Don't make things harder than they have to be! Just do this:

open (FILE,"<$input_file") or die "Couldn't open file $input_file, $!\
+n";
while (<FILE>) {
    chomp;
    if ($_) {
        $entry .= "$_\n";
    } else {
        push @data, $entry;
        $entry = "";
    }
}
close FILE;
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