Kittitornkun, Surin

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Kittitornkun, Surin
Alternative Name
Kittitornkun, S.
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surin.ki@kmitl.ac.th

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    Item type:Publication,
    Multithreading bioinformatics software with OpenMP: SNPHAP case study
    (2010-12-01)
    Ranok, Udom
    ;
    Kittitornkun, Surin
    ;
    Tongsima, Sissades
    This paper presents a parallelization framework for infer- ring haplotypes using an expectation maximization (EM) algorithm. Our framework utilizes GProf profiling tool, OpenMP library, and ompP profiling tool to parallelize the algorithm by determining the hotspot functions, mul- tithreading, and executing them on the Multi-core CPUs. In our experiments, we choose the SNPHAP program for this case study and run it on an 8-core Xeon Linux ma- chine. The results show that our framework can signifi- cantly speedup up to 214% on a large data set with 151 loci of a 10,000 data samples. In addition, deep profiles of multithreaded SNPHAP support our discovery that maxi- mum speedup can be achieved when the number of parallel threads equals to the number of physical cores.