Cosmological simulations of structures and galaxies formations have played a fundamental role in the study of the origin, formation and evolution of the Universe. These studies improved enormously with the use of supercomputers and parallel systems and, recently, grid based systems and Linux clusters. Now we present the new version of the tree N-body parallel code FLY that runs on a PC Linux Cluster using the one side communication paradigm MPI-2 and we show the performances obtained. FLY is included in the Computer Physics Communication Program Library. This new version was developed using the Linux Cluster of CINECA, an IBM Cluster with 1024 Intel Xeon Pentium IV 3.0 Ghz. The results show that it is possible to run a 64 Million particle simulation in less than 15 minutes for each timestep, and the code scalability with the number of processors is achieved. This lead us to propose FLY as a code to run very large N-Body simulations with more than $10^{9}$ particles with the higher resolution of a pure tree code.