https://github.com/z1skgr/simd-instruction-mpi-pthreads-parallism
Parallelism standards for accelerating performance on calculations for detection of positive DNA selection
https://github.com/z1skgr/simd-instruction-mpi-pthreads-parallism
accelerated-computing intel intel-intrinsics linux memory-layout mpi parallel-programming pthreads simd-instructions sse
Last synced: 3 months ago
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Parallelism standards for accelerating performance on calculations for detection of positive DNA selection
- Host: GitHub
- URL: https://github.com/z1skgr/simd-instruction-mpi-pthreads-parallism
- Owner: z1skgr
- Created: 2022-02-23T22:20:10.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-11-19T08:13:37.000Z (7 months ago)
- Last Synced: 2025-01-23T09:11:27.164Z (4 months ago)
- Topics: accelerated-computing, intel, intel-intrinsics, linux, memory-layout, mpi, parallel-programming, pthreads, simd-instructions, sse
- Language: C
- Homepage:
- Size: 866 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# SIMD-instructions/parallism
> Parallelism standards for accelerating performance on calculations for detection of positive DNA selection
## Table of contents
* [General Info](#general-information)
* [Features](#features)
* [Prerequisites](#prerequisites)
* [Setup](#setup)
* [How to run](#how-to-run)
* [Acknowledgements](#acknowledgements)
## 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](https://software.intel.com/sites/landingpage/IntrinsicsGuide)
[MPI](http://mpitutorial.com/tutorials/)
## How to run
1. GCC Installation
```
$ gcc --version
$ sudo apt install gcc
$ sudo apt install lam-runtime
```
Supposing you can navigate the proper folder to compile the desired source code from the terminal
2. MPI Installation
Download the source code [MPI](https://www.mpich.org/downloads/) release
```
$ tar -xzf mpich-X-X-X.tar.gz
$ cd mpich-X-X-X
```
where `X-X-X` mpi version
```
$ ./configure
$ make; sudo make install
```
3. Check MPI version
```
$ mpiexec --version
```
4. LAM installation
```
sudo apt-get install lam-runtime
```
### 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