Re: [gentoo-user] Diagnosing file corruption

[Fernando Rodriguez]

On Wednesday, August 05, 2015 5:34:43 PM Bryan Gardiner wrote:
> Hello list,
>
> On my most recent update, I had some build failures that led me to
> find that some files on my root partition have been corrupted.  This
> is a new Asus N550JK laptop, a mostly-stable amd64 install with
> gentoo-sources-4.0.5 and ext4-root-in-LVM-in-LUKS-on-HDD, and Debian
> lives in there too (no problems showed up verifying Debian's packages;
> I installed Debian on Jul 1 and used it for a week before getting time
> to set up Gentoo).
>
> These are the package merge times, package names, and files that I
> found to be corrupted via qcheck (there were also a couple Python
> headers that I fixed by rebuilding).  They appear to be filled with
> random data.  The binpkg contents in /usr/portage/packages are okay,
> so I don't know when the files were corrupted; their mtimes haven't
> been updated since the packages were installed.
>
> Thu-Jul-30-22:40:23-2015 app-arch/p7zip-9.20.1-r5
/usr/lib64/p7zip/Lang/va.txt
> Thu-Jul-30-22:40:23-2015 app-arch/p7zip-9.20.1-r5
/usr/lib64/p7zip/help/cmdline/switches/large_pages.htm
> Sun-Jul-19-22:34:30-2015 dev-libs/libzip-1.0.1
/usr/share/man/man3/zip_error_get_sys_type.3.bz2
> Sun-Jul-26-22:35:28-2015 dev-python/pygments-2.0.1-r1
/usr/lib64/python2.7/site-packages/pygments/styles/pastie.pyc
> Wed-Jul-08-23:34:56-2015 media-libs/tiff-4.0.3-r6
/usr/share/man/man3/TIFFGetField.3tiff.bz2
> Thu-Jul-30-10:05:31-2015 sci-mathematics/scilab-5.5.2
/usr/share/scilab/modules/compatibility_functions/macros/%b_l_s.bin
> -(from-stage3-on-Jul-8)- sys-apps/acl-2.2.52-r1
/usr/share/man/man3/acl_set_file.3.bz2
>
> I haven't had any unclean shutdowns, it looks like OpenRC is
> unmounting things cleanly on shutdown, and suspend appears to work
> fine.
>
> After I make a fresh backup of my files, how would you recommend
> troubleshooting this?  Run memtest or a hard drive tester?  Since the
> files seemingly corrupted themselves after install without being
> touched, I'm highly suspicious of the hard drive, but would like to
> rule other things out (if say for example that CONFIG_X86_INTEL_PSTATE
> CPU clock booster is dangerous, or nvidia-drivers, or ...).  Haven't
> checked for corruption on /home yet.
>
> This is the disk:
>
>   *-disk
>     description: ATA Disk
>     product: ST1000LM024 HN-M
>     vendor: Seagate
>     physical id: 0.0.0
>     bus info: scsi@4:0.0.0
>     logical name: /dev/sda
>     version: 0001
>     size: 931GiB (1TB)
>     capabilities: gpt-1.00 partitioned partitioned:gpt
>     configuration: ansiversion=5
>     guid=xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx sectorsize=4096
>
> Thanks for any help you can provide,
> Bryan

You can use badblocks to rule out a bad drive (be sure to read the 
documentation first if you haven't). But I would guess that something LUKS 
related is more likely. There may be clues in your log files (probably around 
the time when you installed these packages).

-- 
Fernando Rodriguez