Your reverse puts all 1 million lines in memory.

That's on top of the 2 million indexes you place in memory when only 1 million are needed.

Fix:

use Tie::File;

tie(my @data, 'Tie::File', $fname_in)
   or die("Unable to open \"$fname_in\": $!\n");

open(my $fh_out, '>', $fname_out)
   or die("Unable to create \"$fname_out\": $!\n");

for (my $i=@data; $i--; ) {
   print $fh_out $data[$i];
}

untie @data;
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Although I recommend File::ReadBackwards.

use File::ReadBackwards qw( );

my $fh_in = File::ReadBackwards->new($fname_in)
   or die("Unable to open \"$fname_in\": $!\n");

open(my $fh_out, '>', $fname_out)
   or die("Unable to create \"$fname_out\": $!\n");

while (defined(my $line = $fh_in->readline())) {
   print $fh_out $line;
}
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