You are measuring time across a loop: 


                my @time = localtime(time);
                ...

                for(my $i = 0; $i<= $file_number - 1; $i++){

                           ...


                        for(my $j = $i + 1; $j <= $file_number; $j++){
                                $x = $x + 1;
                                my $m2 = $file_list_array[$j];
                                my ($Nvalue3, $Nvalue4, $Nvalue5) = fi
+nd_common_items($m1, $m2, \%file_gene, 0.1);

                                ...
                        }

                          ...
                }



               my @time = localtime(time);

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However, i did a test and found that the time needed to calculate the overlapping between two files increases with the number of the total files.

Thats actually not what you are measuring - you are measuring the time taken to compare every file with every other file, and of course that time will go up with the number of files! -- Your loop should be close to O(Nlog(N))

In reply to Re: Why does Perl get slower when building a larger hash? (Not due to the memory swapping) by tmharish
in thread Why does Perl get slower when building a larger hash? (Not due to the memory swapping) by chialingh

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