Possible store corrumption

Possible store corrumption

[Jack Hill]

Hi Guix,

I've run guix gc --verify and received the following output:

$ guix gc --verify
reading the store...
checking path existence...
path `/gnu/store/k5qxpr9wswli6lskpp433mrk0ffvxa9q-gcc-6.5.0.tar.xz.drv' disappeared, but it still has valid referrers!
path `/gnu/store/k5vl8jfhjasarib3ya4zpimxb1qm5hbj-expat-2.2.6-guile-builder' disappeared, but it still has valid referrers!
path `/gnu/store/k8r5c77rqzi2jg70x4sk2bf79q9gqbxn-python-minimal-wr?pper-3.7.0.drv' disappeared, removing from database...
path `/gnu/store?k8jx7nmx92dpr65gg2l3avajq4ngwxs7-zlib-1.2.11-guile-builder' is not in the store
path `/gn?/store/k681wjynl5pkmi8bdbbxxvdn2ljvq854-gnome-disk-utility-3.28.3' is not in the store
path `26478' is not in the store

At firt I suspected filesystem corruption, but my store is on btrfs and 
btrfs scrub reports no errors:

$ sudo ./btrfs scrub status /
scrub status for ffa898fe-cd24-400e-8bc7-1865643a2d45
 	scrub started at Mon May 20 16:15:36 2019 and finished after 00:00:42
 	total bytes scrubbed: 19.20GiB with 0 errors

guix gc fails with:

$ guix gc
finding garbage collector roots...
deleting garbage...
guix gc: error: executing SQLite query: database or disk is full

What might be causing these symptoms and how might I resolve them?

Best,
Jack

Re: Possible store corrumption

[Giovanni Biscuolo]

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Hi Jack,

Jack Hill <jackhill@jackhill.us> writes:

> I've run guix gc --verify and received the following output:
>
> $ guix gc --verify
> reading the store...
> checking path existence...
> path `/gnu/store/k5qxpr9wswli6lskpp433mrk0ffvxa9q-gcc-6.5.0.tar.xz.drv' disappeared, but it still has valid referrers!

[...]

> $ guix gc
> finding garbage collector roots...
> deleting garbage...
> guix gc: error: executing SQLite query: database or disk is full
>
> What might be causing these symptoms and how might I resolve them?

Could be a full disk issue?

If you use a dedicated volume for /gnu, what's the result of

 df -h | grep /gnu

?

Otherwise, the result of "df -h | grep /" ?

If your disk/volume is full: I never had similar issues so I cannot
help, I just suggest you to extend your volume if you can

HTH! Gio'.

[...]

-- 
Giovanni Biscuolo

Xelera IT Infrastructures

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Re: Possible store corrumption

[Jack Hill]

On Tue, 21 May 2019, Giovanni Biscuolo wrote:

> Could be a full disk issue?

In this case that was not true. It turned out to be bad memory. When I ran 
a memory test, it aborted do to too many errors, which is not a good sign 
☺. Therefore, I expect what was happening was that data was being 
corrupted in memory, and the bad data was begin written to disk.

Thanks for your help,
Jack