The PCI Express Root Port is a specific port on a computer's motherboard. The Root Port is prone to the same device conflicts and compatibility issues as a regular PCI port.
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The PCI Express Root Port is a port on the root complex -- the portion of the motherboard that contains the host bridge. The host bridge allows the PCI ports to talk to the rest of the computer; this allows components plugged into the PCI Express ports to work with the computer.
The PCI Express Root Port functions the same way as a regular PCI Express port, with the additional function of monitoring the interconnect hierarchy of the PCI ports. This function includes tracking the interconnect bandwidth and making sure that the PCI port hierarchy is functioning properly.
The most common problems with the PCI Express Root Port are related to device IRQ conflicts. While most plug-and-play components set their IRQ numbers automatically, you may occasionally have to set the line manually. Solve IRQ conflict problems by assigning a new IRQ number to the problematic device.