This paper discusses the issue of fault-tolerance in distributed computer systems with tens or hundreds of thousands of diskless processor units. Such systems, like the IBM BlueGene/L, are predicted to be deployed in the next five to ten years. Since a 100,000-processor system is going to be less reliable, scientific applications need to be able to recover from occurring failures more efficiently. In this paper, we adapt the present technique of diskless checkpointing to such huge distributed systems in order to equip existing scientific algorithms with super-scalable fault-tolerance. First, we discuss the method of diskless checkpointing, then we adapt this technique to super-scale architectures and finally we present results from an implementation of the Fast Fourier Transform that uses the adapted technique to achieve super-scale fault-tolerance.