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Old 09-14-2011, 09:56 PM
Sebastiano Pilla
 
Default Yum segmentation fault updating from 5.6 to 5.7

I'm trying to update my CentOS 5.6 boxes to 5.7, and on every single one
of them yum is failing with a segmentation fault: the error happens when
yum is checking the 'base' repository.

[root@picard yum]# yum update
Loaded plugins: downloadonly, fastestmirror, priorities
Determining fastest mirrors
* base: mirrors.ircam.fr
* extras: mirrors.ircam.fr
* updates: mirror.opendoc.net
base | 1.1 kB 00:00
base/primary | 961 kB 00:00
Segmentation fault

Running yum under strace produces lots of output, the last lines are:

access("/var/cache/yum/base/primary.xml.gz.sqlite-journal", F_OK) = -1
ENOENT (No such file or directory)
fstat64(5, {st_mode=S_IFREG|0644, st_size=20480, ...}) = 0
_llseek(5, 0, [0], SEEK_SET) = 0
read(5, "SQLite format 3411@ 21"..., 1024) = 1024
_llseek(5, 2048, [2048], SEEK_SET) = 0
read(5,
"
4"...,
1024) = 1024
fcntl64(5, F_SETLK64, {type=F_UNLCK, whence=SEEK_SET, start=0, len=0},
0xbf86a1c4) = 0
futex(0x7ba0918, FUTEX_WAKE_PRIVATE, 2147483647) = 0
stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
st_size=983757, ...}) = 0
stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
st_size=983757, ...}) = 0
stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
st_size=983757, ...}) = 0
open("/var/cache/yum/base/primary.xml.gz", O_RDONLY|O_LARGEFILE) = 6
_llseek(6, 0, [0], SEEK_CUR) = 0
read(6, "3721310102377/home/buildcentos/CENT"..., 8192) = 8192
--- SIGSEGV (Segmentation fault) @ 0 (0) ---
+++ killed by SIGSEGV +++

It seems that the primary.xml.gz file is somehow corrupted, but I've
already tried a "yum clean all" and a "rm -rf /var/cache/yum/*" without
success.

Apart from being at CentOS 5.6 and all having this problem, the boxes
have very few in common:

- 2 physical machine running 5.6 32-bit, one in my office, the other in
a datacenter
- 1 physical machine running 5.6 64-bit in another datacenter
- 2 KVM VPS running 5.6 32-bit in a third datacenter
- 1 Xen VPS running 5.6 64-bit in a fourth datacenter

There was a thread on the forum some months ago which mentioned this
same problem, but the original poster didn't find a solution (or if he
did, he didn't share it with the forum). Any suggestion is appreciated,
I cannot reinstall those boxes with 6.0 for at least 4/5 months.
_______________________________________________
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Old 09-14-2011, 10:09 PM
Always Learning
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Wed, 2011-09-14 at 23:56 +0200, Sebastiano Pilla wrote:
> I'm trying to update my CentOS 5.6 boxes to 5.7, and on every single one
> of them yum is failing with a segmentation fault: the error happens when
> yum is checking the 'base' repository.

Have you tried

yum clean all


followed by

yum update

?



_______________________________________________
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http://lists.centos.org/mailman/listinfo/centos
 
Old 09-14-2011, 10:18 PM
Craig White
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Sep 14, 2011, at 2:56 PM, Sebastiano Pilla wrote:

> I'm trying to update my CentOS 5.6 boxes to 5.7, and on every single one
> of them yum is failing with a segmentation fault: the error happens when
> yum is checking the 'base' repository.
>
> [root@picard yum]# yum update
> Loaded plugins: downloadonly, fastestmirror, priorities
> Determining fastest mirrors
> * base: mirrors.ircam.fr
> * extras: mirrors.ircam.fr
> * updates: mirror.opendoc.net
> base | 1.1 kB 00:00
> base/primary | 961 kB 00:00
> Segmentation fault
>
> Running yum under strace produces lots of output, the last lines are:
>
> access("/var/cache/yum/base/primary.xml.gz.sqlite-journal", F_OK) = -1
> ENOENT (No such file or directory)
> fstat64(5, {st_mode=S_IFREG|0644, st_size=20480, ...}) = 0
> _llseek(5, 0, [0], SEEK_SET) = 0
> read(5, "SQLite format 3411@ 21"..., 1024) = 1024
> _llseek(5, 2048, [2048], SEEK_SET) = 0
> read(5,
> "
4"...,
> 1024) = 1024
> fcntl64(5, F_SETLK64, {type=F_UNLCK, whence=SEEK_SET, start=0, len=0},
> 0xbf86a1c4) = 0
> futex(0x7ba0918, FUTEX_WAKE_PRIVATE, 2147483647) = 0
> stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
> st_size=983757, ...}) = 0
> stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
> st_size=983757, ...}) = 0
> stat64("/var/cache/yum/base/primary.xml.gz", {st_mode=S_IFREG|0644,
> st_size=983757, ...}) = 0
> open("/var/cache/yum/base/primary.xml.gz", O_RDONLY|O_LARGEFILE) = 6
> _llseek(6, 0, [0], SEEK_CUR) = 0
> read(6, "3721310102377/home/buildcentos/CENT"..., 8192) = 8192
> --- SIGSEGV (Segmentation fault) @ 0 (0) ---
> +++ killed by SIGSEGV +++
>
> It seems that the primary.xml.gz file is somehow corrupted, but I've
> already tried a "yum clean all" and a "rm -rf /var/cache/yum/*" without
> success.
>
> Apart from being at CentOS 5.6 and all having this problem, the boxes
> have very few in common:
>
> - 2 physical machine running 5.6 32-bit, one in my office, the other in
> a datacenter
> - 1 physical machine running 5.6 64-bit in another datacenter
> - 2 KVM VPS running 5.6 32-bit in a third datacenter
> - 1 Xen VPS running 5.6 64-bit in a fourth datacenter
>
> There was a thread on the forum some months ago which mentioned this
> same problem, but the original poster didn't find a solution (or if he
> did, he didn't share it with the forum). Any suggestion is appreciated,
> I cannot reinstall those boxes with 6.0 for at least 4/5 months.
----
make sure that there isn't any yum/rpm processes running...
ps aux|grep yum
ps aux|grep rpm

Once you've determined they aren't running, try...

yum clean metadata
yum clean dbcache

(those should be executed when you execute 'yum clean all' but maybe it ain't gettin' done)

and then
yum update

Craig

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Old 09-14-2011, 10:26 PM
Sebastiano Pilla
 
Default Yum segmentation fault updating from 5.6 to 5.7

Always Learning wrote:
> On Wed, 2011-09-14 at 23:56 +0200, Sebastiano Pilla wrote:
>> I'm trying to update my CentOS 5.6 boxes to 5.7, and on every single one
>> of them yum is failing with a segmentation fault: the error happens when
>> yum is checking the 'base' repository.
>
> Have you tried
>
> yum clean all
>
>
> followed by
>
> yum update
>
> ?

Yes, I've tried it, with the exact same result:

[root@picard ~]# yum clean all
Loaded plugins: downloadonly, fastestmirror, priorities
Cleaning up Everything
Cleaning up list of fastest mirrors
[root@picard ~]# yum update
Loaded plugins: downloadonly, fastestmirror, priorities
Determining fastest mirrors
* base: mirror.opendoc.net
* extras: mirror.opendoc.net
* updates: mirror.opendoc.net
base | 1.1 kB 00:00
base/primary | 961 kB 00:00
Segmentation fault

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Old 09-14-2011, 10:31 PM
Always Learning
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Thu, 2011-09-15 at 00:26 +0200, Sebastiano Pilla wrote:

> Always Learning wrote:
>>
> > Have you tried
> >
> > yum clean all
> >
> >
> > followed by
> >
> > yum update
> >
> > ?
>
> Yes, I've tried it, with the exact same result:
>
> [root@picard ~]# yum clean all
> Loaded plugins: downloadonly, fastestmirror, priorities
> Cleaning up Everything
> Cleaning up list of fastest mirrors
> [root@picard ~]# yum update
> Loaded plugins: downloadonly, fastestmirror, priorities
> Determining fastest mirrors
> * base: mirror.opendoc.net
> * extras: mirror.opendoc.net
> * updates: mirror.opendoc.net
> base | 1.1 kB 00:00
> base/primary | 961 kB 00:00
> Segmentation fault

Can you list, one line for each, the names of the repos
in /etc/yum.repos.d

And list the entire file for your BASE repo in /etc/yum/repos.d - it is
probably named something like

CentOS-Base.repo

Also can you do a

uname -a

and show us the result.

Curious!


--
With best regards,

Paul.
England,
EU.


_______________________________________________
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CentOS@centos.org
http://lists.centos.org/mailman/listinfo/centos
 
Old 09-14-2011, 10:35 PM
Sebastiano Pilla
 
Default Yum segmentation fault updating from 5.6 to 5.7

Always Learning wrote:
> On Thu, 2011-09-15 at 00:26 +0200, Sebastiano Pilla wrote:
>
> Can you list, one line for each, the names of the repos
> in /etc/yum.repos.d

[root@picard ~]# ll /etc/yum.repos.d/
total 20K
-rw-r--r-- 1 root root 1.9K Feb 8 2011 CentOS-Base.repo
-rw-r--r-- 1 root root 631 Feb 8 2011 CentOS-Debuginfo.repo
-rw-r--r-- 1 root root 626 Feb 8 2011 CentOS-Media.repo
-rw-r--r-- 1 root root 4.6K Feb 8 2011 CentOS-Vault.repo

>
> And list the entire file for your BASE repo in /etc/yum/repos.d - it is
> probably named something like
>
> CentOS-Base.repo

(there may be some additional line wrapping inserted by my mail client)

[root@picard ~]# cat /etc/yum.repos.d/CentOS-Base.repo
# CentOS-Base.repo
#
# The mirror system uses the connecting IP address of the client and the
# update status of each mirror to pick mirrors that are updated to and
# geographically close to the client. You should use this for CentOS
updates
# unless you are manually picking other mirrors.
#
# If the mirrorlist= does not work for you, as a fall back you can try the
# remarked out baseurl= line instead.
#
#

[base]
name=CentOS-$releasever - Base
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=os
#baseurl=http://mirror.centos.org/centos/$releasever/os/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#released updates
[updates]
name=CentOS-$releasever - Updates
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=updates
#baseurl=http://mirror.centos.org/centos/$releasever/updates/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#additional packages that may be useful
[extras]
name=CentOS-$releasever - Extras
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=extras
#baseurl=http://mirror.centos.org/centos/$releasever/extras/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#additional packages that extend functionality of existing packages
[centosplus]
name=CentOS-$releasever - Plus
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=centosplu s
#baseurl=http://mirror.centos.org/centos/$releasever/centosplus/$basearch/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#contrib - packages by Centos Users
[contrib]
name=CentOS-$releasever - Contrib
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=contrib
#baseurl=http://mirror.centos.org/centos/$releasever/contrib/$basearch/
gpgcheck=1
enabled=0
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5


> Also can you do a
>
> uname -a
>
> and show us the result.

[root@picard ~]# uname -a
Linux picard.home.lan 2.6.18-238.19.1.el5 #1 SMP Fri Jul 15 07:32:29 EDT
2011 i686 i686 i386 GNU/Linux

Thank you very much for your help.

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Old 09-14-2011, 10:48 PM
Always Learning
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Thu, 2011-09-15 at 00:35 +0200, Sebastiano Pilla wrote:

> Thank you very much for your help.

Please do not forget I am a Learner, not an expert :-)

Please try one thing for me

yum install httpd

It does not matter whether or not you have this already installed. I am
curious to know what type of response you get. You do not have to
install this. It is the reaction from yum that interests me, so you can
reject the installation - if it works.



--
With best regards,

Paul.
England,
EU.


_______________________________________________
CentOS mailing list
CentOS@centos.org
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Old 09-14-2011, 10:49 PM
Keith Roberts
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Thu, 15 Sep 2011, Sebastiano Pilla wrote:

> -rw-r--r-- 1 root root 4.6K Feb 8 2011 CentOS-Vault.repo

Do you need CentOS-Vault, as it includes all the packages
from Centos 5.x upwards IIRC?

Keith

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Old 09-14-2011, 11:01 PM
Always Learning
 
Default Yum segmentation fault updating from 5.6 to 5.7

On Thu, 2011-09-15 at 00:35 +0200, Sebastiano Pilla wrote:

> [root@picard ~]# ll /etc/yum.repos.d/
> total 20K
> -rw-r--r-- 1 root root 1.9K Feb 8 2011 CentOS-Base.repo
> -rw-r--r-- 1 root root 631 Feb 8 2011 CentOS-Debuginfo.repo
> -rw-r--r-- 1 root root 626 Feb 8 2011 CentOS-Media.repo
> -rw-r--r-- 1 root root 4.6K Feb 8 2011 CentOS-Vault.repo

Please add an extra repo to the same directory

name: (your own choice) - something like this: centos-cr.repo

---------------contents---------------------

# CentOS-CR.repo
#
# The continuous release ( CR ) repository contains rpms from the
# next point release of CentOS, which isnt itself released as yet.
#
# Look at http://wiki.centos.org/AdditionalResources/Repositories/CR
# for more details about how this repository works and what users
# should expect to see included / excluded

[cr]
name=CentOS-$releasever - CR
baseurl=http://mirror.centos.org/centos/$releasever/cr/$basearch/
gpgcheck=1
enabled=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5


-------end------------------ (do not include this line)

and try again

yum clean all
yum install httpd

and see what happens.



--
With best regards,

Paul.
England,
EU.


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Old 09-15-2011, 06:19 AM
Sebastiano Pilla
 
Default Yum segmentation fault updating from 5.6 to 5.7

Always Learning wrote:
> Please try one thing for me
>
> yum install httpd
>
> It does not matter whether or not you have this already installed. I am
> curious to know what type of response you get. You do not have to
> install this. It is the reaction from yum that interests me, so you can
> reject the installation - if it works.

Same result:

[root@picard ~]# yum install httpd
Loaded plugins: downloadonly, fastestmirror, priorities
Loading mirror speeds from cached hostfile
* base: mirror.opendoc.net
* extras: mirror.opendoc.net
* updates: mirror.opendoc.net
base | 1.1 kB 00:00
Segmentation fault

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