Thank you very much for your detailed analysis of the log!

On Tue, Apr 4, 2017 at 1:56 PM, Bjorn Helgaas <helgaas@kernel.org> wrote:
>> In particular, these are the lines that seem wrong to me:
>> [    5.920000] pci 0000:00:00.0: bridge configuration invalid ([bus
>> 00-00]), reconfiguring
>> [    5.930000] pci 0000:01:00.0: bridge configuration invalid ([bus
>> 00-00]), reconfiguring
>
> This is normal but possibly worded more alarmingly than necessary.
> Bridges power up with secondary/subordinate bus numbers as zero, so
> this just means nothing has changed their configuration from the
> power-up default.

Right. If the firmware had enumerated the bridge already, though, you
would not see this message because it would have been assigned a bus
number already. Right?

>> [    6.000000] pci 0000:04:00.0: [Firmware Bug]: reg 0x10: invalid BAR
>> (can't size)
>> [    6.010000] pci 0000:06:00.0: [Firmware Bug]: reg 0x10: invalid BAR
>> (can't size)
>
> These are more worrisome.  We discover the size of a BAR by writing
> all ones to it and reading it back, which tells us how many bits of
> the BAR are hard-wired to zero.  This behavior is prescribed by the
> PCI specs, so it's likely a hardware defect.

So, you would say it's a hardware problem of the PCIe cards in
question and I can safely ignore it?

> This is because the xilinx host bridge doesn't support I/O space

Yeah. I knew this, but thanks for confirming.

FYI, there is a bug in the pcie-xilinx bridge wrt legacy interrupts.
I've seen several people discussing the same problem for the altera
bridge and the "NW" xilinx bridge, but somehow this bridge still has
the issue. I've attached a patch that solved the problem for me.
Without it I see:

[    6.230000] ------------[ cut here ]------------
[    6.230000] WARNING: CPU: 0 PID: 1 at
/scratch/terpstra/freedom-u-sdk/linux/kernel/irq/irqdomain.c:365
irq_domain_associate+0x190/0x200
[    6.240000] error: hwirq 0x4 is too large for dummy
[    6.250000] CPU: 0 PID: 1 Comm: swapper Not tainted
4.11.0-rc1-661305-g4f97179 #12
[    6.250000] Call Trace:
[    6.260000] [<ffffffff80288660>] walk_stackframe+0x0/0x104
[    6.260000] [<ffffffff80288800>] show_stack+0x38/0x50
[    6.270000] [<ffffffff803c6e30>] dump_stack+0x2c/0x40
[    6.270000] [<ffffffff8028c600>] __warn+0x118/0x130
[    6.280000] [<ffffffff8028c658>] warn_slowpath_fmt+0x40/0x54
[    6.280000] [<ffffffff802c02a8>] irq_domain_associate+0x18c/0x200
[    6.290000] [<ffffffff802c0a3c>] irq_create_mapping+0x90/0xe4
[    6.300000] [<ffffffff802c0be4>] irq_create_fwspec_mapping+0x154/0x288
[    6.300000] [<ffffffff802c0d7c>] irq_create_of_mapping+0x64/0x84
[    6.310000] [<ffffffff804f9cb8>] of_irq_parse_and_map_pci+0x38/0x50
[    6.310000] [<ffffffff80407e00>] pci_fixup_irqs+0x6c/0x114
[    6.320000] [<ffffffff80408e64>] xilinx_pcie_probe+0x308/0x3f0
[    6.330000] [<ffffffff8042cba4>] platform_drv_probe+0x3c/0x88
[    6.330000] [<ffffffff8042aec0>] really_probe+0xbc/0x260
[    6.340000] [<ffffffff8042b138>] __driver_attach+0xd4/0xdc
[    6.340000] [<ffffffff80429200>] bus_for_each_dev+0x68/0xb8
[    6.350000] [<ffffffff8042b640>] driver_attach+0x24/0x38
[    6.350000] [<ffffffff80429db8>] bus_add_driver+0x1b4/0x22c
[    6.360000] [<ffffffff8042bdc0>] driver_register+0x68/0x12c
[    6.360000] [<ffffffff8042da78>] __platform_driver_register+0x48/0x5c
[    6.370000] [<ffffffff8000db38>] xilinx_pcie_driver_init+0x20/0x34
[    6.380000] [<ffffffff80000d48>] do_one_initcall+0x98/0x140
[    6.380000] [<ffffffff80000f38>] kernel_init_freeable+0x148/0x218
[    6.390000] [<ffffffff805ad19c>] kernel_init+0x18/0x114
[    6.390000] [<ffffffff80286cac>] ret_from_syscall+0xc/0x10
[    6.400000] ---[ end trace 8023adf5befc91e0 ]---

... that said, I am not confident my patch is the right fix. So
consider this a bug report + work-around only. :)

> Yeah, everything seems mostly working.  The "invalid BAR" things
> *could* be an issue -- those registers are not what the PCI spec says
> they should be.

The devices in question are:
04:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd.
RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 06)
06:00.0 SATA controller: Marvell Technology Group Ltd. 88SE9230 PCIe
SATA 6Gb/s Controller (rev 11)

I am going to plug them in to an Intel machine with 4.11 and see if I
get the same warnings.