Do you have a particular need to execute the 16 processes in parallel? If not, use system.

for (0..16) {
   my $idx = $_ || '';  # Don't actually include '0' in the file name.

   my $in_file  = "perloutput$idx.txt";
   my $out_file = "output$idx.txt";

   my $rv = system("chirp_md5sum $in_file > $out_file");

   die("Error launching child: $!\n")                    if $rv == -1;
   die(sprintf("Child died with signal %d\n", $rv & 127))if $rv & 127;
   die(sprintf("Child returned error %d\n, $rv >> 8))    if $rv;
}
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