Analysing and Optimizing SNPHAP using Radix-2 Computation and OpenMP

Ratthaslip Ranokphanuwat, Apisit Rattanatranurak, Surin Kittitornkun, and Sissades Tongsima


SNPHAP, Radix-2, OpenMP, Optimization


In this paper, the run time complexity of SNPHAP, which is a haplotype inference tool, is extensively examined. The analysis is based on our previous work in terms of profiling and run-time complexity function. To reduce the run time complexity and enhance its performance, a Radix-2 computation and OpenMP multithreading are applied. The optimized results are compared with both original and compiler optimized versions on an AMD A6-3650 Linux machine. Due to the Radix-2 technique, the complexity is drastically reduced. In addition, the theoretical Speedup is consistent with the experimental one. Furthermore, up to 1,303% Speedup is achievable as a result of OpenMP multithreading.

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