The perl Cookbook has a recipe on using alarm to solve your problem. See 16.22 if you have the book.

Here is the code it uses

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

eval {
   alarm(1200); # 20 minutes
   # long-time operations here
   alarm(0);
};
if ($@) {
   if ($@ =~ /timeout/) {
      #timed out, do what you will here
   }
   else {
      die; # propagate the unexpected exception
   }
}
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