G3.1.3.5 is pretty clear on that
G3.1.3.5 Hot-Water Pumps (Systems 1, 5, and 7).
The baseline building design hot-water pump power shall
be 19 W/gpm. The pumping system shall be modeled as
primary-only with continuous variable flow. Hot-water
systems serving 120,000 ft2 or more shall be modeled
with variable-speed drives, and systems serving less than
120,000 ft2 shall be modeled as riding the pump curve.
So, just one pump (put it just after the supply side inlet or just before the supply side outlet), either constant or variable.
By the way for chillers, when they say (G3.1.3.10) that if you have 300 tons or more you need a primary secondary pumping system... That doesn't mean you should put one pump per chiller, and then one pump on the supply side. What it means is that you should have a constant speed pump on the supply side (typically right after the supply inlet node) and one variable speed pump on the demand side, typically right after the demand side supply inlet node. If you use the HVACTemplate:ChillerWaterLoop and select ConstantPrimaryVariableSecondaryas pumping configuration, that's what you get...See attached