Sebastiano Pilla
2011-Sep-14 21:56 UTC
[CentOS] 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 at 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 3\0\4\0\1\1\0@ \0\0\0\21\0\0\0\0"..., 1024) =
1024
_llseek(5, 2048, [2048], SEEK_SET) = 0
read(5,
"\r\0\0\0\0\4\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"...,
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, "\37\213\10\10\0\0\0\0\2\377/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.
Always Learning
2011-Sep-14 22:09 UTC
[CentOS] 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 ?
Craig White
2011-Sep-14 22:18 UTC
[CentOS] 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 at 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 3\0\4\0\1\1\0@ \0\0\0\21\0\0\0\0"..., 1024) = 1024 > _llseek(5, 2048, [2048], SEEK_SET) = 0 > read(5, > "\r\0\0\0\0\4\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0"..., > 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, "\37\213\10\10\0\0\0\0\2\377/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