I've run into this same issue and resolved by wrapping calls in an eval block, like below. This only works on *NIX boxes though -- Windows doesn't support signals per se.

my $timeout = 20;

my $result = eval {
    local $SIG{ALRM} = sub { die "timed out\n" };
  
    alarm $timeout;
    my $result = send_command();
    alarm 0;

    return $result;
};
if ($@) {
    print "command timed out\n";
    do_something_else();
}
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