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Old 09-15-2011, 10:31 PM
Craig White
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Sep 15, 2011, at 3:22 PM, Sebastiano Pilla wrote:

> Josh Miller wrote:
>> On 09/15/2011 02:45 PM, Sebastiano Pilla wrote:
>>> Craig White wrote:
>>>> mv /var/cache/yum/base/primary.xml.gz/sqlite /tmp
>>>>
>>>> and try again I suppose - yes, that file is supposed to be much larger - I suspect that it will create a new 'copy' of that file if it fails to find it.
>>> Unfortunately yum recreates the same corrupted file, even if I move it
>>> out or delete it:
>>
>> Are you behind a proxy?
>
> No, there are no proxies between this box and the Internet (and all the
> other boxes where the same problem appears aren't behind proxies either).
>
> Based on what I'm seeing, I do not think that yum is downloading a
> corrupt sqlite database, rather than it is creating a corrupt database
> all by itself. I have however no definite confirmation of this and I
> would like to have one before filing a bug against yum.
----
I would agree with your assessment but perhaps you can remove/reinstall sqlite but the thing that I don't understand is you said there was no output from rpm -Va which should mean that the sqlite installed verified correctly so there's no reason to be optimistic that removing/reinstalling sqlite will have any positive impact.

Also note - you can file a bug against yum but I suspect that it will go nowhere because there are so many installations that haven't had this issue and yet you suggested that you have multiple systems exhibiting this same problem which suggests that there's something in the methodologies you employ.

Craig
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Old 09-15-2011, 11:05 PM
Kahlil Hodgson
 
Default Yum segmentation fault updating from 5.6 to 5.7

On 16/09/11 08:22, Sebastiano Pilla wrote:
> Based on what I'm seeing, I do not think that yum is downloading a
> corrupt sqlite database, rather than it is creating a corrupt database
> all by itself. I have however no definite confirmation of this and I
> would like to have one before filing a bug against yum.

Perhaps some python/sqlite/gzip library used by yum is
broken/incompatible. Do you have anything under /usr/local that may be
overriding the distro packages? Perhaps an NFS mount that is shared by
all affected servers?

Kal
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Old 09-16-2011, 01:15 PM
 
Default Yum segmentation fault updating from 5.6 to 5.7

Kahlil Hodgson wrote:
> On 16/09/11 08:22, Sebastiano Pilla wrote:
>> Based on what I'm seeing, I do not think that yum is downloading a
>> corrupt sqlite database, rather than it is creating a corrupt database
>> all by itself. I have however no definite confirmation of this and I
>> would like to have one before filing a bug against yum.
>
> Perhaps some python/sqlite/gzip library used by yum is
> broken/incompatible. Do you have anything under /usr/local that may be
> overriding the distro packages? Perhaps an NFS mount that is shared by
> all affected servers?

Has anyone in this thread - I may have missed some posts last night -
suggested yum reinstall yum?

mark

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Old 09-16-2011, 01:25 PM
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Fri, 16 Sep 2011 09:15:23 -0400, m.roth@5-cent.us wrote:
> Has anyone in this thread - I may have missed some posts last night -
> suggested yum reinstall yum?

This wasn't suggested yet, so I've tried it and it fails in the same
way (not unexpectedly, I would say):

[root@picard ~]# yum reinstall yum
Loaded plugins: downloadonly, fastestmirror, priorities
Setting up Reinstall Process
Determining fastest mirrors
* base: mirrors.ircam.fr
* updates: mirrors.ircam.fr
base | 1.1 kB 00:00
base/primary | 961 kB 00:02
Segmentation fault

Trying again without plugins:

[root@picard ~]# yum clean all
Loaded plugins: downloadonly, fastestmirror, priorities
Cleaning up Everything
Cleaning up list of fastest mirrors
[root@picard ~]# yum --noplugins reinstall yum
Setting up Reinstall Process
base | 1.1 kB 00:00
base/primary | 961 kB 00:01
Segmentation fault
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Old 09-16-2011, 01:38 PM
 
Default Yum segmentation fault updating from 5.6 to 5.7

sebastiano@datafaber.net wrote:
> On Fri, 16 Sep 2011 09:15:23 -0400, m.roth@5-cent.us wrote:
>> Has anyone in this thread - I may have missed some posts last night -
>> suggested yum reinstall yum?
>
> This wasn't suggested yet, so I've tried it and it fails in the same
> way (not unexpectedly, I would say):

Next thought: d/l the rpm for yum, uninstall yum via rpm -e, and then
install it via rpm -Ivh

mark

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Old 09-16-2011, 01:39 PM
 
Default Yum segmentation fault updating from 5.6 to 5.7

sebastiano@datafaber.net wrote:
> On Fri, 16 Sep 2011 09:15:23 -0400, m.roth@5-cent.us wrote:
>> Has anyone in this thread - I may have missed some posts last night -
>> suggested yum reinstall yum?
>
> This wasn't suggested yet, so I've tried it and it fails in the same
> way (not unexpectedly, I would say):

Oh, *right*: before you reinstall, try rpm --rebuilddb.

Also, have you seen any errors in messages?

mark

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Old 09-16-2011, 01:51 PM
William Hooper
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Thu, Sep 15, 2011 at 9:18 AM, <sebastiano@datafaber.net> wrote:
[snip]
> So either several mirrors all have the same corrupted file, or my box
> is generating a corrupted file each time. I would tend towards the
> second hypothesis, since other people have successfully updated their
> 5.6 installations to 5.7.

Have you added any non-CentOS versions of any of the packages that yum
uses (python, sqlite, etc)?

--
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Old 09-16-2011, 03:26 PM
 
Default Yum segmentation fault updating from 5.6 to 5.7

I've finally managed to update one of my boxes to 5.7. I did it in a
very roundabout way, which however confirms that at least in my boxes
there's something wrong in the way yum creates the sqlite databases.

I've basically followed the guide at
http://wiki.centos.org/HowTos/CreateLocalMirror to create my own mirror
of the 5.7 'os' and 'updates' directories, created the yum repository
with 'createrepo -d' to pre-create the sqlite database and made this
mirror accessible to the other boxes via HTTP.

I then created a /etc/yum.repos.d/Local.repo file which specifies my
private mirror for the [base] and [updates] repositories, commented out
everything in the /etc/yum.repos.d/CentOS-Base.repo and ran

yum clean all
yum update

Everything updated flawlessly and the box restarted normally with the
newer kernel.

Now, this doesn't solve the original yum problem, but at least confirms
that the creation of a corrupted sqlite database was indeed the real
issue.

Many thanks to all the people on the list who have suggestions and
advice, particularly to Alain Péan who pointed me in the right
direction.

Have a nice weekend
Sebastiano Pilla
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Old 09-16-2011, 04:33 PM
Alain Péan
 
Default Yum segmentation fault updating from 5.6 to 5.7

Le 16/09/2011 17:26, sebastiano@datafaber.net a écrit :
> Many thanks to all the people on the list who have suggestions and
> advice, particularly to Alain Péan who pointed me in the right
> direction.

You are welcome, but I don't know how my suggestions lead you to the
idea to setup a local repo

But I am glad it is working now for you.

Cheers,
Alain

--
================================================== ========
Alain Péan - LPP/CNRS
Administrateur Système/Réseau
Laboratoire de Physique des Plasmas - UMR 7648
Observatoire de Saint-Maur
4, av de Neptune, Bat. A
94100 Saint-Maur des Fossés
Tel : 01-45-11-42-39 - Fax : 01-48-89-44-33
================================================== ========

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Old 09-16-2011, 06:16 PM
"Denniston, Todd A CIV NAVSURFWARCENDIV Crane"
 
Default Yum segmentation fault updating from 5.6 to 5.7

> -----Original Message-----
> From: centos-bounces@centos.org [mailto:centos-bounces@centos.org] On
> Behalf Of sebastiano@datafaber.net
> Sent: Friday, September 16, 2011 11:27
> To: centos@centos.org
> Subject: Re: [CentOS] Yum segmentation fault updating from 5.6 to 5.7
>
> I've finally managed to update one of my boxes to 5.7. I did it in a
> very roundabout way, which however confirms that at least in my boxes
> there's something wrong in the way yum creates the sqlite databases.
>
> I've basically followed the guide at
> http://wiki.centos.org/HowTos/CreateLocalMirror to create my own mirror

Which uses rsync instead of http.

> of the 5.7 'os' and 'updates' directories, created the yum repository
> with 'createrepo -d' to pre-create the sqlite database and made this
> mirror accessible to the other boxes via HTTP.
>
> I then created a /etc/yum.repos.d/Local.repo file which specifies my
> private mirror for the [base] and [updates] repositories, commented out
> everything in the /etc/yum.repos.d/CentOS-Base.repo and ran
>
> yum clean all
> yum update
>
> Everything updated flawlessly and the box restarted normally with the
> newer kernel.
>
> Now, this doesn't solve the original yum problem, but at least confirms
> that the creation of a corrupted sqlite database was indeed the real
> issue.
>
> Many thanks to all the people on the list who have suggestions and
> advice, particularly to Alain Péan who pointed me in the right
> direction.
>

For, what to me is, an interesting data point, I would suggest doing the following now that you have a local known good copy:
On a machine that was still faulting:

for i in /var/cache/yum/base/
/PATHTOLOCALREPO/5.7/os/<arch>/repodata/
/var/cache/yum/updates/
/PATHTOLOCALREPO/5.7/updates/<arch>/repodata/
do
ls -l $i
md5sum $i/*
done
#you may want to unroll the for, into four terminals, for your own sanity.
#you'll have two sqlite files in each /var/cache dirs you can ignore

My bet... some isp between you and the internet is transparent proxying*** to reduce their downloading bandwidth, and they keep cache too long, the error will clear just as soon as their cache clears or you force it by wgeting the broken file with the --no-cache flag. [got the tee-shirt]

But now that you have a local mirror, the updates should go faster in the future.

*** I know you keep indicating no proxy is _known_ to you in the path to the mirrors, but it is pretty much the only thing that makes any sense.
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