Density functional theory (DFT) has become the most widely used quantum mechanical method in material science simulations. Due to the change of computer architectures, and the corresponding change in the scope of problems amenable by the DFT method, the algorithms used in the DFT calculations are also changing. In this talk, I will discuss a few commonly used ground state based algorithms for large scale DFT calculations. I will also discuss what it will take to speed up the DFT molecular dynamics simulations by a thousand times, and the self-consistent problems often encountered in large system simulations. Some of our recent effort in implementing our planewave DFT code in GPU will also be discussed. Finally, I will present a method using auxiliary periodic boundary conditions to solve an open boundary condition scattering state problem in quantum transport calculations.