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This paper considers both one-way and two-way relaying systems with multiple relays between two terminal nodes where all nodes have multiple-input multiple-output (MIMO) antennas. We propose a unified algorithm which computes the optimal linear transceivers jointly at the source node and the relay nodes for amplify-and-forward (AF) protocols. First, optimization designs based on the sum-rate and the mean-square error (MSE) criteria are formulated for the two-way AF relaying channel. Due to non-convexity of the given problems, the proposed schemes iteratively identify local-optimal source and relay filters by deriving the gradients of the cost functions for a gradient descent algorithm. Then, the proposed algorithm can optimize a one-way multiple relay system as a special case of the two-way channel. Finally, we prove the global optimality of the maximum sum-rate scheme under an asymptotically large antenna assumption. From simulation results, it is confirmed that the proposed methods yield the near optimum result for the MIMO multiple relay channel even with a moderate number of antennas. Consequently, we show that the proposed algorithm outperforms conventional schemes in terms of the sum-rate and the error performance for both one-way and two-way protocols.