[solved] update to 3.0.26 partially failed - any suggestions?

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pdwalker
Posts: 1038
Joined: 18 Mar 2015 09:16

[solved] update to 3.0.26 partially failed - any suggestions?

Post by pdwalker » 11 Jan 2018 08:56

[problem resolved - see my last post in this thread]

I just updated, and my EFA has partially blown up.

First I did a yum update and rebooted the server.

Next, I ran the update - and during the update, the server spontaneously rebooted.

After the reboot, the efa update appeared to complete without further error. I also added the symlink according to the post here: viewtopic.php?f=13&t=2892#p11492 then I rebooted one final time.

The end result is that I appear to be sending/receiving mail correctly, but the web interface is bust.

Code: Select all

[root@efa run]# service httpd start
Starting httpd: httpd: Syntax error on line 221 of /etc/httpd/conf/httpd.conf: 
Syntax error on line 9 of /etc/httpd/conf.d/php.conf: 
Cannot load /etc/httpd/modules/libphp7.so into server: libargon2.so.0: 
cannot open shared object file: No such file or directory
[FAILED]
I'm not sure what this libargon2 is, but it appears to be installed:

Code: Select all

[root@efa run]# yum list |grep argon
libargon2.x86_64                          20161029-2.el6.remi         installed
argon2.x86_64                             20161029-2.el6.remi         remi-safe
libargon2-devel.x86_64                    20161029-2.el6.remi         remi-safe
This may or my not be relevant. I see that php is upgraded, however running php from the command line results in this:
[root@efa log]# php --version

Code: Select all

PHP Warning:  PHP Startup: Unable to load dynamic library '/usr/lib64/php/modules/ldap' - /usr/lib64/php/modules/ldap: cannot open shared object file: No such file or directory in Unknown on line 0
PHP Warning:  PHP Startup: Unable to load dynamic library '/usr/lib64/php/modules/mbstring' - /usr/lib64/php/modules/mbstring: cannot open shared object file: No such file or directory in Unknown on line 0
PHP 5.3.3 (cli) (built: Mar 22 2017 12:27:09)
Copyright (c) 1997-2010 The PHP Group
Zend Engine v2.3.0, Copyright (c) 1998-2010 Zend Technologies
This is everything php related installed

Code: Select all

[root@efa log]# yum list |grep php|grep installed
php-cli.x86_64                            7.2.1-1.el6.remi            installed
php-common.x86_64                         7.2.1-1.el6.remi            installed
php-gd.x86_64                             7.2.1-1.el6.remi            installed
php-json.x86_64                           7.2.1-1.el6.remi            installed
php-mysqlnd.x86_64                        7.2.1-1.el6.remi            installed
php-pdo.x86_64                            7.2.1-1.el6.remi            installed
php-pecl-mcrypt.x86_64                    1.0.1-4.el6.remi.7.2        installed
php-pecl-zip.x86_64                       1.15.2-1.el6.remi.7.2       installed
php-xml.x86_64                            7.2.1-1.el6.remi            installed
I've attached the two log files, the earlier one from the failed updated caused by the reboot, and the second where things ran to completion.

If anyone has any suggestions or hints on how I can get apache running again, it would be greatly appreciated.
Attachments
update-2018-01-11-15-56-27.txt.zip
(3.47 KiB) Downloaded 5 times
update-2018-01-11-16-03-02.txt.zip
(3.06 KiB) Downloaded 6 times
Last edited by pdwalker on 12 Jan 2018 07:14, edited 3 times in total.

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pdwalker
Posts: 1038
Joined: 18 Mar 2015 09:16

[not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by pdwalker » 11 Jan 2018 09:10

ok, I was able to diagnose my own problem.

Since httpd was complaining about libargon2, and I couldn't find libargon2 on my server even though yum thought it was installed, I did a yum reinstall libargon2.

and lo and behold, libargon2 really came to be
and httpd was happy to run.

However, accessing the UI resulted in the following error:
The PHP extension xml is missing
which means I have at least more than one package not correctly installed but marked as installed.

Update to follow as I work through reinstalling the packages

User avatar
pdwalker
Posts: 1038
Joined: 18 Mar 2015 09:16

Re: [not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by pdwalker » 11 Jan 2018 09:41

I am able to reinstall the following packages

Code: Select all

yum reinstall libargon2
yum reinstall php-xml 
yum reinstall libxslt
yum reinstall php-mbstring
yum reinstall php-json
yum reinstall libmcrypt libwebp libxslt libzip5
yum reinstall php-ldap
yum reinstall gd-last
yum reinstall php-ldap
yum reinstall php-pecl-mcrypt
yum reinstall php-pecl-zip
yum reinstall php
yum reinstall php-mysqlnd
but the following packages results in lots of yum errors: php-cli php-common php-gd php-pdo
[root@efa modules]# yum reinstall php-common
Loaded plugins: fastestmirror, security
Setting up Reinstall Process
Loading mirror speeds from cached hostfile
* EFA: dl2.efa-project.org
* base: centos.uhost.hk
* epel: mirrors.nipa.cloud
* extras: centos.uhost.hk
* mariadb: nyc2.mirrors.digitalocean.com
* remi-php72: mirror.innosol.asia
* remi-safe: mirror.innosol.asia
* updates: mirrors.neusoft.edu.cn
Resolving Dependencies
--> Running transaction check
---> Package php-common.x86_64 0:5.3.3-49.el6 will be reinstalled
---> Package php-common.x86_64 0:7.2.1-1.el6.remi will be reinstalled
--> Processing Dependency: php-json(x86-64) = 7.2.1-1.el6.remi for package: php-common-7.2.1-1.el6.remi.x86_64
---> Package php-json.x86_64 0:7.2.1-1.el6.remi will be obsoleted
--> Processing Dependency: php-json(x86-64) = 7.2.1-1.el6.remi for package: php-common-7.2.1-1.el6.remi.x86_64
--> Processing Dependency: php-json(x86-64) = 7.2.1-1.el6.remi for package: php-common-7.2.1-1.el6.remi.x86_64
---> Package php-pecl-zip.x86_64 0:1.15.2-1.el6.remi.7.2 will be obsoleted
--> Finished Dependency Resolution
Error: Package: php-common-7.2.1-1.el6.remi.x86_64 (remi-php72)
Requires: php-json(x86-64) = 7.2.1-1.el6.remi
Removing: php-json-7.2.1-1.el6.remi.x86_64 (@remi-php72)
php-json(x86-64) = 7.2.1-1.el6.remi
Obsoleted By: php-common-5.3.3-49.el6.x86_64 (base)
Not found
Available: php-json-7.2.0-2.el6.remi.x86_64 (remi-php72)
php-json(x86-64) = 7.2.0-2.el6.remi
Error: Package: php-common-7.2.1-1.el6.remi.x86_64 (installed)
Requires: php-json(x86-64) = 7.2.1-1.el6.remi
Removing: php-json-7.2.1-1.el6.remi.x86_64 (@remi-php72)
php-json(x86-64) = 7.2.1-1.el6.remi
Obsoleted By: php-common-5.3.3-49.el6.x86_64 (base)
Not found
Available: php-json-7.2.0-2.el6.remi.x86_64 (remi-php72)
php-json(x86-64) = 7.2.0-2.el6.remi
You could try using --skip-broken to work around the problem
** Found 4 pre-existing rpmdb problem(s), 'yum check' output follows:
php-cli-7.2.1-1.el6.remi.x86_64 is a duplicate with php-cli-5.3.3-49.el6.x86_64
php-common-7.2.1-1.el6.remi.x86_64 is a duplicate with php-common-5.3.3-49.el6.x86_64
php-gd-7.2.1-1.el6.remi.x86_64 is a duplicate with php-gd-5.3.3-49.el6.x86_64
php-pdo-7.2.1-1.el6.remi.x86_64 is a duplicate with php-pdo-5.3.3-49.el6.x86_64
So it seems that rpm thinks that both the original and the newer package is installed. Lovely.

Any ideas on how to resolve this? I'm runninng a "yum check" but it's still running and I don't know how long it'll take to complete.

henk
Posts: 134
Joined: 14 Dec 2015 22:16

Re: [not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by henk » 11 Jan 2018 10:07

Rebooting during the upgrade..........

did you edit /etc/yum.conf and comment out the exclude?

# PUT YOUR REPOS HERE OR IN separate files named file.repo
# in /etc/yum.repos.d
#exclude=kernel* MariaDB* postfix* mailscanner* MailScanner* clamav* clamd* open-vm-tools*
#exclude=kernel* postfix* mailscanner* MailScanner* clamav* clamd* open-vm-tools*


yum list |grep php|grep installed list no packages at all

[root@sansspam ~]# yum list |grep argon
libargon2.x86_64 20161029-2.el6.remi @remi-safe
argon2.x86_64 20161029-2.el6.remi remi-safe
libargon2-devel.x86_64 20161029-2.el6.remi remi-safe

[root@sansspam ~]# yum list |grep php|grep installed

[root@sansspam ~]# yum list |grep php
* remi-php72: remi.mirror.wearetriple.com
php.x86_64 7.2.1-1.el6.remi @remi-php72
php-cli.x86_64 7.2.1-1.el6.remi @remi-php72
php-common.x86_64 7.2.1-1.el6.remi @remi-php72
php-gd.x86_64 7.2.1-1.el6.remi @remi-php72
php-json.x86_64 7.2.1-1.el6.remi @remi-php72
php-ldap.x86_64 7.2.1-1.el6.remi @remi-php72
php-mbstring.x86_64 7.2.1-1.el6.remi @remi-php72
php-mysqlnd.x86_64 7.2.1-1.el6.remi @remi-php72
php-pdo.x86_64 7.2.1-1.el6.remi @remi-php72
php-pecl-mcrypt.x86_64 1.0.1-4.el6.remi.7.2 @remi-php72
php-pecl-zip.x86_64 1.15.2-1.el6.remi.7.2 @remi-php72
php-xml.x86_64 7.2.1-1.el6.remi @remi-php72
apcu-panel.noarch 5.1.9-1.el6.remi.7.2 remi-php72
cups-php.x86_64 1:1.4.2-78.el6_9 updates
graphviz-php.x86_64 2.26.0-10.el6 base
phan.noarch 0.11.0-1.el6.remi.7.2 remi-php72
php-Analog.noarch 1.0.0-3.git9ab4c9e.el6 epel


however

[root@sansspam log]# yum list installed |grep php
php.x86_64 7.2.1-1.el6.remi @remi-php72
php-cli.x86_64 7.2.1-1.el6.remi @remi-php72
php-common.x86_64 7.2.1-1.el6.remi @remi-php72
php-gd.x86_64 7.2.1-1.el6.remi @remi-php72
php-json.x86_64 7.2.1-1.el6.remi @remi-php72
php-ldap.x86_64 7.2.1-1.el6.remi @remi-php72
php-mbstring.x86_64 7.2.1-1.el6.remi @remi-php72
php-mysqlnd.x86_64 7.2.1-1.el6.remi @remi-php72
php-pdo.x86_64 7.2.1-1.el6.remi @remi-php72
php-pecl-mcrypt.x86_64 1.0.1-4.el6.remi.7.2
@remi-php72
php-pecl-zip.x86_64 1.15.2-1.el6.remi.7.2
@remi-php72
php-xml.x86_64 7.2.1-1.el6.remi @remi-php72


My yum log showing a 2 stage update ( 3-1 and 6-1)

Jan 03 10:20:44 Updated: kernel-firmware-2.6.32-696.16.1.el6.noarch
Jan 03 10:20:52 Installed: kernel-2.6.32-696.16.1.el6.x86_64
Jan 03 10:20:53 Updated: kernel-headers-2.6.32-696.16.1.el6.x86_64
Jan 03 10:20:57 Installed: kernel-devel-2.6.32-696.16.1.el6.x86_64
Jan 03 10:25:51 Erased: kernel-devel
Jan 03 10:25:54 Erased: kernel
Jan 03 10:27:05 Updated: clamav-db-0.99.2-3.el6.x86_64
Jan 03 10:27:07 Updated: clamav-0.99.2-3.el6.x86_64
Jan 03 10:27:07 Updated: clamd-0.99.2-3.el6.x86_64
Jan 03 10:27:24 Updated: MailScanner-5.0.7-1.noarch
Jan 03 10:27:49 Installed: remi-release-6.9-1.el6.remi.noarch
Jan 03 10:28:11 Installed: php-json-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:11 Updated: php-common-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:11 Installed: libargon2-20161029-2.el6.remi.x86_64
Jan 03 10:28:13 Updated: php-cli-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:13 Updated: php-pdo-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:13 Installed: libwebp-0.4.3-3.el6.x86_64
Jan 03 10:28:13 Installed: gd-last-2.2.5-1.el6.remi.x86_64
Jan 03 10:28:13 Installed: libmcrypt-2.5.8-9.el6.x86_64
Jan 03 10:28:13 Installed: libzip5-1.4.0-2.el6.remi.x86_64
Jan 03 10:28:13 Installed: php-pecl-zip-1.15.2-1.el6.remi.7.2.x86_64
Jan 03 10:28:13 Installed: php-pecl-mcrypt-1.0.1-4.el6.remi.7.2.x86_64
Jan 03 10:28:13 Updated: php-gd-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:13 Installed: php-mysqlnd-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:14 Updated: php-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:14 Installed: php-ldap-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:14 Updated: php-mbstring-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:14 Installed: php-xml-7.2.0-2.el6.remi.x86_64
Jan 03 10:28:14 Erased: php-mysql
Jan 06 10:00:34 Updated: php-json-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:35 Updated: php-common-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:36 Updated: php-cli-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:36 Updated: php-pdo-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:42 Updated: kernel-firmware-2.6.32-696.18.7.el6.noarch
Jan 06 10:00:53 Installed: kernel-2.6.32-696.18.7.el6.x86_64
Jan 06 10:00:53 Updated: php-mysqlnd-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:54 Updated: php-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:54 Updated: php-ldap-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:54 Updated: php-xml-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:54 Updated: php-gd-7.2.1-1.el6.remi.x86_64
Jan 06 10:00:55 Updated: php-mbstring-7.2.1-1.el6.remi.x86_64
Jan 06 10:01:03 Installed: kernel-devel-2.6.32-696.18.7.el6.x86_64
Jan 06 10:01:03 Updated: 1:microcode_ctl-1.17-25.2.el6_9.x86_64
Jan 06 10:01:04 Updated: kernel-headers-2.6.32-696.18.7.el6.x86_64
Jan 06 10:55:04 Erased: kernel-devel
Jan 06 10:55:07 Erased: kernel

User avatar
pdwalker
Posts: 1038
Joined: 18 Mar 2015 09:16

Re: [not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by pdwalker » 11 Jan 2018 10:16

Hi henk,

the reboot during the upgrade wasn't intential. The server just... went away without warning.

As for yum.conf, the exclude line was empty, even before the upgrade. I don't know when that changed.

What version of centos are you running? Looks like 7 while I'm running 6 - which is why I think our yum commands differ.

I think my problem is a boggled up rpm installed package database. I've done some google searches and it's not an uncommon problem so I'll see of one of those solutions corrects my issue.

henk
Posts: 134
Joined: 14 Dec 2015 22:16

Re: [not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by henk » 11 Jan 2018 11:28

just kidding about the spontaneous rebout ;)

Due the errors ( full tekst index related) in mysql, I already upgraded only mysql before the upgrade.
viewtopic.php?f=13&t=2827

I also removed old kernels, to get some free space.

Code: Select all

package-cleanup --oldkernels --count=1
[root@sansspam log]# df -h
Filesystem Size Used Avail Use% Mounted on
/dev/mapper/vg_00-lv_root
7.8G 4.0G 3.5G 54% /
tmpfs 1.9G 64K 1.9G 1% /dev/shm
/dev/sda1 485M 39M 421M 9% /boot
/dev/mapper/vg_00-lv_tmp
976M 1.5M 924M 1% /tmp
/dev/mapper/vg_00-lv_var
86G 1.1G 80G 2% /var
none 1.9G 56K 1.9G 1% /var/spool/MailScanner/incoming


Could you repeat the upgrade?

I did stop cron,

Code: Select all

service crond stop 
service munin-node stop 
then upgraded. Don't want cron jobs ( or munin) during upgrade process!

Still on centos 6, wating for the centos7 version :)
[root@sansspam log]# cat /etc/centos-release
CentOS release 6.9 (Final)
[root@sansspam log]# uname -a
Linux sansspam.private.lan 2.6.32-696.18.7.el6.x86_64 #1 SMP Thu Jan 4 17:31:22 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

I wil take a look at the upgrade logs, and compare with my logs
Last edited by henk on 11 Jan 2018 13:12, edited 1 time in total.

henk
Posts: 134
Joined: 14 Dec 2015 22:16

Re: [not quite solved] update to 3.0.26 partially failed - any suggestions?

Post by henk » 11 Jan 2018 12:15

efa_update.zip
(4.48 KiB) Downloaded 5 times
just compared the logs. Checkout my log. (Stil using windooows,I Used Notepad++ to compare the 2 files)

We use different repos , should not be a prolem.

Due the unsheduled reboot, you could explain the next line:
There are unfinished transactions remaining. You might consider running yum-complete-transaction first to finish them.

Comparing the update proces will show quite some differences.

even the EFA upgrade script is different. ( left side is me)
update-2018-01-11-16-03-0.png
update-2018-01-11-16-03-0.png (27.79 KiB) Viewed 3174 times
in the first stage of the update, I do not have
* remi-php72: rpms.remirepo.net
* remi-safe: rpms.remirepo.net

my log
Cleaning repos: EFA base epel extras mariadb terabithia updates
Examining /var/tmp/yum-root-d2YhfH/remi-release-6.rpm: remi-release-6.9-1.el6.remi.noarch
Marking /var/tmp/yum-root-d2YhfH/remi-release-6.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package remi-release.noarch 0:6.9-1.el6.remi will be installed
--> Finished Dependency Resolution

your log
Cleaning repos: EFA base epel extras mariadb remi-php72 remi-safe updates
Examining /var/tmp/yum-root-jKZC0c/remi-release-6.rpm: remi-release-6.9-1.el6.remi.noarch
/var/tmp/yum-root-jKZC0c/remi-release-6.rpm: does not update installed package.

I miss this part after the Dependency Resolution in your log.

Installing:
php-ldap x86_64 7.2.0-2.el6.remi remi-php72 63 k
php-mysqlnd x86_64 7.2.0-2.el6.remi remi-php72 205 k
replacing php-mysql.x86_64 5.3.3-49.el6
php-pecl-mcrypt x86_64 1.0.1-4.el6.remi.7.2 remi-php72 26 k
php-pecl-zip x86_64 1.15.2-1.el6.remi.7.2 remi-php72 45 k
php-xml x86_64 7.2.0-2.el6.remi remi-php72 173 k
Updating:
php x86_64 7.2.0-2.el6.remi remi-php72 2.9 M
php-cli x86_64 7.2.0-2.el6.remi remi-php72 4.3 M
php-common x86_64 7.2.0-2.el6.remi remi-php72 1.0 M
php-gd x86_64 7.2.0-2.el6.remi remi-php72 69 k
Installing for dependencies:
gd-last x86_64 2.2.5-1.el6.remi remi-safe 128 k
libargon2 x86_64 20161029-2.el6.remi remi-safe 21 k
libmcrypt x86_64 2.5.8-9.el6 epel 96 k
libwebp x86_64 0.4.3-3.el6 epel 210 k
libzip5 x86_64 1.4.0-2.el6.remi remi-safe 60 k
php-json x86_64 7.2.0-2.el6.remi remi-php72 56 k
Updating for dependencies:
php-mbstring x86_64 7.2.0-2.el6.remi remi-php72 1.0 M
php-pdo x86_64 7.2.0-2.el6.remi remi-php72 108 k

User avatar
pdwalker
Posts: 1038
Joined: 18 Mar 2015 09:16

Re: [solved] update to 3.0.26 partially failed - any suggestions?

Post by pdwalker » 12 Jan 2018 07:13

Hi henk,

I am not sure why our upgrade scripts are different. There may have been a silent revision we weren't told about.

As for why my packages are different from yours, it could be because I've installed different things on my efa server over time, thus needing packages updated that you do not have installed. Just guessing, but it is a likely answer.

As for the solution:

Code: Select all

[root@efa modules]# yum check
Loaded plugins: fastestmirror, security

[after a very long time]

php-cli-7.2.1-1.el6.remi.x86_64 is a duplicate with php-cli-5.3.3-49.el6.x86_64
php-common-7.2.1-1.el6.remi.x86_64 is a duplicate with php-common-5.3.3-49.el6.x86_64
php-gd-7.2.1-1.el6.remi.x86_64 is a duplicate with php-gd-5.3.3-49.el6.x86_64
php-json-7.2.1-1.el6.remi.x86_64 is obsoleted by php-common-5.3.3-49.el6.x86_64
php-pdo-7.2.1-1.el6.remi.x86_64 is a duplicate with php-pdo-5.3.3-49.el6.x86_64
php-pecl-zip-1.15.2-1.el6.remi.7.2.x86_64 is obsoleted by php-common-5.3.3-49.el6.x86_64
Right, time to clean out those failed dupes

Code: Select all

[root@efa modules]# rpm -e --nodeps --justdb php-pecl-zip-1.15.2
[root@efa modules]# rpm -e --nodeps --justdb php-pdo-7.2.1
[root@efa modules]# rpm -e --nodeps --justdb php-json-7.2.1
[root@efa modules]# rpm -e --nodeps --justdb php-gd-7.2.1
[root@efa modules]# rpm -e --nodeps --justdb php-common-7.2.1
[root@efa modules]# rpm -e --nodeps --justdb php-cli-7.2.1
and then reinstall

Code: Select all

[root@efa modules]# yum update
[root@efa modules]# yum update php-pecl-zip
now apache is behaving, and php is now version 7.2.1

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