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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:

 

Scroll pdf title
titleS1 settings for booting from SPI Flash memory.

switch

S1A
(EEPROM serial data)

S1B
(M2)

S1C
(M1)

S1D
(/MR master reset)

S2
(PS_EN)

state

0 = ON

0 = ON

0 = ON

1 = OFF

X = do note care

state

1 = OFF

0 = ON

0 = ON

1 = OFF

FX2 PON

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.