compare two files and send out equal values

You need to put

inB.seekg(0, inB.beg) 

to the end of the outer while loop. Else you will stay at the end of inB and will read nothing after processing of the first entry of inA

Another problem may be that you are using float for A and B. Try int (or string), as float may not behave as you expect with ==. Refer to this question for details: What is the most effective way for float and double comparison?.

This code worked on my platform:

... while (inA >> A) { inB.clear(); inB.seekg(0, inB.beg); while (inB >> B) { if (A == B) { outA << A << "\t" << B << endl; } } } 

Notice the inB.clear() and inB.seekg(...), A and B are strings.

By the way, this method only good for quick-and-dirty implementation, it's not optimal for big files, as you get N * M complexity (N - size of FileA, M - size of FileB). By using hash set you may get to nearly linear (N + M) complexity.

Example of hash set implementation (C++11):

#include <string> #include <iostream> #include <fstream> #include <unordered_set> using namespace std; int main() { string A, B; ifstream inA("FileA"); // input stream ifstream inB("FileB"); // second instream ofstream outA("OutA.txt"); // output stream unordered_set<string> setA; while (inA >> A) { setA.insert(A); } while (inB >> B) { if (setA.count(B)) { outA << A << "\t" << B << endl; } } return 0; } 

Are both the files small enough to read into memory?

You could try something similar to the following:

int main(int argc, char**argv) { std::vector<std::string> a; std::vector<std::string> b; ofstream outA("OutA.txt"); // output stream ifstream inA("FileA"); // input stream ifstream inB("FileB"); // second instream std::string value; inA >> value; //read first line (and don't use - discarding header) while (inA >> A) { a.push_back(A);} //populate first vector inB >> value; //read first line (and don't use - discarding header) while (inB >> B) { b.push_back(B);} //populate first vector //std::sort will perform a pretty efficient sort std::sort(a.begin(),a.end()); std::sort(b.begin(),b.end()); //now that it is sorted, comparing is easier for (std::vector<std::string>::iterator ita=a.begin(), std::vector<std::string>::iterator itb=b.begin(); ita!=a.end(), itb!=b.end();) { if(*ita > *itb) itb++; else if(*ita < *itb) ita++; else outA << *ita <<'\n'; } return 0; } 

Reads both files into memory, sorts them both, and then compares them. The comparison only has to go through each file once, which reduces the complexity immensely O(a+b) instead of O(a*b). Of course the sorting will have an overhead, but this should be more efficient for larger files, and for shorter files it should be sufficiently fast still. (unless comparing lots and lots (and lots) of small files). I believe with std::sort the worst case for all this is O(aloga + blogb) which is better than O(a*b)

In the end I fixed it like so

#include <cmath> #include <cstdlib> #include <string> #include <iomanip> #include <iostream> #include <fstream> #include <ctime> using namespace std; //Globals, to allow being called from several functions //main program int main() { string A, B; ifstream inA("FileA.txt"); //input stream ifstream inB("FileB.txt") ;//second instream ofstream outA("OutA.txt"); //output stream while(inA>>A){//take in first stream while(inB>>B){//whilst thats happening take in second stream if (A==B){//do they match? If so then send out the value outA<<A<<"\t"<<B<<endl; //THIS IS JUST SHOW A DOES = B! } }//end of B loop inB.clear();//now clear the second stream (B) inB.seekg(0, inB.beg);//return to start of stream B }//move onto second input in stream A, and repeat return 0; }