Hi Chris,
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Did you contact Altera about 'reconfiguration busy' being asserted for ~6ms? Did anyone confirm your timing on another part?
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I didn't contact Altera about this aspect (my discussions with them were regarding the failure to meet timing). I don't recall if I tested this on multiple parts.
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Did you determine if a longer reset period before allowing altgx_reconfig to start improves link negotiation for 4x ?
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I didn't try. Have you?
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Was this support entry posted thanks to your design? www altera com/support/kdb/solutions/rd12172009_309.html
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I don't think so. I do recall seeing recommendations like this, though many of the example designs neglect to implement it.
Cheers,
Dave