Alex JF

Smith-Waterman with OpenMP and OpenMPI

  • Category: Distributed Systems
  • Authors: Alexandre Fonseca, Anh Thu Vu
  • Start date: 2012/09
  • Version: 1.0
  • Status: Finished

This project was created as an assigment for the Algorithms and Models for Parallel Programming course during my 1st semester at UPC.

In this project we were tasked with the implementation of parallel versions of the Smith-Waterman algorithm for sequence alignment using OpenMP and OpenMPI.

We also had to develop theoretical models for the performance of the parallelization and compare it with the results obtained through experimentation with the actual implementation.

In the end, we presented our results for several different implementations of the parallelization:

  • OpenMPI without row-level interleaving.
  • OpenMPI with row-level interleaving.
  • OpenMP using tasks.
  • OpenMPI + OpenMP.

For details about the implementation and evaluation, refer to the attached report.

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