Yep-- use open(). Like so:

use File::Copy;

open(PROGRAM_OUT, "| $runbin/$program.x") 
    or die "Couldn't open '$runbin/$program.x': $!; stopped";
copy(\*STDIN, PROGRAM_OUT) or die "Couldn't copy: $!; stopped";
close(PROGRAM_OUT) or die "Error while closing: $!/$?; stopped";
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Untested.

That runs your FORTRAN process, copying STDIN to it, then checks the error code on file close.

Update: Actually, system() by itself should work fine... it inherits your STDIN from the main program. So if you get rid of the redirection and temporary file, it should work fine. So just

system("$runbin/$program") == 0
    or die("'$runbin/$program' failed: returned signal @{[ $? >> 8 ]} 
+stopped";
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stephen