Hello Yiannis,
If I understand you correctly, you want to synchronize your analog input and analog output that are started by a trigger on the analog input board. If you don't want to use the RTSI lines, your best bet is to export the AI Sample Clock and then read it in to the AO board. There is an example on ni.com called DAQmx - Synchronized AIAO Shared Clock. It appears to be having techincal issues so I have attached the example below. To export ai/sampleclock, use DAQmx Export Signal.vi after Get Terminal Name with Device Prefix.vi. Export Sample Clock to PFI3 (There are only connections between the sample clock and PCI3/4/8/9). Connect PFI3 on your AI board to PFI0 on your AO board (with a wire). Then change the source for the AO Timing.vi to Devx/PFI0. If you want to do triggering, stick the DAQmx Trigger.vi between the Timing property node and the DAQmx Start.vi on the AI task. I have shown how to do this in the modified version below. Please take a look at it and let me know if you have any questions. If you still get an error please take a screenshot of it and post to the forum. Have a great day!
Sincerely,
Marni S.