CentOS - Dec 2016 - Problem with yum on CentOS Linux release 7.2.1511 (Core) with 3.10.0-327.36.3.el7.x86_64 kernel

Everyone,

I am at a loss on this problem would appreciate some guidance as to
where to start to fix it.

I noticed that my home gateway server was not being updated with the
new kernel and other software, and when I ran yum it aborted with the
following notices.  I tried a yum clean all, but this did not fix the
problem.  I thought the problem may be related to one of the repos, but
I have other machines in the same network that update properly.  I
disabled all repos except the BASE to try to simply the problem and
still the same problem.

Any help would be appreciated.

Thanks,

Greg Ennis


Loaded plugins: aliases, changelog, fastestmirror, langpacks, product-
id, search-
??????????????: disabled-repos, subscription-manager, tmprepo, verify,
versionlock
This system is not registered with Subscription Management. You can use
subscription-manager to register.
base??????????????????????????????????????????????????????????| 3.6
kB??00:00:00?????
(1/2): base/7/x86_64/group_gz?????????????????????????????????| 155
kB??00:00:00?????
(2/2): base/7/x86_64/primary_db???????????????????????????????| 5.6
MB??00:00:01?????
Determining fastest mirrors
?* base: centos.mirror.lstn.net
Traceback (most recent call last):
? File "/usr/bin/yum", line 29, in <module>
????yummain.user_main(sys.argv[1:], exit_code=True)
? File "/usr/share/yum-cli/yummain.py", line 365, in user_main
????errcode = main(args)
? File "/usr/share/yum-cli/yummain.py", line 174, in main
????result, resultmsgs = base.doCommands()
? File "/usr/share/yum-cli/cli.py", line 573, in doCommands
????return self.yum_cli_commands[self.basecmd].doCommand(self,
self.basecmd, self.extcmds)
? File "/usr/share/yum-cli/yumcommands.py", line 500, in doCommand
????ret = base.updatePkgs(extcmds, update_to=(basecmd == 'update-to'))
? File "/usr/share/yum-cli/cli.py", line 1015, in updatePkgs
????self.update()
? File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 5114,
in update
????tx_return.extend(self.update(po=new))
? File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 5328,
in update
????available_pkg, updated_pkg)
? File "/usr/lib/python2.7/site-packages/yum/__init__.py", line 5033,
in _add_up_txmbr
????txmbr = self.tsInfo.addUpdate(upkg, ipkg)
? File "/usr/lib/python2.7/site-packages/yum/transactioninfo.py", line
518, in addUpdate
????self.add(txmbr)
? File "/usr/lib/python2.7/site-packages/yum/transactioninfo.py", line
289, in add
????self.addUpdated(oldpo, txmember.po)
? File "/usr/lib/python2.7/site-packages/yum/transactioninfo.py", line
547, in addUpdated
????txmbr = TransactionMember(po)
? File "/usr/lib/python2.7/site-packages/yum/transactioninfo.py", line
830, in __init__
????po.yumdb_info.get('from_repo')
? File "/usr/lib/python2.7/site-packages/yum/rpmsack.py", line 1946,
in
get
????res = self._read(attr)
? File "/usr/lib/python2.7/site-packages/yum/rpmsack.py", line 1861,
in
_read
????info = misc.stat_f(fn, ignore_EACCES=True)
? File "/usr/lib/python2.7/site-packages/yum/misc.py", line 962, in
stat_f
????return os.stat(filename)
OSError: [Errno 5] Input/output error:
'/var/lib/yum/yumdb/f/27ef8f508b150c2162f1bdcb1bc41713836b88ee-fence-
agents-ipdu-4.0.11-27.el7_2.9-x86_64/from_repo'

Am 14.12.2016 um 14:44 schrieb Gregory P. Ennis:
> Everyone,
>
> I am at a loss on this problem would appreciate some guidance as to
> where to start to fix it.
>
> I noticed that my home gateway server was not being updated with the
> new kernel and other software, and when I ran yum it aborted with the
> following notices.  I tried a yum clean all, but this did not fix the
> problem.  I thought the problem may be related to one of the repos, but
> I have other machines in the same network that update properly.  I
> disabled all repos except the BASE to try to simply the problem and
> still the same problem.
>
> Any help would be appreciated.
>
> Thanks,
>
> Greg Ennis
>
>
> Loaded plugins: aliases, changelog, fastestmirror, langpacks, product-
> id, search-
>               : disabled-repos, subscription-manager, tmprepo, verify,
> versionlock
> This system is not registered with Subscription Management. You can use
> subscription-manager to register.
> base                                                          | 3.6
> kB  00:00:00
> (1/2): base/7/x86_64/group_gz                                 | 155
> kB  00:00:00
> (2/2): base/7/x86_64/primary_db                               | 5.6
> MB  00:00:01
> Determining fastest mirrors
>  * base: centos.mirror.lstn.net
> Traceback (most recent call last):
[ ...
> OSError: [Errno 5] Input/output error:
> '/var/lib/yum/yumdb/f/27ef8f508b150c2162f1bdcb1bc41713836b88ee-fence-
> agents-ipdu-4.0.11-27.el7_2.9-x86_64/from_repo'
Such an I/O error indicates either a phyisical problem (storage broken) 
or filesystem full or read-only.

Do other opertions besides a "yum update" work properly? Specificly do
disk operations succeed?
Do you see any error messages in /var/log/messages respectively by 
"journalctl -b"?

Regards

Alexander

Am 14.12.2016 um 14:44 schrieb Gregory P. Ennis:
> Everyone,
>
> I am at a loss on this problem would appreciate some guidance as to
> where to start to fix it.
>
> I noticed that my home gateway server was not being updated with the
> new kernel and other software, and when I ran yum it aborted with the
> following notices.  I tried a yum clean all, but this did not fix the
> problem.  I thought the problem may be related to one of the repos, but
> I have other machines in the same network that update properly.  I
> disabled all repos except the BASE to try to simply the problem and
> still the same problem.
>
> Any help would be appreciated.
>
> Thanks,
>
> Greg Ennis
>
>
> Loaded plugins: aliases, changelog, fastestmirror, langpacks, product-
> id, search-
>               : disabled-repos, subscription-manager, tmprepo, verify,
> versionlock
> This system is not registered with Subscription Management. You can use
> subscription-manager to register.
> base                                                          | 3.6
> kB  00:00:00
> (1/2): base/7/x86_64/group_gz                                 | 155
> kB  00:00:00
> (2/2): base/7/x86_64/primary_db                               | 5.6
> MB  00:00:01
> Determining fastest mirrors
>  * base: centos.mirror.lstn.net
> Traceback (most recent call last):
[ ...
> OSError: [Errno 5] Input/output error:
> '/var/lib/yum/yumdb/f/27ef8f508b150c2162f1bdcb1bc41713836b88ee-fence-
> agents-ipdu-4.0.11-27.el7_2.9-x86_64/from_repo'
Such an I/O error indicates either a phyisical problem (storage broken) 
or filesystem full or read-only.

Do other opertions besides a "yum update" work properly? Specificly do
disk operations succeed?
Do you see any error messages in /var/log/messages respectively by 
"journalctl -b"?

Regards

Alexander


--------------------------------

Alexander,

Thanks for your assistance.  I have not identified any problems with the
drive, and have no difficulty reading or writing from the disc.  E-mail
is going in and out without a problem. I have not identified any other
problem with the machine.

The disc space seems ok to me, here is the result of df 

> [root at localhost ~]# df -v
> Filesystem                    1K-blocks      Used  Available Use% Mounted
on
> /dev/mapper/centos_hmwk-root   52403200  12425172   39978028  24% /
> devtmpfs                         863512         0     863512   0% /dev
> tmpfs                            879348         0     879348   0% /dev/shm
> tmpfs                            879348     58216     821132   7% /run
> tmpfs                            879348         0     879348   0%
/sys/fs/cgroup
> /dev/mapper/centos_hmwk-u0   1023500000 571429000  452071000  56% /u0
> /dev/mapper/centos_hmwk-u1   1023500000 160669800  862830200  16% /u1
> /dev/mapper/centos_hmwk-home   52403200     96148   52307052   1% /home
> /dev/mapper/centos_hmwk-u2   1023500000 310892544  712607456  31% /u2
> /dev/mapper/centos_hmwk-u3    213371092     34736  213336356   1% /u3
> /dev/mapper/centos_hmwk-u     511750000  66208428  445541572  13% /u
> /dev/sda2                        508588    366236     142352  73% /boot
> /dev/sda1                        204580      9640     194940   5% /boot/efi
> /dev/sdd1                    2884105400  53040472 2684536980   2%
/media/usbdrive
> tmpfs                            175872         0     175872   0%
/run/user/0

Am 14.12.2016 um 14:44 schrieb Gregory P. Ennis:
> Everyone,
> 
> I am at a loss on this problem would appreciate some guidance as to
> where to start to fix it.
> 
> I noticed that my home gateway server was not being updated with the
> new kernel and other software, and when I ran yum it aborted with the
> following notices.??I tried a yum clean all, but this did not fix the
> problem.??I thought the problem may be related to one of the repos,
> but
> I have other machines in the same network that update properly.??I
> disabled all repos except the BASE to try to simply the problem and
> still the same problem.
> 
> Any help would be appreciated.
> 
> Thanks,
> 
> Greg Ennis
> 
> 
> Loaded plugins: aliases, changelog, fastestmirror, langpacks,
> product-
> id, search-
> ??????????????: disabled-repos, subscription-manager, tmprepo,
> verify,
> versionlock
> This system is not registered with Subscription Management. You can
> use
> subscription-manager to register.
> base??????????????????????????????????????????????????????????| 3.6
> kB??00:00:00
> (1/2): base/7/x86_64/group_gz?????????????????????????????????| 155
> kB??00:00:00
> (2/2): base/7/x86_64/primary_db???????????????????????????????| 5.6
> MB??00:00:01
> Determining fastest mirrors
> ?* base: centos.mirror.lstn.net
> Traceback (most recent call last):
[ ...
> OSError: [Errno 5] Input/output error:
> '/var/lib/yum/yumdb/f/27ef8f508b150c2162f1bdcb1bc41713836b88ee-fence-
> agents-ipdu-4.0.11-27.el7_2.9-x86_64/from_repo'
Such an I/O error indicates either a phyisical problem (storage
broken)?
or filesystem full or read-only.

Do other opertions besides a "yum update" work properly? Specificly
do?
disk operations succeed?
Do you see any error messages in /var/log/messages respectively by?
"journalctl -b"?

Regards

Alexander

----------------------------------------------------------------------

Alexander,

After monitoring journalctl -b output, I am getting the following error
messages.  I am not sure what these error messages mean, but it causes
me to believe you are correct that I have a disc problem?  Is that
correct?

Greg


Dec 15 17:20:06 HmWk smartd[961]: Device: /dev/sda [SAT], 220 Currently
unreadable (pending) sectors
Dec 15 17:20:06 HmWk smartd[961]: Device: /dev/sda [SAT], 30 Offline
uncorrectable sectors

Dec 15 17:24:22 HmWk kernel: ata1.00: exception Emask 0x0 SAct 0x400000
SErr 0x40000 action 0x0
Dec 15 17:24:22 HmWk kernel: ata1.00: irq_stat 0x40000008
Dec 15 17:24:22 HmWk kernel: ata1: SError: { CommWake }
Dec 15 17:24:22 HmWk kernel: ata1.00: failed command: READ FPDMA QUEUED
Dec 15 17:24:22 HmWk kernel: ata1.00: cmd
60/08:b0:28:c4:cc/00:00:04:00:00/40 tag 22 ncq 4096 in
????????????????????????????????????????????????res
41/40:00:28:c4:cc/00:00:04:00:00/40 Emask 0x409 (media error) <F>
Dec 15 17:24:22 HmWk kernel: ata1.00: status: { DRDY ERR }
Dec 15 17:24:22 HmWk kernel: ata1.00: error: { UNC }

Dec 15 17:24:22 HmWk kernel: blk_update_request: I/O error, dev sda,
sector 80528424
Dec 15 17:24:22 HmWk kernel: ata1: EH complete
Dec 15 17:24:22 HmWk kernel: XFS (dm-1): metadata I/O error: block
0x4b6d428 ("xfs_trans_read_buf_map") error 5 numblks 8