In this paper, we study the physical layer security (PLS) problem in the dual hop orthogonal frequency division multiplexing (OFDM) based wireless communication system. First, we consider a single user single relay system and study a joint power optimization problem at the source and relay subject to individual power constraint at the two nodes. The aim is to maximize the end to end secrecy rate with optimal power allocation over different sub-carriers. Later, we consider a more general multi-user multi-relay scenario. Under high SNR approximation for end to end secrecy rate, an optimization problem is formulated to jointly optimize power allocation at the BS, the relay selection, sub-carrier assignment to users and the power loading at each of the relaying node. The target is to maximize the overall security of the system subject to independent power budget limits at each transmitting node and the OFDMA based exclusive sub-carrier allocation constraints. A joint optimization solution is obtained through duality theory. Dual decomposition allows to exploit convex optimization techniques to find the power loading at the source and relay nodes. Further, an optimization for power loading at relaying nodes along with relay selection and sub carrier assignment for the fixed power allocation at the BS is also studied. Lastly, a sub-optimal scheme that explores joint power allocation at all transmitting nodes for the fixed subcarrier allocation and relay assignment is investigated. Finally, simulation results are presented to validate the performance of the proposed schemes.