Found and fixed the problem. In my case the kernel was trying to check
the secondary GUID partition table (GPT), where there was a bad sector -
in this case in the second-to-last sector on the disk (and outside of
all partitions). Except on my system there also was no GUID partition
table - no primary GPT, no secondary GPT, as it's using a standard old
msdos partition table. Parted has no problem seeing that as the case.
But the kernel - some bright programmer thought the kernel should not
only check for a primary GPT, but even after finding none there, and
even after booting using the msdos partition table, that the kernel
should obsess if it finds a bad sector where the secondary GPT would be
- if the system even had one - and try to read that sector again and
again, thus crippling the system for no good reason at all.

Anyway, "hdparm --repair-sector ######## --yes-i-know-what-i-am-doing
/dev/sda" totally fixed the problem.

In summary, GPT support has only shown up in more recent kernels. So if
other READ FPDMA QUEUED bug reports are right that it's more recent
kernels implicated, there's some chance that this brain-dead GPT code
has bitten more people than me. The question would be: is the sector
you're having trouble with after or before those allocated to your
partitions? If so, that would explain why running e2fsck -c isn't going
to fix them, and why the problem will persist even if your disk looks
clean. You can as it turns out confirm the bad sector with smartctl, and
it's folks on the list for that who pointed me towards the problem with
GPT - which of course I wasn't looking for because the system that had
the problem has never had a GPT.

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https://bugs.launchpad.net/bugs/550559

Title:
  hdd problems, failed command: READ FPDMA QUEUED

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