Speedup on NVIDIA Tesla C1060. Speedup due the GPU alone is almost constant because once the threshold for the number of threads that can be launched is met, there is no further increase in speedup. Speedup due to HCP+GPU increases with the increase in the size of the structure due to the O(nlogn) scaling of the HCP approximation. Baseline: No-approximation CPU implementation optimized by hand-tuned SSE Intrinsics and parallelized across 16 cores.
Daga and Feng BMC Bioinformatics 2012 13(Suppl 5):S4 doi:10.1186/1471-2105-13-S5-S4