Basically I have two compactRIOs with different modules on it. The first compactRIO has an NI-9401 (8-CH, 5 V/TTL Bidirectional C Series DIO Module) and the second compactRIO have one NI-9205 (32-CH, +/-10V, 16-Bit Analog Input Module), one NI-9239 (4-CH, 24-Bit Analog Input Module), and one NI-9236 (8-CH, Quarter Bridge Strain Gauge Module). I will use the NI-9401 module from the first cRIO to trigger the NI-9205, NI-9239, and NI-9236 modules on the second cRIO to start acquiring data. The first cRIO is the controller and the second cRIO is the embedded controller.
There is no direct way to do triggering between the chassis like I think you want. You will have to do ethernet communication (shared variables or network streams, or however you want to implement it) between the two devices to link them up. I would have an RT VI on the controller that is constantly monitoring the IO pins of the 9401 (so scan engine mode), and transmitting their states to the other RIO. You could then trigger off of this data. That said, why do you need two RIOs for this application?
Thanks for the advice, I really appreciate it! I'm using two cRIOs because of the number of channels I need for acquiring data. Can I create the two RT Targets (two cRIO) in one project or do I have to create two separate LabVIEW project?
One project will be best. Just add both of them to the project by right clicking on the project name in project explorer, and add them individually from the new targets and devices window.