Looks like your code had 2 loops, each counting to +6 million

foreach my $che (@b){
  @aa=split(/\s/,$che);

  foreach my $kh (@a){
    @bb=split(/\s/,$kh);

    for ($l=0;$l<=$#bb;$l++){
      for ($m=0;$m<=$#aa;$m++){

      ## this code executes 6 million x 6 million times
      if(($bb[$l] eq $aa[$m]) ){
      ..

      }
    }
  }
}
[download]

But within the 6 million words, there are only few thousand different ones so your loops were checking the same word thousand of times more than required. By holding the unique words from file1 in a hash you don't have to loop through 6 million words every time to find a match with a word from file2

hi i don't understand this part of code

 my @match = grep $uniq1{$_}, @words; what i understand : here we search for $uniq1{$_} in @words

we know that @words contain the current line, but $uniq1{$_} what does it contain? and if $uniq1{$_} contain the line of the file N°1 how to browse(iterate) it and how to change from a value to another

while (<FICC>) {
  my @words = split /\s+/,lc $_;
  ++$uniq1{$_} for @words;
}
[download]

$uniq1{$_} contains all the words from file1 like a dictionary. $uniq1{'anyword'} will be undef or 0 if 'anyword' was not in file1.
Try a simple example

#!perl
my %uniq1= (
  cow => 1,
  dog => 1,
  fox => 1,
);

my @words = ('ant','bat','cat','dog','eel','fox');
my @match = grep $uniq1{$_}, @words;
print "@match\n"
[download]

poj