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]) ){
      ..

      }
    }
  }
}