Error message
xillybus: FPGA reported a fatal error.Meaning
This fatal error messages is issues when the FPGA's hardware PCIe core flags that the PCIe link has rendered unreliable. This is a result of reaching a condition which is prohibited by the PCI Express specification.
This can happen as a result of faulty physical hardware (wire crosstalk, clock jitter etc.) or bugs in either end of the PCIe link.
This low-level communication takes place in Xilinx' PCIe core, which Xillybus relies on. This hardware problem is most likely unrelated to Xillybus (neither kernel module nor FPGA core).
The host driver stops any activity as soon as this condition occurs. Subsequent messages may be a result of this. It is possible that some data was corrupted just before this error was reported.
This fatal condition has occurred in the past as a result of ACPM being allowed to switch the physical layer into the L0s state, but the host driver now disables ACPM altogether.
Recommended action
This is a serious condition, which is most likely not related to Xillybus. Unless its reason is obvious (such as pulling out the PCIe card from its slot in the middle of operation), it's warmly recommended to investigate your hardware further.
Reports about this condition are welcome. As has been done in the past, this may be solved with a workaround to buggy hardware.
To get Xillybus working again, power the computer off, reconfigure the FPGA and power the computer on again.