Zentyal Forum, Linux Small Business Server
Zentyal Server => Installation and Upgrades => Topic started by: scottdr on March 29, 2024, 11:29:26 pm
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I wanted to upload a PDF attachment to show dialogue boxes with this report, but was unable to do so. The PDF was 179KB but there was no upload space.
Hope it helps
My attempt at carrying out an upgrade to Zentyal Version 8 from an up to date version of Zentyal 7.1.1
Platform: QEMU-KVM Hypervsisor host on HPE Proliant DL380 Gen9 running Ubuntu 22.04.4 LTS server with updates to 28th March 2024 including ESM updates.
VM 8vCPU, 8G Ram scsi drives on *.qcow2 2 x virtio bridge network connections
The dialogue below is misleading as it suggests that the Upgrade is finished and you can click close, but leave it open, In a separate shell monitor dpkg.log for progress ‘tail -f /var/log/dkpg.log’
Even though it will display ‘Finishing the upgrade’ watch the dpkg.log for the update finished message before clicking on ‘Close’
From dkpg.log
Click Close on Upgrading to Zentyal 8.0 dialogue and then reboot the system.
A stop job for Zentyal will delay the reboot for 1min 30sec
When the system restarted, the Zentyal logger daemon repeatedly stopped and started which might be a clue to issues ahead.
On restart, the Dashboard looked OK, but the Antivirus service failed to start. Also, the mysql service also failed due to permission issues on lock directory and missing log folder /var/log/mysql
This prevented the zentyal-core update script running to complete the install process.
Mar 29 11:23:28 hcs-zentyal6 systemd[1]: mysql.service: Start request repeated too quickly.
Mar 29 11:23:28 hcs-zentyal6 systemd[1]: mysql.service: Failed with result 'exit-code'.
░░ Subject: Unit failed
░░ Defined-By: systemd
░░ Support: http://www.ubuntu.com/support
░░ The unit mysql.service has entered the 'failed' state with result 'exit-code'.
Mar 29 11:23:28 hcs-zentyal6 systemd[1]: Failed to start MySQL Community Server.
░░ Subject: A start job for unit mysql.service has failed
░░ Defined-By: systemd
░░ Support: http://www.ubuntu.com/support
░░ A start job for unit mysql.service has finished with a failure.
░░ The job identifier is 9012 and the job result is failed.
Setting up zentyal-core (8.0.0) ...
Connection DB Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
dpkg: error processing package zentyal-core (--configure):
installed zentyal-core package post-installation script subprocess returned error exit status 2
Errors were encountered while processing:
zentyal-core
E: Sub-process /usr/bin/dpkg returned an error code (1)
Had to create a folder for mysql /var/log/mysql and chown mysql to that folder for mysql to start
Now clamav failing
Unable to work out clamav issues
Removed Antivirus module from Zentyal and rebooted
Mysql failed again, so had to chown mysql /var/log/mysql
Setting up zentyal-core (8.0.0) ...
Synchronizing state of apparmor.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install disable apparmor
sed: can't read /etc/apt/apt.conf.d/20auto-upgrades: No such file or directory
dpkg: error processing package zentyal-core (--configure):
installed zentyal-core package post-installation script subprocess returned error exit status 2
Errors were encountered while processing:
zentyal-core
E: Sub-process /usr/bin/dpkg returned an error code (1)
Removed Antivirus module, mailfilter and antivirus
Unable to process /etc/apt/apt.conf.d/20auto-upgrades: No such file or directory
Gave up!! Reverted VM to V7.1.1 with no outstanding updates as at 29th March 2024
Hope this helps somebody.
Thank you Zentyal for the community version.
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Hi scottdr,
I have had the same issues although I didn’t close any dialog boxes until I was sure it had finished all tasks. Eventually you have to reboot into the new server and antivirus was stoped but the rest was working. I managed to set the 20autostart and 50xxxx files to get to work, but the update process of zentyal-core never finished and is now stuck on expecting the unattended package which is not installed and can not be installed because of the unfinished installation proces of zentyal-core. I think that this is the bottleneck of all the problems.
I would advise to install the Debian unattended package before upgrading to Zentyal 8. Probably this will help to upgrade without issues. Once I have fixed my upgrade I will check this approach but maybe someone has a chance to test this theory before I can.
I also hope the the Zentyal community finds a way to finish the stuck unattended installation so we don’t have to fall back or restore to the earlier version.
C.
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https://forum.zentyal.org/index.php/topic,35672.0.html
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Good morning,
Stuck there too...
sed: can't read /etc/apt/apt.conf.d/20auto-upgrades: No such file or directory <------- This file is provided by the .deb.package unattended-upgrades, which will be downloaded and installed manually.
dpkg: error processing package zentyal-core (--configure):
installed zentyal-core package post-installation script subprocess returned error exit status 2
Errors were encountered while processing:
zentyal-core
E: Sub-process /usr/bin/dpkg returned an error code (1)
Solution:
cd /tmp
sudo apt download unattended-upgrades
sudo dpkg -i unattended-upgrades.deb (fill correct name of the pack downloaded previously)
sudo dpkg zentyal-core --configure
The stalled deb packs and unfinished configs have just gone after that,
HTH,
RSalles
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Hi all,
First of all, thank you for reporting the issues you got during the upgrade. Unfortunately, in the tests we did before releasing the script, we did not encounter those errors. Could you tell me how was installed your Zentyal 7.1 server? I mean:
1. It was installed through the official Zentyal 7.1 ISO?
2. It was upgraded from other versions such as Zentyal 7.0, if so, what was the original version?
3. It was installed in a working Ubuntu Server or Ubuntu Desktop?
At this moment, we are working on fixing the following errors:
1. Mysql log directory (/var/log/mysql/).
2. Missing APT file (/etc/apt/apt.conf.d/20auto-upgrades)
Finally, about the Antivirus issue, do you have any log or something that we can analyze?
Best regards, Daniel Joven.
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Hi Daniel,
i updated my zentyal today with zentyal-core 7.1.2 and zentyal-core 8.0.1. The update process worked fine.
After that i restarted the server and e_mail, fetchmail and antivirus stoped working. After deinstall and reinstall the antivirus and mailfilter componets e-mail and fetchmail works fine.
Antivirus does not work. After restart the antivirus it seems to work for about 30 seconds. then the service stops again.
var/log/clamav/clamav.log tells the following:
Fri Apr 12 17:27:17 2024 -> +++ Started at Fri Apr 12 17:27:17 2024
Fri Apr 12 17:27:17 2024 -> Received 0 file descriptor(s) from systemd.
Fri Apr 12 17:27:17 2024 -> clamd daemon 0.103.11 (OS: linux-gnu, ARCH: x86_64, CPU: x86_64)
Fri Apr 12 17:27:17 2024 -> Log file size limited to 4294967295 bytes.
Fri Apr 12 17:27:17 2024 -> Reading databases from /var/lib/clamav
Fri Apr 12 17:27:17 2024 -> Not loading PUA signatures.
Fri Apr 12 17:27:17 2024 -> Bytecode: Security mode set to "TrustSigned".
Fri Apr 12 17:27:27 2024 -> Loaded 8690518 signatures.
Fri Apr 12 17:27:30 2024 -> ERROR: LOCAL: Socket file /var/run/clamav/clamd.ctl could not be bound: Permission denied
Regards
Charles
EDIT:
Changed the owner of /var/run/clamav to user "clamav" and it works for me (drwxr-xr-x 2 clamav root)
Charles
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Same symptoms here for Antivirus - start from GUI, stops after about 30 secs
Exact same log entry
The following file does not exist in my system:
/var/run/clamav/clamd.ctl
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Daniel Joven:
It install official Zentyal ISO :
- probably 5(...)->6(...)->7(...)->8 - problem with mysql and and missing apt
- 7(...)->8 problem with missing apt, mysql ok
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running the following and accepting defaults seems to do the trick:
dpkg-reconfigure clamav-daemon
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Hi,
We are debugging the antivirus issue, we believe three things should be analyzed:
1. The server was not rebooted after the upgrade, so the directory /var/run/clamav does not belong to the owner clamav.
2. You have a persistent stub and because of that, the module’s configuration is old.
3. ClamAV databases are not updated. It requires sudo freshclam
Meanwhile, we do the required tests, you should try the following:
1. Update the internal database:
sudo freshclam
2. Make sure the module is enabled through the Zentyal GUI.
3. Ensure the directory /var/run/clamav belongs to clamav as chapderprinz suggested.
sudo chown -R clamav /var/run/clamav/
4. Restart the module through the CLI:
sudo zs antivirus restart
If the issue persists, you can try to restart the service through Systemd and then, check the log files.
sudo systemctl restart clamav-daemon
sudo journalctl -u clamav-daemon
Log files:
- /var/log/zentyal/zentyal.log
- /var/log/syslog
- /var/log/clamav/clamav.log
Best regards, Daniel Joven.
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Hi,
We have updated the official documentation with the mentioned steps in my previous answer about the Antivirus module. Below you have the links.
* https://doc.zentyal.org/en/upgrade.html#antivirus-module
* https://doc.zentyal.org/es/upgrade.html#modulo-de-antivirus
Again, thank you for reporting the issues.
Best regards, Daniel Joven.
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Hi,
I made a upgrade by the web page official guide but the webmail module is disappeared after the upgrade, and when i try to reinstall it in that case i got the following error message:
The following packages have unmet dependencies:
libgnustep-base1.26 : Depends: gnustep-base-common (= 1.26.0-7) but 1.28.0-4build1 is to be installed
Depends: libicu66 (>= 66.1-1~) but it is not installable
Somebody can help in this case.
BR,
GáborS
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Hi,
I made a upgrade by the web page official guide but the webmail module is disappeared after the upgrade, and when i try to reinstall it in that case i got the following error message:
The following packages have unmet dependencies:
libgnustep-base1.26 : Depends: gnustep-base-common (= 1.26.0-7) but 1.28.0-4build1 is to be installed
Depends: libicu66 (>= 66.1-1~) but it is not installable
Somebody can help in this case.
BR,
GáborS
Hi Gábor,
Below you have a few questions that might help you to find the issue with the Webmail module:
1. Did you confirm that all the Zentyal packages are correctly installed and there is anything broken or removed?
dpkg -l | egrep ‘zen(buntu|tyal)-’
dpkg -l | egrep -v ‘^ii’
lsb_release -a
2. Did you ensure that you are using the right repositories? Perhaps you have an old Zentyal repository that is causing the issue.
sudo apt update
3. Did you check where the webmail module and its main dependency is going to be installed?
sudo apt policy zentyal-sogo
sudo apt policy sogo
sudo apt policy gnustep-base-common
Hope the above helps you.
Best regards, Daniel Joven.
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Hi Daniel,
I appreciate your help,
Before i started the upgrade I did all of the check steps and I didn't see any error
Yes, the proper and up-to-date repository data will be used.
The first time when I wrote I used a live server clone this server contains the webmail module and this module is actively used. But today I created an empty 7.0 server, during the upgrade from 7.0 to 8.0 I didn't experience any issues but when I tried to deploy the webmail module it showed same error
BR,
GáborS
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I had some issues after upgrading too, with both the Antivirus and MySQL, resolved with the help of steps provided by Daniel - thank you!
Hi,
We are debugging the antivirus issue, we believe three things should be analyzed:
1. The server was not rebooted after the upgrade, so the directory /var/run/clamav does not belong to the owner clamav.
Ensure the directory /var/run/clamav belongs to clamav as chapderprinz suggested.
sudo chown -R clamav /var/run/clamav/
4. Restart the module through the CLI:
sudo zs antivirus restart
... <snip> ..
Best regards, Daniel Joven.
That fixed the same antivirus issue for us.
And the MySQL error on trying to login:
2024/04/26 11:04:02 ERROR> MyDBEngine.pm:200 EBox::MyDBEngine::_connect - Connection DB Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
at Connection DB Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
at /usr/share/perl5/EBox/MyDBEngine.pm line 200
The following fixed that issue (copied from another post by Daniel and edited down a bit):
check mysql running status:
sudo systemctl status mysql
Status, inactive:
○ mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; disabled; vendor preset: enabled)
Active: inactive (dead)
If it is stopped (inactive), run the following commands:
mkdir /var/log/mysql/
chown -R mysql:adm /var/log/mysql
chmod -R 0770 /var/log/mysql
systemctl restart mysql
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Hi Daniel,
I appreciate your help,
Before i started the upgrade I did all of the check steps and I didn't see any error
Yes, the proper and up-to-date repository data will be used.
The first time when I wrote I used a live server clone this server contains the webmail module and this module is actively used. But today I created an empty 7.0 server, during the upgrade from 7.0 to 8.0 I didn't experience any issues but when I tried to deploy the webmail module it showed same error
BR,
GáborS
Hi,
The script uninstalls temporarily the zentyal-webmail package and installs it later. Also, it does a database backup and restores it, just to avoid any issues during this process. Unfortunately, without the required information, we cannot know what might happen in your upgrade. You must schedule another upgrade and in case you get the same error, you must run the mentioned commands and also, analyze the following log files:
- /var/log/zentyal/upgrade.log
- /var/log/zentyal/zentyal.log
- /var/log/dpkg.log
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I had some issues after upgrading too, with both the Antivirus and MySQL, resolved with the help of steps provided by Daniel - thank you!
Hi,
We are debugging the antivirus issue, we believe three things should be analyzed:
1. The server was not rebooted after the upgrade, so the directory /var/run/clamav does not belong to the owner clamav.
Ensure the directory /var/run/clamav belongs to clamav as chapderprinz suggested.
sudo chown -R clamav /var/run/clamav/
4. Restart the module through the CLI:
sudo zs antivirus restart
... <snip> ..
Best regards, Daniel Joven.
That fixed the same antivirus issue for us.
And the MySQL error on trying to login:
2024/04/26 11:04:02 ERROR> MyDBEngine.pm:200 EBox::MyDBEngine::_connect - Connection DB Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
at Connection DB Error: Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)
at /usr/share/perl5/EBox/MyDBEngine.pm line 200
The following fixed that issue (copied from another post by Daniel and edited down a bit):
check mysql running status:
sudo systemctl status mysql
Status, inactive:
○ mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; disabled; vendor preset: enabled)
Active: inactive (dead)
If it is stopped (inactive), run the following commands:
mkdir /var/log/mysql/
chown -R mysql:adm /var/log/mysql
chmod -R 0770 /var/log/mysql
systemctl restart mysql
Status Update on 29/04/2024 - issues returned
Issues continue: We have been getting intermittent network connectivity issues since the upgrade, with users on DHCP leased IP's. Static IP systems (couple of users and various printers and servers) seem unaffected - I am suspecting the DHCP, but not totally sure it is the issue. Our address elase time was very short (2 hours), so have updated this to a 24-hour lease duration.
Looking at the /var/log/syslog file we also see several entries for the following error that seems to relate to DNS:
Apr 29 09:28:43 titan sh[3185911]: ERROR(runtime): uncaught exception - (5, 'WERR_ACCESS_DENIED')
Apr 29 09:28:43 titan sh[3185911]: File "/usr/lib/python3/dist-packages/samba/netcmd/__init__.py", line 186, in _run
Apr 29 09:28:43 titan sh[3185911]: return self.run(*args, **kwargs)
Apr 29 09:28:43 titan sh[3185911]: File "/usr/lib/python3/dist-packages/samba/netcmd/dns.py", line 1235, in run
Apr 29 09:28:43 titan sh[3185911]: raise e
Apr 29 09:28:43 titan sh[3185911]: File "/usr/lib/python3/dist-packages/samba/netcmd/dns.py", line 1223, in run
Apr 29 09:28:43 titan sh[3185911]: dns_conn.DnssrvUpdateRecord2(dnsserver.DNS_CLIENT_VERSION_LONGHORN,
But are unsure if this had anyhting to do with the connectivity issues, as the entry occured again more recently in the file (12:17), but no-one raised query that it had given them a problem at that time.
Additionally, the AntiVirus and MySql issues returned on our PDC (which also runs the DHCP service), with the antivirus stopping and not restarting.
Tried to reset the permission on the clamav folder, but result was the directory not found:
sudo chown -R clamav /var/run/clamav/
chown: cannot access '/var/run/clamav/': No such file or directory
So as per the upgrade guidance instructions on https://doc.zentyal.org/en/upgrade.html#antivirus-module (https://doc.zentyal.org/en/upgrade.html#antivirus-module) re-ran the dpkg command for clamav:
sudo dpkg-reconfigure clamav-daemon
Service still failed to start. Result in the error log showed:
Mon Apr 29 11:48:30 2024 -> ERROR: LOCAL: Could not create socket directory: /var/run/clamav: Permission denied
47 Mon Apr 29 11:48:30 2024 -> ERROR: LOCAL: Socket file /var/run/clamav/clamd.ctl could not be bound: No such file or directory
I re-ran the clamav config
sudo dpkg-reconfigure clamav-daemon
This time, I selected YES to handling the configuration file automatically - the opposite to the upgrade guidance. Went through that accepting the defaults - it recreated the missing /var/run/clamav/ folder for us, and added the missing clamd.ctl file.
This seems to have sorted it, the service has remained running for the last 15 minutes...
MySQL
The mysql error occurred again when trying to check the DHCP module from the web admin (though the dashboard was displaying OK).
Checked the mysql status in CLI:
~$ sudo systemctl status mysql
[sudo] password for copeadmin:
○ mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; disabled; vendor preset: enabled)
Active: [b]inactive[/b] (dead)
Checked the current permissions in the mysql log directory:
~$ sudo ls -lh /var/log/mysql
total 12K
-rw-r----- 1 mysql adm 0 Apr 29 00:00 error.log
-rw-r----- 1 mysql adm 20 Apr 28 00:00 error.log.1.gz
-rw-r----- 1 mysql adm 20 Apr 27 00:00 error.log.2.gz
-rw-r----- 1 mysql mysql 942 Apr 26 19:05 error.log.3.gz
Note the difference in owner for file dated 26/04, when it ought to match the other 3 files (mysql:adm). This had previously been corrected on 26/04 in the morning. I had rebooted the server after office hours, but afraid I can't recall exact time - I don't think it was as late as 19:00 though.
So reapplied the permission chown commands:
sudo chown -R mysql:adm /var/log/mysql
sudo chmod -R 0770 /var/log/mysql
Result:
~$ sudo ls -lh /var/log/mysql
total 12K
-rwxrwx--- 1 mysql adm 0 Apr 29 00:00 error.log
-rwxrwx--- 1 mysql adm 20 Apr 28 00:00 error.log.1.gz
-rwxrwx--- 1 mysql adm 20 Apr 27 00:00 error.log.2.gz
-rwxrwx--- 1 mysql adm 942 Apr 26 19:05 error.log.3.gz
And then restarted mysql again.
sudo systemctl restart mysql
And check status again - OK:
~$ sudo systemctl status mysql
● mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; disabled; vendor preset: enabled)
Active: active (running) since Mon 2024-04-29 10:24:57 BST; 4s ago
Process: 3236229 ExecStartPre=/usr/share/mysql/mysql-systemd-start pre (code=exited, status=0/SUCCESS)
Main PID: 3236248 (mysqld)
Status: "Server is operational"
Tasks: 39 (limit: 7071)
Memory: 437.9M
CPU: 1.527s
CGroup: /system.slice/mysql.service
└─3236248 /usr/sbin/mysqld
So it's OK again for now - but worrying I had to re-apply the permission changes on the log directory again. I don't want to be having to re-apply this every day!
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Hi AlecM,
About the mysql issue, a few things I saw in your output:
1. The service is not enabled, so when the server is rebooted, it does not start.
# To confirm that it is disabled
sudo systemctl is-enabled mysql
# To enable
sudo systemctl enable mysql
2. The permission behavior is probably caused by logrotate, you can check this out by analyzing the configuration file /etc/logrotate.d/mysql-server
NOTE: You should check the permissions of the folder as well (sudo ls -ld /var/log/mysql/)
If it is possible, just fix step 1 and only check step 2 but do not make any changes, let’s see tomorrow when the system rotates the logs if the issue is fixed or if a change must be done in the mentioned configuration file.
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Thanks Daniel!
You were quite correct, our mysql was not set to start with the system.
~$ sudo systemctl is-enabled mysql
disabled
So enabled as you indicated:
~$ sudo systemctl enable mysql
Synchronizing state of mysql.service with SysV service script with /lib/systemd/systemd-sysv-install.
Executing: /lib/systemd/systemd-sysv-install enable mysql
Created symlink /etc/systemd/system/multi-user.target.wants/mysql.service → /lib/systemd/system/mysql.service.
Checked the permissions on the log folder - I think it's correct? (mysql:adm)
~$ sudo ls -ld /var/log/mysql/
drwxrwx--- 2 mysql adm 4096 Apr 30 00:00 /var/log/mysql/
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Hi Daniel,
Here is the requested logs...
https://nextcloud.bemutatjuk.eu/index.php/s/s83n9s4oc8rGLH2
Please let me know if you need more information in this case.
Hi Daniel,
I appreciate your help,
Before i started the upgrade I did all of the check steps and I didn't see any error
Yes, the proper and up-to-date repository data will be used.
The first time when I wrote I used a live server clone this server contains the webmail module and this module is actively used. But today I created an empty 7.0 server, during the upgrade from 7.0 to 8.0 I didn't experience any issues but when I tried to deploy the webmail module it showed same error
BR,
GáborS
Hi,
The script uninstalls temporarily the zentyal-webmail package and installs it later. Also, it does a database backup and restores it, just to avoid any issues during this process. Unfortunately, without the required information, we cannot know what might happen in your upgrade. You must schedule another upgrade and in case you get the same error, you must run the mentioned commands and also, analyze the following log files:
- /var/log/zentyal/upgrade.log
- /var/log/zentyal/zentyal.log
- /var/log/dpkg.log