my %data;

foreach my $x (1..5000) {
	$data{$x} = {} unless $data{$x};
	foreach my $y (1..1000) {
		$data{$x}{$y} = {} unless $data{$x}{$y};
	}
}

real	0m4.075s
user	0m3.767s
sys	0m0.289s