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SIMD-instructions/parallism

Parallelism standards for accelerating performance on calculations for detection of positive DNA selection

Table of contents

General Information

Streaming SIMD Extensions (SSE), MPI and Pthreads for parallelization the calculation of a simplified form of OMEGA statistical, to detect positive selection in DNA sequences.

Repeated for a set of N DNA sites, extract statistical OMEGA outputs

$$num = \frac{L+R}{\left(\frac{m*(m-1.0)}{2.0}\right) + \left(\frac{n*(n-1.0)}{2.0}\right)}$$
$$den= \frac{C-L-R}{m*n}$$
$$\omega= \frac{num}{den+0.01}$$

The above calculations are repeated iteratively for a set of N DNA sites, $N$ is a variable for which $N ≥ 1$ . All input data is arranged in arrays of length N (user variable).

Interested for

$$max_{\omega}$$ $$min_{\omega}$$ $$avg_{\omega}$$

BONUS: Implementation of a different memory layout for better performance with SSE commands.

Features

  • Reference
  • SSE instructions
  • Parallel standards (pthreads/MPI) + SSE

The implementation was guided by the reference file Benchmarked on Intel(R) Core(TM) i7-1065G7 @ 1.30GHz 1.50 GHz with 8GB DDR3 memory.

Prerequisites

SIMD
MPI

How to run

  1. GCC installation
$ gcc --version
$ sudo apt install gcc

Supposing you can navigate the proper folder to compile the desired source code from the terminal

Reference

gcc -o reference reference.c
./reference 'N'

SSE

gcc -o jam jam.c
./jam 'N'
gcc -o unroll unroll.c
./unroll 'N'

Add -msse4.2 library

gcc -o SSE SSE.c -msse4.2
./SSE 'N'

Pthreads

gcc -pthread SSE_pthreads.c -o SSE_pthreads -msse4.2
./SSE_pthreads 'N' 'N_threads'

MPI

mpicc -pthread SSE_Mpthreads.c -o SSE_Mpthreads -msse4.2 -lm
lamboot -v host
mpiexec -n 'N_proc' ./SSE_Mpthreads 'N' 'N_threads'

Bonus

gcc -o bonus bonus.c -msse4.2
./bonus 'N'

Setup

Script variables initialized as:

  • N = 10000000.
  • Threads = [2 4]
  • Processors = [2 4].

Acknowledgements

  • This project was created for the requirements of the lesson Architecture of Parallel and Distributed Computers