apeNEXT is the latest generation of massively parallel machines optimized for simulating QCD formulated on a lattice (LQCD). In autumn 2005 the commissioning of several large-scale installations of apeNEXT started, which will provide a total of 15 TFlops of compute power. This fully custom designed computer has been developed by an European collaboration composed of groups from INFN (Italy), DESY (Germany) and CNRS (France). We will give an overview on the system architecture and place particular emphasis to the system software, i.e. the programming environment and the operating system. In this talk we will present and analyze performance numbers and finally report on experiences gained during the first months of machine operation.