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This paper presents a global optimization approach for three layers of grid stack. In grid environment, the Quality of Service (QoS) needs to be supported at every layer of the grid architecture. However, less attention has been paid to incorporating QoS at multiple layers of the grid architecture. The primary objective of most existing scheduling mechanisms is to improve QoS at single grid layer, while the QoS optimization at multiple grid layers is seldom considered. In the paper, we consider the requirements of fabric layer, collective layer and application layer at the same time, and propose a global optimization approach for three layers of grid stack. The paper deals with global optimization as optimization decomposition. The global optimization for three layers of grid stack can be decomposed into three sub-problems at different grid layers: resource allocation at the fabric layer, service integration at the collective layer, and application QoS optimization problem at the application layer. A distributed iterative algorithm for three-layer optimization is proposed. The convergence of the iterative algorithm is proved. The simulations are conducted to test Three-Layer Optimization Algorithm.