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I have set the ddr controller to run at half rate (125MHz/2=62.5MHz), doubled the burst and now Nios runs fine, no need of pipeline bridge.
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you can put your cpu and other peripherial (jtag pio etc) to work on 62.5 and your ddr2 to work on 125 (normally using clock crossing without pipeline).
if your cpu will work with clock over 65 mhz you NEED to put pipeline bridge........and peripherial does not work fine with high values of clocks..... is better you put cpu and ram to work with clocks over peripherials clock....
try it..........
cheers
Franz Wagner