Smith-waterman算法 openmp+mpi实现

最新推荐文章于 2023-09-28 15:19:28 发布

GG_wang

最新推荐文章于 2023-09-28 15:19:28 发布

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分类专栏： C/C++ 算法

本文链接：https://blog.csdn.net/gg_wang/article/details/28102373

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本文介绍了使用OpenMP和MPI并行实现Smith-Waterman算法时遇到的问题，并提供了完整的C语言代码示例。该算法用于生物信息学中的序列比对，代码包括文件读取、矩阵计算和输出对齐结果。然而，在混合使用MPI和OpenMP时，可能出现一些挑战，作者希望寻求解决方案。

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//此Smith-Waterman 算法分别用mpi与openmp实现是没问题的，但是两个混合编程的时候就会出各种问题，希望懂的能够给指条明路。。。万分感谢

#include <omp.h>
#include <time.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <mpi.h>
/*File pointers*/
FILE *ptr_file_1, *ptr_file_2,*ptr_file_3;	//test file pointers

/*Definitions*/
#define TRUE 1
#define FALSE 0
#define Match 1
#define MissMatch -1
#define GapPenalty 2
#define MAXLEN 20

/*Global Variables*/
char inputC[5];		//user input character
int inputI;
int StrLen1,StrLen2;
int intcheck = TRUE;

char holder, ch;
int filelen1 = 0;
int filelen2 = 0;
int filelen3 = 0;
int i,j,k,l,m,n,lenA,lenB,compval,top,left,left_top,rows,columns,contrl;
char FASTA1[MAXLEN],FASTA2[MAXLEN]; 
char dash = '-';

char strA[MAXLEN];			//holds 1st string to be aligned in character array		
char strB[MAXLEN];			//holds 2nd string to be aligned in character array 
int HiScore;			//holds value of highest scoring alignment(s).
int HiScorePos[2];		//holds the position of the HiScore
int SWArray[MAXLEN][MAXLEN];	//S-W Matrix

char MaxA[MAXLEN];
char MaxB[MAXLEN];
char OptA[MAXLEN];
char OptB[MAXLEN];

int MaxAcounter = 1;	//MaxA counter	
int MaxBcounter = 1;	//MaxB counter
int cont = TRUE;
int check;


int rank,size;
MPI_Status status;
int buff[3];



/*ALIGNMENT FUNCTION*/
int Align(int PosA,int PosB) {

	/*Function Variables*/
	int relmax = -1;		//hold highest value in sub columns and rows
	int relmaxpos[2];		//holds position of relmax

	if(SWArray[PosA-1][PosB-1] == 0) {
		cont = FALSE;
	}

	while(cont == TRUE) {	//until the diagonal of the current cell has a value of zero
		
		/*Find relmax in sub columns and rows*/
		for(i=PosA; i>0; --i) {
	
			if(rel