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

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

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

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