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In order to have the module to configure from its SPI Flash memory next time it is (re)booted, ensure one of following DIP switch settings:
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Table 31: S1 settings for booting from SPI Flash memory.
For your convenience, a reference video is available on the TrenzElectronic's Channel at YouTube.
For further reference, please read Xilinx XAPP974: Indirect Programming of SPI Serial Flash PROMs with Spartan-3A FPGAs.