How do I fix a boot error: "failed command: READ FPDMA QUEUED"

Parsnip, thank you for your help!
OK, I'll give that a go. I did see that solution after some web searching, but I noted that after the boot disabled NCQ - see dmesg log above, line 5.077665- the error still came up 3 times more, so I thought I'd ask if there were other resolutions.
I found a command to disable NCQ- from the Wiki entry on Libata at https://ata.wiki.kernel.org/index.php/Libata_FAQ:
$ echo 1 > /sys/block/sdX/device/queue_depth

I wonder if you could help me, where do I put it (so to speak) so that it runs every boot?

Cheers,
Dan

BTW, this motherboard uses the AMD SB850 for SATA controller; and the problem has come up on my ssd system disk (OCZ Agility 30GB), my data disk (Hitachi P7K 500 GB) and my backup disk (an old Hitachi 2.5" 250 GB), not sure why it switches.
Dan

OK, I have puzzled it out... tried 3 methods and the third worked for me. Disabling NCQ on my SSD system disk (OCZ Agility) with the kernel command line solved the problem. Funny that the errors showed up first on my Hitachi spinning disk; then when I took it out, switched to the ssd. Oh well.

For other newbies with this problem:

The actual command is inserted in /etc/default/grub:

GRUB_CMDLINE_LINUX="libata.force=1.00:noncq"

where 1.00 is the ATA port and device number of the misbehaving drive.

Then in terminal run: "sudo update-grub" to make the changes.
Check the /boot/grub/grub.cfg file to see that the changes are in there. Presto, reboot!

New log results, see /var/log/dmesg:

[ 1.700190] ata1.00: FORCE: horkage modified (noncq)
[ 1.700368] ata1.00: HPA unlocked: 62531183 -> 62533296, native 62533296
[ 1.700395] ata1.00: ATA-8: OCZ-AGILITY, 1.6, max UDMA/133
[ 1.700421] ata1.00: 62533296 sectors, multi 1: LBA48 NCQ (not used)
[ 1.701750] ata2.00: HPA unlocked: 488388911 -> 488397168, native 488397168
[ 1.701972] ata2.00: ATA-8: Hitachi HTS543225L9A300, FBEOC40C, max UDMA/133
[ 1.701999] ata2.00: 488397168 sectors, multi 0: LBA48 NCQ (depth 31/32), AA
[ 1.702249] ata1.00: configured for UDMA/133
[ 1.703265] ata2.00: configured for UDMA/133
[ 1.711655] ata5.00: ATA-8: Hitachi HDP725050GLA360, GM4OA50E, max UDMA/133
[ 1.711683] ata5.00: 976773168 sectors, multi 0: LBA48 NCQ (depth 31/32), AA
[ 1.712694] ata5.00: configured for UDMA/133

Note: I only had to disable NCQ for the SSD (ATA1), no idea why the problem was showing up prior on the Hitachi drive (ATA5).

Thanks actionparsnip, that solved my question.

Great share, hopefully this will help others.

Glad you got the gold.

Today I have the boot issue again. It looks like the order that udev starts the controllers (if that's the right term) is somewhat arbitrary, so the ATA port assignments shift. Today, my SSD is ata3, not ata1, and so it started with NCQ and I got the errors and the boot delay.

My question now is, does anyone know of a way to disable NCQ with an option or rule for udev, so that it applies to all devices?

Here are two consecutive boots:
This one (yesterday) starts up AHCI first and gave the J-Micron PATA controller ata7&8:

[ 1.383604] udev: starting version 151
[ 1.403300] ahci 0000:00:11.0: version 3.0
[ 1.403311] alloc irq_desc for 19 on node 0
[ 1.403313] alloc kstat_irqs on node 0
[ 1.403322] ahci 0000:00:11.0: PCI INT A -> GSI 19 (level, low) -> IRQ 19
[ 1.403391] alloc irq_desc for 27 on node 0
[ 1.403392] alloc kstat_irqs on node 0
[ 1.403400] ahci 0000:00:11.0: irq 27 for MSI/MSI-X
[ 1.403481] ahci 0000:00:11.0: AHCI 0001.0200 32 slots 6 ports 6 Gbps 0x3f impl SATA mode
[ 1.403511] ahci 0000:00:11.0: flags: 64bit ncq sntf ilck pm led clo pmp pio slum part

This one (today) assigned the J-Micron first and gave it ata 1&2:
[ 1.383445] udev: starting version 151
[ 1.404241] pata_jmicron 0000:05:00.1: PCI INT B -> GSI 17 (level, low) -> IRQ 17
[ 1.404299] pata_jmicron 0000:05:00.1: setting latency timer to 64
[ 1.405248] ahci 0000:00:11.0: version 3.0
[ 1.405257] alloc irq_desc for 19 on node 0
[ 1.405258] alloc kstat_irqs on node 0
[ 1.405266] ahci 0000:00:11.0: PCI INT A -> GSI 19 (level, low) -> IRQ 19
[ 1.405331] alloc irq_desc for 27 on node 0
[ 1.405332] alloc kstat_irqs on node 0
[ 1.405339] ahci 0000:00:11.0: irq 27 for MSI/MSI-X
[ 1.405417] ahci 0000:00:11.0: AHCI 0001.0200 32 slots 6 ports 6 Gbps 0x3f impl SATA mode
[ 1.405447] ahci 0000:00:11.0: flags: 64bit ncq sntf ilck pm led clo pmp pio slum part

So because the grub command is specific to a numbered port (ata1), my boot problem reappears since the SSD is now on ata3.
More weird.

It's been a while since this thread was active, but it helped me out today.
> The actual command is inserted in /etc/default/grub:
> GRUB_CMDLINE_LINUX="libata.force=1.00:noncq"

This did it for me on Ubuntu 10.04

I had a world of weirdness with 11.04 and have gone retro to 10.04. I'll wait and see how 12.04 looks next year ;^)
I also realized something with my hardware (a CQ40 laptop with Hitachi ATA), that it didn't take well to the journaled file systems, so rolling back to the ext2 file system cleared up some grief, and with this fix I can now boot Ubuntu in less than a minute. Thanks DD!
Yeah, I should take this knowledge and try 11.04 again, but after having a 2-week hobby of re-installing and picking the nits out of the thing and having it go to doo-doo every time I think that's enough.

I ran into the same issue after upgrading from 14.04 to 16.04 64 bit and the line mentioned above did the trick.
Thank you very much for it. That shortens the booting at least by 30 seconds.