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I know about DMA and that it would be more efficient. However, in this case the goal is different - neither efficiency, no consistency are the issues.
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Ok.
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I think it might be a HW issue ... Mmapping /dev/mem at PCIe BAR address was also tried with the same result: reads work as expected, writes cause system reboot.
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In this thread
http://www.alteraforum.com/forum/showthread.php?t=35678 there is a zip file containing a program called pci_debug. Could you try that. I've used it on the Cyclone IV GX kit, the Stratix IV GX kit, and the DE4, and it works fine on all of them. If you find writes causing your system to crash still, then it definitely sounds like a hardware issue.
Cheers,
Dave