If you've got them in two arrays, don't use a nested loop as that is over 3 million comparisons that you'll have to make. Instead, use a hash for one of them.

my %search;
@search{ @keys2 } = undef;
my @found;
foreach my $key (@keys1) {
    push @found => $key if exists $search{$key};
}
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When that's done, @found will have the duplicate keys. You'll only have a few thousand iterations instead of a few million.

Cheers,
Ovid

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