A primary clock is a clock that defines a timing reference for your design and that is used by the timing engine to derive the timing path requirements and the phase relationship with other clocks. Their insertion delay is calculated from the clock source point (driver pin/port where the clock is defined) to the clock pins of the sequential cells to which it fans out.
For this reason, it is important to define the primary clocks on objects that correspond to the boundary of the design, so that their delay, and indirectly their skew, can be accurately computed.
The following sections describe the typical primary clock roots.