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This paper builds a real time Programmable LDPC Decoder for decoding codes specified in IEEE 802.16 standard and discusses their performance under various decoding algorithms. Out of the decoding algorithms, the modified Min-Sum SPA is selected for implementation and optimization on a reconfigurable instruction cell architecture. Different general and architecture specific optimization techniques are applied to enhance the throughput. With the architecture, a throughput of 20 Mbps has been achieved.