Internal fluid flow

Does anyone have experience simulating internal fluid flow through a cylinder with internal baffles and side exit holes? I want to see how the fluid acts inside and outside of the cylinder. I can't seem to get the fluid to come out of the exit holes when the holes are capped.

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Watertight volume with outlets assigned to your exit holes

Assuming you have extracted the fluid volume and it is watertight, then you need to assign the exit holes as Faces->Outlets from the Physics Tool Palette.

What are the error/warning messages you are seeing, if any?

I would suggest extruding the exit holes, to form a better path, away from the likely high velocity and pressure gradients near your exit holes. For more see the section "5. Keep inlets and outlets away from velocity and pressure gradients" in "5 Tips for CFD Flow Volume Creation."