86 3.0 GHz processors, 32 MB L4 cache shared among 4 CPUs, 4 MB L3 cache, 8 GB of memory | 14x [10] |
| EARTH | hmmpfam | 50 HMM profiles and 38192 sequences | A cluster that consists of 128 nodes, each with two 500 MHz Pentium III processors | 222.8x [11] | |
|
| |||||
| Distributed memory parallelism | PVM | hmmsearch | 1 HMM profile and 100 MB of nr database | A cluster with 4 nodes, each node consists of two 2.66 GHz Intel Xeon processors with 2.5 GB memory per node | 4.56x [9] |
| MPI | hmmsearch | 5.90x [9] | |||
| MPI + I/O optimizations | hmmsearch | One 236-state HMM profile and nr database | A cluster that consists of 1056 nodes, each equipped with two 3.2 GHz Intel Xeon processors, 2 GB RAM | 221x [12] | |
| hmmpfam | 1.6 GB of Pfam database and nr databases | 328x [12] | |||
|
| |||||
| Heterogeneous approach | MPI + SSE2 | hmmsearch | 1 HMM profile and 100 MB of nr database | A cluster with 4 nodes, each node consists of two 2.66 GHz Intel Xeon processors with 2.5 GB memory per node | 7.71x [13] |