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I have 2 test stations that use the PCI 6533 DIO, I had a a requirement to build another test station and had to go with the PXIe 6536. I am in the process of updating all my VI's that use Traditional DAQ drivers to DAQmx. I have come across a problem that has beaten me up. The code works on the PCI6533 cards. I have taken a Logic analyzer and captured a plot of the good DIO. When I am using the PXIe 6536 would appear to be loaded down or nonexistent when testing a UUT. When no UUT present and I test just the DIO it seems to be there. My question is what has changed between the 2 types of DIO's that would load down a signal like this. There has got to be some line or something that is loading it all down.
What is the input impendance of your UUT? Digging through the PXIe-6536, I found a 50 Ohm output impedance spec. I couldn't find anything similar for the PCI-6533. So the impedance mismatch is likely your problem.
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Note that the output impedence spec is 50Ω, but input impedence is "High-impedance" (50 kΩ to ground). It's hard to give you much more information without knowing your application though.