The alarm code might look something like this:

$SIG{ALRM} = sub { die "timeout"; };

eval {
    alarm(60);    # shouldn't take more than a minute
    # do something here
    alarm(0);    # if the last op finished, cancel the alarm
};

if ($@ =~ /timeout/) {
    # you know it didn't finish
} else {
    # continue
}
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Shamelessly adapted from the Perl Cookbook, though I once wrote code like this anyway.