I am using a recent version of u-boot (git from the past couple of weeks) and have an LSI SAS adapter on a canyonlands board. What I see happening is that u-boot reads the bist bit, then does numerous bar accesses, then sets the bist fail and latency words. Once the bist is set to fail, the lsi adapter doesn't respond to anything else and so Linux fails to see it when it boots. I've tried turning off pcie support in u-boot, in that case the bist did not get written but Linux kernel crashed during the init of the adapter. The LSI adapter does work fine in a ubuntu PC, so the hardware is likely good. This adapter is an LSISAS2008 gen 2 pcie board. On the PC it uses both IO and MEM spaces.
I am unsure what to try next -- Linux should not assume any state about the adapter -- on the other hand, if u-boot does cause the board to go into an unrecoverable state, there isn't much the kernel can do about that. any help / suggestions / experiments would be much appreciated.
Thanks Ayman