this is a little garbled, but i assume from the database fields you mention that the goal is to build a table of number of visits by each source to each destination?

one good approach to this kind of problem: first draw up the data structure which is most suited to holding the information you have in the relations you want, then write a script in two parts: first to build that structure, then to use it. in the end you'll often find some way of eliminating the middle step and - in your case - writing to the database directly as you while though the file.

in this case i'd suggest that the data structure you want is something like:

$totals = (
    $source => {
        $destination => $count,
    },
);
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ie, a hash of hashrefs each of which refers to a { destination => count } pair. which is easily built:

my %totals;
while (<LOGFILE>) {
    $totals{$1}->{$2}++ if m/(...)(...)(...)/;
}
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and then you just need to loop on the constructed hash to feed it all into the database, with something like:

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} };
}
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incidentally, and in case i've completely missed the point, the main trouble you're probably having is illustrated here:

  %ips = ( $src => "$dst");
  foreach $ws (keys(%ips)) {
    ...
  }
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The %ips hash will have exactly one key, $src, so looping on it isn't doing much. Which suggests that you haven't quite grasped how perl's hashes work and how much they can do for you. Some time with perldata, perldsc and perllol will help, along with a bit of strictness and if possible the perl cookbook.