I think the synchronization is not the problem. I synchronized the boards using the 10 MHz backplane clock. This should work.
However, the sample rate of the PXI-6115 is 20MHz/3 = 6,666,666.50 Hz, the frequency of the square wave is 1000 Hz. These are not multiples, so sometimes there is a sample less.
The sample rate should be at least 6 MHz, unfortunately this is not a dividend of the PXI-6115 board clock.
Is it possible with the PXI-6115 or the PXI-5411 to route not the board clock timebase, but the actual sample rate timebase (so the 6,666,666.50 Hz signal in case of the PXI-6115) to the RTSI-bus to use it as an external clock for another board?
Or does the PXI-6115 have some sort of high resolution clock mode?
Thanks again,
DeWit