Efficient resource allocation with hybrid precoder design is essential for massive MIMO systems operating in millimeter wave (mmW) domain. Owing to a higher energy efficiency and a lower complexity of a partially connected hybrid architecture, in this letter, we propose a joint deep convolutional neural network (CNN) based scheme for precoder design and antenna selection of a partially connected massive MIMO hybrid system. Precoder design and antenna selection is formulated as a regression and classification problem, respectively, for CNN. The channel data is fed to the first CNN network which outputs a subset of selected antennas having the optimal spectral efficiency. This subset is again fed to the second CNN to obtain the block diagonal precoder for a partially connected architecture. Simulation results verifies the superiority of CNN based approach over conventional iterative and alternating minimization (alt-min) algorithms. Moreover, the proposed scheme is computationally efficient and is not very sensitive to channel irregularities.