my $pid = open2(*HIS_OUT, *HIS_IN, "/my/application" ) || die $!;
my $now = time(); # you may want something more precise, whatever.
while (<HIS_OUT>) {
  chomp;
  do_something_to($_);
  if ($now and time - $now > 4) {
    print HIS_IN "quit\n";
    $now = undef; # don't keep doing this.
  }
}