A multithreading methodology with OpenMP on multi-core CPUs: SNPHAP case study

Abstract

This paper presents a multithreading methodology for OpenMP library. The methodology can be applied to convert existing sequential and demanding programs to be multithreaded programs with OpenMP running on the Multi-core CPUs. In our experiments, we apply this methodology to SNPHAP, which is one of the best haplotype inference bioinformatics program in terms of speed. The results show that our significant achievement is the maximum Speedup 316% for Intel Xeon E5405 (8-core 2.0 GHz) and 410% for Intel Xeon E5520 (8-Core with HyperThreading 2.66GHz) faster than its own sequential version. © 2011 IEEE.