  Nuclear pasta topology is an essential ingredient to determine transport
properties in the inner crust of neutron stars. We perform semi-classical
molecular dynamics simulations of nuclear pasta for proton fractions $Y_p=0.30$
and $Y_p=0.40$ near one third of nuclear saturation density,
$n=0.05\,\mathrm{fm}^{-3}$, at a temperature $T=1.0\,\mathrm{MeV}$. Our
simulations are, to our knowledge, the largest nuclear pasta simulations to
date and contain up to $3\,276\,800$ nucleons in the $Y_p=0.30$ and $819\,200$
nucleons in the $Y_p=0.40$ case. An algorithm to determine which nucleons are
part of a given sub-domain in the system is presented. By comparing runs of
different sizes we study finite size effects, equilibration time, the formation
of multiple domains and defects in the pasta structures, as well as the
structure factor dependence on simulation size. Although we find qualitative
agreement between the topological structure and the structure factors of runs
with $51\,200$ nucleons and those with $819\,200$ nucleons or more, we show
that simulations with hundreds of thousands of nucleons may be necessary to
accurately predict pasta transport properties.
