With all of these suggestions, I came up with the following hack (ugly, but it works). Just for the sake of reference, this works for me.

use Tk;
use strict;
require Tk::ProgressBar;
require Tk::Button;

$|++;

my (
    $mw,
    $progressBar,
    $cancelCalButton,
    $runCalButton,
    $cancel,
   );

my @data = (0 .. 100);
my $dataIndex;

my $guiPid = $$;
my $childPid;

pipe(FROM_PARENT, TO_CHILD) or die "pipe: $!\n";
pipe(FROM_CHILD, TO_PARENT) or die "pipe: $!\n";
select((select(TO_CHILD), $| = 1)[0]);
select((select(TO_PARENT), $| = 1)[0]);

if ($childPid = fork()){
  close FROM_PARENT;
  close TO_PARENT;
} else {
  die "cannot fork :$!\n" unless defined $childPid;
  close FROM_CHILD;
  close TO_CHILD;
  while(my $line = <FROM_PARENT>){
    chomp($line);
    print "Chid got from parent $line\n";
    sleep(10);
    if ($line == 100){
      kill('USR1',$guiPid); #tell the GUI child is done with work
      next;
    }
    kill('USR2',$guiPid); #tell the GUI child has update info
    print "sending stuff to parent\n";
    print TO_PARENT "$line\n";
  }
  print "Done with child\n";
  exit();
}

$mw = MainWindow->new();
$cancelCalButton = $mw->Button(-text=>"cancel", -command=>\&cancel)->p
+ack();
$runCalButton = $mw->Button(-text=>"run",-command=>\&doit)->pack();
$progressBar = $mw->ProgressBar()->pack();
$mw->repeat(100,sub{$mw->idletasks});

$SIG{USR1} = sub {
  $cancel = 1;
  $progressBar->value(0);
  $cancelCalButton->configure(-state=>"disabled");
  $mw->idletasks;
};

$SIG{USR2} = sub {
  $runCalButton->configure(-state=>"normal");
  print "Got USR2 request\n";
  my $value = <FROM_CHILD>;
  print "parent got $value from child\n";
  return if ($cancel);
  $progressBar->value($value);
  $runCalButton->configure(-state=>"disabled");
  print TO_CHILD "$data[$dataIndex++]\n";
};

MainLoop;

sub doit {

  $runCalButton->configure(-state=>"disabled");
  $cancelCalButton->configure(-state=>"normal");
  $mw->update;
  $cancel = 0;
  $dataIndex = 0;
  print TO_CHILD "$data[$dataIndex++]\n";
}

sub cancel {
  print "@@@@@@@@@ Got Cancel button @@@@@@@@@\n";
  kill('USR1',$$);
}
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