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Hi Sing,
I had the same question a few days ago
To your questions:
1: My observation is that the CLKRUN_EN pin floats to ground. But in theory, it could also float to any other voltage level. Each time the XIO2001 reads this pin as "1", the secondary clock will stop during the pauses between PCI traffic. If the PCI devices on the XIO's PCI-Bus are target-only, this will not harm as long as they do not rely on a continiously running PCI-Clock for local operation (e.g. supervising an input and generating an interrupt if it gets high).
2: My observation is that the EXT_ARB_EN pin floats to ground. But in theory, it could also float to any other voltage level. Each time the XIO2001 reads this pin as "1", the internal arbiter will stop working and any subsequent access to the PCI-Bus will fail.
3: As Yaser wrote, no fix.
4: Pull CLKRUN_EN high and see that the PCI-Clock stops. Remove the Pullup, and the PCI-Clock will start running again.
Pull EXT_ARB_EN high and see that it is no longer possible to access PCI-Devices on the XIO's PCI-Bus. Remove the Pullup and see that your PCI-Devices are back.
Regards, Niels