It sounds like you want something like this:

#!/usr/bin/perl
use warnings;
use strict;
use Socket;

my $hostfile = '/tmp/jn/hosts';
my $logfile  = '/tmp/jn/logforthisserver.log';

open HOSTFILE, '<', $hostfile or die "Cannot open '$hostfile' $!";

my %unique_ips;
while ( <HOSTFILE> ) {
    next if /^(?:#|\s*$)/;
    my $ip = inet_aton( ( split )[ 0 ] );
    $unique_ips{ $ip }++;
    }

close HOSTFILE;


open LOGFILE, '>', $logfile or die "Cannot open '$logfile' $!";

for my $ip ( sort keys %unique_ips ) {
    print LOGFILE inet_ntoa( $ip ), "\n";
    }

close LOGFILE;
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