$totals = (
	$source => {
		$destination => $count,
	},
);

##</code><code>##

my %totals;
while (<LOGFILE>) {
    $totals{$1}->{$2}++ if m/(...)(...)(...)/;
}

##</code><code>##

my $sth = $dbh->prepare('insert into totals (srcIP, dstIP, visit_count) values (?, ?, ?)');
foreach my $source (keys %totals) {
	$sth->execute($source, $_, $totals{$source}->{$_}) for keys %{ $totals{$source} };
}

##</code><code>##

  %ips = ( $src => "$dst");
  foreach $ws (keys(%ips)) {
    ...
  }