You can catch the kill signal in your script and kill the thread on the server with this code: 
my $thread_id = $dbh->{thread_id};
my $new_dbh = $dbh->clone();
$new_dbh->{InactiveDestroy} = 0;
$new_dbh->do("KILL $thread_id");

[download]
(Taken from DBIx::Timeout)

In reply to Re: DBI mysql slow queries, hanging threads by perrin
in thread DBI mysql slow queries, hanging threads by Anonymous Monk

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