GNDに繋がってるってうるさい

ERROR:Xst:2033 - Port I of Input buffer XLXI_2/u_mem_controller/u_ddr2_infrastructure/DIFF_ENDED_CLKS_INST.SYS_CLK_INST is connected to GND

ERROR:Xst:2033 - Port IB of Input buffer XLXI_2/u_mem_controller/u_ddr2_infrastructure/DIFF_ENDED_CLKS_INST.SYS_CLK_INST is connected to GND

ERROR:Xst:2033 - Port I of Input buffer XLXI_2/u_mem_controller/u_ddr2_infrastructure/DIFF_ENDED_CLKS_INST.IDLY_CLK_INST is connected to GND

ERROR:Xst:2033 - Port IB of Input buffer XLXI_2/u_mem_controller/u_ddr2_infrastructure/DIFF_ENDED_CLKS_INST.IDLY_CLK_INST is connected to GND

ERROR:Xst:1847 - Design checking failed

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PIN定義のUCFファイルがトップモジュールに無いと起きるエラーですよ。