I think you might like this sub I wrote based on stuff I saw in perlipc. You can pass your timeout as a switch --timeout=N if you don't like the timeout of 15 seconds. I use it for calling an external script which does OCR of PDF files. If your $cmd has space-separated switches, they will be turned into more @args. Using multi-parameter open is much faster than backticks since you don't invoke a shell, and you don't have to deal with shell-mangling your filenames (so they don't need quotes if they contain spaces, eg).

sub execute {  # exec with timeout
   my ($cmd,@args)=@_;
   my $timeout=15;  # seconds
   my ($result,$pid,$i,$time);
   if ($args[$#args]=~/^--?timeout=(\d+)$/i) {  # or pass as last arg
      $timeout=$1;
      pop @args;
   }
   $i=index($cmd,' ');   # args appended to command?
   if ($i>-1) {
      unshift @args,split(/\s+/,substr($cmd,$i+1));   # could be more 
+than one
      $cmd=substr($cmd,0,$i);
   }
   eval {
        local $SIG{ALRM} = sub { die "alarm\n" }; # NB: \n required
        local($/)=undef;
        alarm $timeout;
        $time=time if debug_has(EXEC);
        $pid=open(CMD,'-|',$cmd,@args);   # run without shell overhead
        if ($pid) {
           $result=<CMD>;
           close CMD;
        }
        alarm 0;
    };
    if ($@) {
        $result='TIMEOUT' if $@ eq "alarm\n";   
    }
    $result;
}
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Hope that helps. SSF