You should not use qx// for anything that involves more than just `command options`. Playing around with STDIN and STDOUT is much more, you need the Good Old open().

open my $pipe , '|' , $scriptname or die "...";
print $pipe "This goes to the parallel program's STDIN".

...
[download]

`perldoc -f open` and `perldoc perlopentut` will help you.

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