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TSW14J56EVM: Rev B vs Rev D boards and firmware

Part Number: TSW14J56EVM

We have two TSW14J56EVM Rev B boards. In order to prototype our application we need access to the FPGA source code to modify the triggering behavior. The page for EVM has a link for TSW14J56REVD firmware. What is the difference between Rev B and Rev D boards? Can we use Rev D firmware source for the Rev B board? Will it damage the board? Is it compatible?

Another problem the published Rev D firmware synthesizes and fits just fine in Quartus 14.0 but has lots of intra and inter clock setup and hold timing violations for various speed models. Can we safely ignore those?