我正在尝试使用pthread以并行方式实现串行算法。 以下是我写的代码 -
#include <iostream>
#include <fstream>
#include <cstdlib>
#include <string>
#include <cmath>
#include <sys/time.h>
#include <pthread.h>
#include <stdlib.h>
#include <unistd.h>
#include <stdio.h>
#include <ctime>
#include <vector>
#include <map>
#include <sstream>
using namespace std;
double similarity_score(char a,char b);
double find_array_max(double array[],int length);
void insert_at(char arr[], int n, int idx, char val);
void checkfile(int open, char filename[]);
void *main_algo(void* rank);
double valueChanger(int p1 , int p2);
string read_sequence(ifstream& f);
int ind;
double mu,delta;
double H_max = 0.;
int N_a; // get the actual lengths of the sequences
int N_b;
int** H;
int count_gap = 6;
int matrix_i = 1;
double temp[4];
char *nameof_seq_a;
char *nameof_seq_b;
string seq_a,seq_b;
int bigCount;
int start_i;
int stop_i;
int start_j;
int stop_j;
int stopSituation;
int k;
map<int,int> mymap;
std::string strValue;
std::stringstream out;
std::stringstream out2;
double value;
int main(int argc, char** argv){
// read info from arguments
if(argc!=5){
cout<<"Give me the propen number of input arguments:"<<endl<<"1 : mu"<<endl;
cout<<"2 : delta"<<endl<<"3 : filename sequence A"<<endl<<"4 : filename sequence B"<<endl;
cout<<"5 : maximal length N of sequences"<<endl;exit(1);
}
mu = atof(argv[1]);
delta = atof(argv[2]);
/////////////////////////////////
// give it the filenames
nameof_seq_a = argv[3];
nameof_seq_b = argv[4];
//int N_max = atoi(argv[5]);
// read the sequences into two vectors:
ifstream stream_seq_b; // first define the input-streams for seq_a and seq_b
stream_seq_b.open(nameof_seq_b); // the same for seq_b
checkfile(! stream_seq_b,nameof_seq_b);
seq_b = read_sequence(stream_seq_b);
ifstream stream_seq_a;
stream_seq_a.open(nameof_seq_a); // open the file for input
checkfile(! stream_seq_a,nameof_seq_a); // check, whether the file was opened successfully
seq_a = read_sequence(stream_seq_a);
// string s_a=seq_a,s_b=seq_b;
N_a = seq_a.length(); // get the actual lengths of the sequences
N_b = seq_b.length();
cout<<"N_a length "<<N_a<<endl;
cout<<"N_b length "<<N_b<<endl;
////////////////////////////////////////////////
// initialize H
int temp1 = N_a+1;
int temp2 = N_b+1;
// call to main algorithm
bigCount = N_a;
stopSituation = (N_a + N_b -1) / count_gap;
cout<<"--------Big Count----"<<bigCount<<endl;
cout<<"--------stopSituation----"<<stopSituation<<endl;
//cout<<"--------Matrix_i-------"<<matrix_i<<endl;
while(matrix_i <= stopSituation+1){
//cout<<"--------MATRIX_I----"<<matrix_i<<endl;
pthread_t myThreads[matrix_i];
for(k = 1; k < matrix_i +1 ; k++){
if(k == 1){
start_i = 1;
stop_j = (count_gap * (matrix_i))+1;
}
else if(k == matrix_i){
start_i = (count_gap * (k-1)) + 1;
stop_j = count_gap +1;
}
else{
start_i = (count_gap * (k-1)) + 1;
stop_j = (count_gap * ((matrix_i - k)+1))+1;
}
start_j = (count_gap * (matrix_i - k))+1;
stop_i = (count_gap * k)+1;
//main_algo();
pthread_create(&myThreads[k], NULL,main_algo, (void*)k);
}
//wait until all threads finish
for(k = 1; k<matrix_i+1; k++){
pthread_join(myThreads[k],NULL);
}
//sleep(1);
if(matrix_i > 1)
{
}
matrix_i++;
}
// Print the matrix H to the console
cout<<"**************** Max is = "<<H_max<<endl;
mymap.clear();
} // END of main
/////////////////////////////////////////////////////////////////////////////
// auxiliary functions used by main:
/////////////////////////////////////////////////////////////////////////////
void checkfile(int open, char filename[]){
if (open){cout << "Error: Can't open the file "<<filename<<endl;exit(1);}
else cout<<"Opened file "<<filename<<endl;
}
/////////////////////////////////////////////////////////////////////////////
double valueChanger(int p1 , int p2){
out.str(std::string());
out2.str(std::string());
out << p1;
out2 << p2;
strValue = out.str()+out2.str();
double value_new = atoi(strValue.c_str());
return value_new;
}
void *main_algo(void* rank){
//void main_algo(){
// algorithm
for(int i=start_i;i<stop_i;i++){
if(i > N_a) {
break;
}
for(int j=start_j;j<stop_j;j++){
if(j > N_b){
break;
}
int iCheck = i-1;
int jCheck = j-1;
value = valueChanger(iCheck , jCheck);
//double myVal = H[iCheck][jCheck];
double myVal;
if ( mymap.find(value) == mymap.end() ) {
// not found
myVal = 0;
} else {
// found
myVal = mymap.find(value)->second;
}
if(seq_a[i-1]==seq_b[j-1]){
temp[0]= myVal+1.0;
}
else{
temp[0]= myVal-mu;
}
value = valueChanger(i-1 , j-1);
if ( mymap.find(value) == mymap.end() ) {
// not found
temp[1] = 0;
} else {
// found
temp[1] = mymap.find(value)->second-delta;
}
value = valueChanger(i , j-1);
if ( mymap.find(value) == mymap.end() ) {
// not found
temp[2] = 0;
} else {
// found
temp[2] = mymap.find(value)->second-delta;
}
temp[3] = 0.;
value = valueChanger(i , j);
mymap[value] = find_array_max(temp,4);
if( H_max < mymap[value] ){
H_max = mymap[value];
}
}
}
cout<<"Done"<< my_rank<<endl;
}
double similarity_score(char a,char b){
double result;
if(a==b){
result=1.;
}
else{
result=-mu;
}
return result;
}
/////////////////////////////////////////////////////////////////////////////
double find_array_max(double array[],int length){
double max = array[0]; // start with max = first element
for(int i = 1; i<length; i++){
if(array[i] > max){
max = array[i];
}
}
return max; // return highest value in array
}
/////////////////////////////////////////////////////////////////////////////
string read_sequence(ifstream& f)
{
// overflows.
string seq;
char line[5000];
while( f.good() )
{
f.getline(line,5000);
// cout << "Line:" << line << endl;
if( line[0] == 0 || line[0]=='#' )
continue;
for(int i = 0; line[i] != 0; ++i)
{
int c = toupper(line[i]);
// cout << char(c);
if( c != 'A' && c != 'G' && c != 'C' && c != 'T' )
continue;
seq.push_back(char(c));
}
}
return seq;
}
这里，当我执行这个程序时，我得到以下错误
*** Error in `./myProg': double free or corruption (fasttop): 0xb5300480 ***
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(+0x767e2)[0xb74e67e2]
/lib/i386-linux-gnu/libc.so.6(+0x77530)[0xb74e7530]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZdlPv+0x1f)[0xb7689aaf]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1b)[0xb76ee5ab]
/usr/lib/i386-linux-gnu/libstdc++.so.6(+0xad5f0)[0xb76ee5f0]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZNSs6assignERKSs+0x82)[0xb76efde2]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZNSsaSERKSs+0x23)[0xb76efe33]
./myProg[0x80499dc]
./myProg[0x8049c2f]
/lib/i386-linux-gnu/libpthread.so.0(+0x6d78)[0xb7730d78]
/lib/i386-linux-gnu/libc.so.6(clone+0x5e)[0xb75613de]
======= Memory map: ========
*** Error in `./myProg': double free or corruption (fasttop): 0x0829c8f8 ***
======= Backtrace: =========
/lib/i386-linux-gnu/libc.so.6(+0x767e2)[0xb74e67e2]
/lib/i386-linux-gnu/libc.so.6(+0x77530)[0xb74e7530]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZdlPv+0x1f)[0xb7689aaf]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1b)[0xb76ee5ab]
/usr/lib/i386-linux-gnu/libstdc++.so.6(+0xad5f0)[0xb76ee5f0]
/usr/lib/i386-linux-gnu/libstdc++.so.6(_ZNSsaSERKSs+0x23)[0xb76efe33]
./myProg[0x80499dc]
./myProg[0x8049aee]
/lib/i386-linux-gnu/libpthread.so.0(+0x6d78)[0xb7730d78]
Aborted (core dumped)
请随意复制并执行以下两个陈述 - 1）g ++ [name] .cpp -o [name] -lpthread 2）./ [name] 1 1 filetoread.txt filetoread2.txt
请更新我在编写代码时遇到的任何错误。 谢谢!!!!
答案 0 :(得分：0)
您需要使用互斥锁（或其他锁定机制）保护任何非线程安全的变量（例如std :: map）。由于您正在使用pthread，请查看pthread_mutex_lock，pthread_mutex_unlock和pthread_mutex_destroy。
答案 1 :(得分：0)
如果您想要进行多线程处理，可以使用以下注释：