Autors: Ko S.-H., Gancheva, V. S.
Title: An Approach for Parallel Reading in Multiple Sequence Alignment
Keywords: bioinformatics; ClustalW-MPI; MPI-I/O; multiple sequence alignment; parallel reading

Abstract: We propose an approach for faster file reading of multiple sequence alignment input through the use of MPI-I/O over a subset of MPI cores. The idea is to allow a subset of MPI cores that perform I/O operations and to broadcast locally on individual neighbors, so the code is less sensitive to the stability of the parallel file system. It is achieved by creating a number of subgroups under a global MPI communicator. The size of each subgroup and the buffer size of each reading operation are tuned through the synthetic benchmark. We verify the performance of our approach by comparing it with the traditional way of "sequential file reading and global broadcast", and apply it to the existing MPI version of multiple sequence alignment software ClustalW. In the production run over 8192 BlueGene/Q cores, the current approach provides 6.8 times acceleration of the existing ClustalW-MPI implementation.



    International Conference Automatics and Informatics, ICAI 2020, 2020, Bulgaria, DOI 10.1109/ICAI50593.2020.9311347

    Copyright IEEE

    Цитирания (Citation/s):
    1. Muhammad Ishaq, Asfandyar Khan, Mazliham Mohd Su’ud, Muhammad Mansoor Alam, Javed Iqbal Bangash, Abdullah Khan, "An Improved Strategy for Task Scheduling in the Parallel Computational Alignment of Multiple Sequences", Computational and Mathematical Methods in Medicine, vol. 2022, Article ID 8691646, 11 pages, 2022. - 2022 - в издания, индексирани в Scopus или Web of Science

    Вид: публикация в международен форум, публикация в реферирано издание, индексирана в Scopus