Question

I have an array of char pointers of length 175,000. Each pointer points to a c-string array of length 100, each character is either 1 or 0. I need to compare the difference between the strings.

char* arr[175000];

So far, I have two for loops where I compare every string with every other string. The comparison functions basically take two c-strings and returns an integer which is the number of differences of the arrays.

This is taking really long on my 4-core machine. Last time I left it to run for 45min and it never finished executing. Please advise of a faster solution or some optimizations.

---

Example:

000010
000001

have a difference of 2 since the last two bits do not match.

After i calculate the difference i store the value in another array

                int holder;

                for(int x = 0;x < UsedTableSpace; x++){
                    int min = 10000000;

                    for(int y = 0; y < UsedTableSpace; y++){

                        if(x != y){
                            //compr calculates difference between two c-string arrays
                            int tempDiff =compr(similarity[x]->matrix, similarity[y]->matrix);

                            if(tempDiff < min){
                                min = tempDiff;
                                holder = y;
                            }
                        }       
                    }
                    similarity[holder]->inbound++;

                }

Answer 1

One simple optimization is to compare the strings only once. If the difference between A and B is 12, the difference between B and A is also 12. Your running time is going to drop almost half.

In code:

int compr(const char* a, const char* b) {
  int d = 0, i;
  for (i=0; i < 100; ++i)
    if (a[i] != b[i]) ++d;
  return d;
}

void main_function(...) {

    for(int x = 0;x < UsedTableSpace; x++){
        int min = 10000000;

        for(int y = x + 1; y < UsedTableSpace; y++){

            //compr calculates difference between two c-string arrays
            int tempDiff = compr(similarity[x]->matrix, similarity[y]->matrix);

            if(tempDiff < min){
                min = tempDiff;
                holder = y;
            }
        }
        similarity[holder]->inbound++;
    }
}

Notice the second-th for loop, I’ve changed the start index.

Some other optimizations is running the run method on separate threads to take advantage of your 4 cores.