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Recent advances in deep neural network demand more than millions of parameters to handle and mandate the high-performance computing resources with improved efficiency. The cross-bar array architecture has been considered as one of the promising deep learning architectures that shows a significant computing gain over the conventional processors. To investigate the feasibility of the architecture, we examine non-idealities and their impact on the performance. Specifically, we study the impact of failed cells due to the initialization process of the resistive memory based cross-bar array. Unlike the conventional memory array, individual memory elements cannot be rerouted and, thus, may have a critical impact on model accuracy. We categorize the possible failures and propose hardware implementation that minimizes catastrophic failures. Such hardware optimization bounds the possible logical value of the failed cells and gives us opportunities to compensate for the loss of accuracy via off-line training. By introducing the random weight defects during the training, we show that the model becomes more resilient on the device initialization failures, therefore, less prone to degrade the inference performance due to the failed devices. Our study sheds light on the hardware and software co-optimization procedure to cope with potentially catastrophic failures in the cross-bar array.