$ time perl foo.pl

real    0m9.204s
user    0m3.697s
sys     0m1.387s
$ cat foo.pl
#!/usr/bin/perl -w
use strict;
use warnings;

open F1, 'sort s1|' or die "opening file 1";
open F2, 'sort s2|' or die "opening file 2";

open OU1, '>', 'uniq.1' or die;
open OU2, '>', 'uniq.2' or die;
open OU3, '>', 'common' or die;

# Prime the pump
my $in1 = <F1>;
my $in2 = <F2>;

while (1) {
        last if !defined($in1) and !defined($in2);

        if (!defined($in1)) {
            # File 1 is empty, rest of File 2 is unique
            print OU2 $in2;
            $in2 = <F2>;
        }
        elsif (!defined($in2)) {
            # File 2 is empty, rest of File 1 is unique
            print OU1 $in1;
            $in1 = <F1>;
        }
        elsif ($in1 eq $in2) {
            # Line common to both
            print OU3 $in1;
            $in1 = <F1>;
            $in2 = <F2>;
        }
        elsif ($in1 lt $in2) {
            # Line unique to File 1
            print OU1 $in1;
            $in1 = <F1>;
        }
        else {
            # Line unique to File 2
            print OU2 $in2;
            $in2 = <F2>;
        }
}