Ubuntu
mysql-8.0 package

package mysql-server-8.0 8.0.19-0ubuntu0.19.10.3 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1

Bug #1864958 reported by Andy Wylde on 2020-02-27

This bug report is a duplicate of: Bug #1612517: Server fails to start after upgrade because of customized config and obsolete/renamed directives. Edit Remove

This bug affects 10 people

Affects		Status	Importance	Assigned to	Milestone
	mysql-8.0 (Ubuntu)	Incomplete	Undecided	Lars Tangvald

Bug Description

Setting up mysql-server-8.0 (8.0.19-0ubuntu0.19.10.3) ...
Renaming removed key_buffer and myisam-recover options (if present)
mysqld will log errors to /var/log/mysql/error.log
2020-02-27T06:03:40.533679Z 0 [ERROR] [MY-010946] [Server] Failed to start mysqld daemon. Check mysqld error log.
Warning: Unable to start the server.
Job for mysql.service failed because the control process exited with error code.
See "systemctl status mysql.service" and "journalctl -xe" for details.
invoke-rc.d: initscript mysql, action "start" failed.
● mysql.service - MySQL Community Server
   Loaded: loaded (/lib/systemd/system/mysql.service; enabled; vendor preset: enabled)
   Active: activating (auto-restart) (Result: exit-code) since Wed 2020-02-26 23:03:56 MST; 13ms ago
  Process: 39335 ExecStartPre=/usr/share/mysql/mysql-systemd-start pre (code=exited, status=0/SUCCESS)
  Process: 39356 ExecStart=/usr/sbin/mysqld (code=exited, status=1/FAILURE)
Main PID: 39356 (code=exited, status=1/FAILURE)
   Status: "Data Dictionary upgrade from MySQL 5.7 in progress"
invoke-rc.d: release upgrade in progress, error is not fatal
Setting up mysql-server (8.0.19-0ubuntu0.19.10.3) ...

Upgrade complete

The upgrade has completed but there were errors during the upgrade
process.

ProblemType: Package
DistroRelease: Ubuntu 19.10
Package: mysql-server-8.0 8.0.19-0ubuntu0.19.10.3
ProcVersionSignature: Ubuntu 5.0.0-38.41-generic 5.0.21
Uname: Linux 5.0.0-38-generic x86_64
ApportVersion: 2.20.11-0ubuntu8.4
Architecture: amd64
Date: Wed Feb 26 22:57:41 2020
ErrorMessage: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1
Logs.var.log.daemon.log:

MySQLConf.etc.mysql.conf.d.mysql.cnf: [mysql]
MySQLConf.etc.mysql.conf.d.mysqldump.cnf:
[mysqldump]
quick
quote-names
max_allowed_packet = 16M
MySQLConf.etc.mysql.mysql.conf.d.mysqld_safe_syslog.cnf:
[mysqld_safe]
syslog
MySQLVarLibDirListing: ['debian-5.7.flag', 'auto.cnf', 'chillercity.tar.gz', 'server-cert.pem', 'chiller', 'mysql', 'ib_buffer_pool', 'client-cert.pem', 'mysql_upgrade_info', 'ca-key.pem', 'Quickbooks', 'Chiller', 'performance_schema', 'binlog.index', 'ca.pem', 'IP_Phones', 'private_key.pem', 'ib_logfile0', 'server-key.pem', 'public_key.pem', 'voce_test', 'chillercity', '#innodb_temp', 'sys', 'Chiller.tar.gz', 'client-key.pem', 'ibdata1', 'ib_logfile1', 'Interwrx_Support', 'voip_billing']
ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-5.0.0-38-generic root=UUID=6670a550-b39f-11e8-9502-00155d0aa50e ro maybe-ubiquity
Python3Details: /usr/bin/python3.7, Python 3.7.5, python3-minimal, 3.7.5-1
PythonDetails: /usr/bin/python2.7, Python 2.7.17, python-minimal, 2.7.17-1
RelatedPackageVersions:
dpkg 1.19.7ubuntu2
apt 1.9.4
SourcePackage: mysql-8.0
Title: package mysql-server-8.0 8.0.19-0ubuntu0.19.10.3 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1
UpgradeStatus: Upgraded to eoan on 2020-02-27 (0 days ago)
modified.conffile..etc.mysql.mysql.conf.d.mysqld.cnf: [modified]
mtime.conffile..etc.mysql.mysql.conf.d.mysqld.cnf: 2020-02-26T22:57:10.341115

Tags:

Revision history for this message

Andy Wylde (andywylde) wrote on 2020-02-27:

.etc.apparmor.d.usr.sbin.mysqld.txt Edit (2.0 KiB, text/plain; charset="utf-8")
AptOrdering.txt Edit (21.9 KiB, text/plain; charset="utf-8")
AuditLog.txt Edit (466.6 KiB, text/plain; charset="utf-8")
Dependencies.txt Edit (2.2 KiB, text/plain; charset="utf-8")
Df.txt Edit (463 bytes, text/plain; charset="utf-8")
Dmesg.txt Edit (51.0 KiB, text/plain; charset="utf-8")
DpkgHistoryLog.txt Edit (72.8 KiB, text/plain; charset="utf-8")
DpkgTerminalLog.txt Edit (125.9 KiB, text/plain; charset="utf-8")
DuplicateSignature.txt Edit (2.0 KiB, text/plain; charset="utf-8")
KernLog.txt Edit (3.2 KiB, text/plain; charset="utf-8")
Logs.var.log.mysql.error.log.txt Edit (89.2 KiB, text/plain; charset="utf-8")
MySQLConf.etc.mysql.my.cnf.txt Edit (682 bytes, text/plain; charset="utf-8")
MySQLConf.etc.mysql.mysql.cnf.txt Edit (682 bytes, text/plain; charset="utf-8")
MySQLConf.etc.mysql.mysql.conf.d.mysql.cnf.txt Edit (132 bytes, text/plain; charset="utf-8")
MySQLConf.etc.mysql.mysql.conf.d.mysqld.cnf.txt Edit (3.1 KiB, text/plain; charset="utf-8")
MySQLConf.etc.mysql.mysql.conf.d.mysqld.cnf.bak.txt Edit (3.0 KiB, text/plain; charset="utf-8")
MySQLConf.etc.mysql.mysql.conf.d.mysqld.cnf.dpkg-dist.txt Edit (2.1 KiB, text/plain; charset="utf-8")
ProcCpuinfoMinimal.txt Edit (904 bytes, text/plain; charset="utf-8")

Apport retracing service (apport) on 2020-02-27

tags:

removed: need-duplicate-check

Revision history for this message

Andy Wylde (andywylde) wrote on 2020-02-27:

Download full text (5.4 KiB)

I tried the usual to fix this bug .....

apt --fix-broken install
apt install mysql-server

and while it did fix a broken dependency it still reported status as Upgrade in Progress 5.7 to 8.0 ...

However in inspecting the SQL error log it seems that the upgrade was stuck on on infinite loop trying
(and failing) to upgrade the same table over and over ......

2020-02-27T06:33:22.196147Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 7625
2020-02-27T06:33:22.220027Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T06:33:25.927054Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_group is not found in InnoDB dictionary
2020-02-27T06:33:25.927427Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_group
2020-02-27T06:33:25.935839Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T06:33:25.936212Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T06:33:25.942545Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T06:33:25.942987Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T06:33:33.946118Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T06:33:33.946879Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-02-27T06:33:35.557598Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-0ubuntu0.19.10.3) (Ubuntu).
2020-02-27T06:33:36.706904Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.
2020-02-27T06:33:36.711302Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 7698
2020-02-27T06:33:36.734882Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T06:33:39.938288Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_group is not found in InnoDB dictionary
2020-02-27T06:33:39.938929Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_group
2020-02-27T06:33:39.948222Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T06:33:39.948637Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T06:33:39.955979Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T06:33:39.956409Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T06:33:48.102907Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T06:33:48.103689Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-02-27T06:33:49.688120Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-0ubuntu0.19.10.3) (Ubuntu).
2020-02-27T06:33:50.699200Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.

and so on ad-infinitum ........

I tried the usual to fix this bug .....

apt --fix-broken install
 apt install mysql-server

and while it did fix a broken dependency it still reported status as Upgrade in Progress 5.7 to 8.0 ...

However in inspecting the SQL error log it seems that the upgrade was stuck on on infinite loop trying 
(and failing) to upgrade the same table over and over ......

2020-02-27T06:33:22.196147Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 7625
2020-02-27T06:33:22.220027Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T06:33:25.927054Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_group is not found in InnoDB dictionary
2020-02-27T06:33:25.927427Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_group
2020-02-27T06:33:25.935839Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T06:33:25.936212Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T06:33:25.942545Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T06:33:25.942987Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T06:33:33.946118Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T06:33:33.946879Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-02-27T06:33:35.557598Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-0ubuntu0.19.10.3)  (Ubuntu).
2020-02-27T06:33:36.706904Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.
2020-02-27T06:33:36.711302Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 7698
2020-02-27T06:33:36.734882Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T06:33:39.938288Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_group is not found in InnoDB dictionary
2020-02-27T06:33:39.938929Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_group
2020-02-27T06:33:39.948222Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T06:33:39.948637Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T06:33:39.955979Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T06:33:39.956409Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T06:33:48.102907Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T06:33:48.103689Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-02-27T06:33:49.688120Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-0ubuntu0.19.10.3)  (Ubuntu).
2020-02-27T06:33:50.699200Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.

and so on ad-infinitum ......

I moved the entire directory  containing this database to my home directory and without even having to restart it the upgrade completed and started mysql.   It seems the problem is not with the upgrade itself but in the fact that the upgrade gets stuck in an infinite loop when it fails to be able to upgrade a database.  I will figure out what it doesn't like about the table later.

2020-02-27T06:34:38.735613Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T06:34:38.736004Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T06:34:38.743030Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T06:34:38.743455Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T06:34:46.810865Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T06:34:46.811643Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-02-27T06:34:48.419798Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.19-0ubuntu0.19.10.3)  (Ubuntu).
2020-02-27T06:34:49.426926Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.
2020-02-27T06:34:49.431041Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 8032
2020-02-27T06:34:49.452924Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T06:35:06.351247Z 2 [System] [MY-011003] [Server] Finished populating Data Dictionary tables with data.
2020-02-27T06:35:08.591061Z 5 [System] [MY-013381] [Server] Server upgrade from '50700' to '80019' started.
2020-02-27T06:35:23.759966Z 5 [System] [MY-013381] [Server] Server upgrade from '50700' to '80019' completed.
2020-02-27T06:35:23.945776Z 0 [Warning] [MY-010068] [Server] CA certificate ca.pem is self signed.
2020-02-27T06:35:24.001095Z 0 [System] [MY-010931] [Server] /usr/sbin/mysqld: ready for connections. Version: '8.0.19-0ubuntu0.19.10.3'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu).
2020-02-27T06:35:24.163996Z 0 [System] [MY-011323] [Server] X Plugin ready for connections. Socket: '/var/run/mysqld/mysqlx.sock' bind-address: '::' port: 33060

Revision history for this message

Christian Ehrhardt  (paelzer) wrote on 2020-02-28:

The initial upgrade was at 2020-02-27T05:57:24.644898Z

And that already has thrown the same issues:
2020-02-27T05:57:11.390065Z 0 [Warning] [MY-011068] [Server] The syntax 'expire-logs-days' is deprecated and will be removed in a future release. Please use binlog_expire_logs_seconds instead.
2020-02-27T05:57:11.397089Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.19-0ubuntu0.19.10.3) starting as process 17204
2020-02-27T05:57:11.463144Z 1 [System] [MY-011012] [Server] Starting upgrade of data directory.
2020-02-27T05:57:15.889595Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_group is not found in InnoDB dictionary
2020-02-27T05:57:15.889989Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_group
2020-02-27T05:57:15.899648Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/root_contact is not found in InnoDB dictionary
2020-02-27T05:57:15.900108Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.root_contact
2020-02-27T05:57:15.908185Z 2 [ERROR] [MY-012083] [InnoDB] Table IP_Phones/Company is not found in InnoDB dictionary
2020-02-27T05:57:15.908587Z 2 [ERROR] [MY-010767] [Server] Error in fixing SE data for IP_Phones.Company
2020-02-27T05:57:24.583660Z 0 [ERROR] [MY-010022] [Server] Failed to Populate DD tables.
2020-02-27T05:57:24.584837Z 0 [ERROR] [MY-010119] [Server] Aborting

That is the same error that repeats later on.

Changed in mysql-8.0 (Ubuntu):
assignee:	nobody → Lars Tangvald (lars-tangvald)

Revision history for this message

Christian Ehrhardt  (paelzer) wrote on 2020-02-28:

That seems to be a mysql specific upgrade issue, I'm subscribing and assigning Lars for subject-matter expertise e.g. if it is a known and common issue.

Revision history for this message

Lars Tangvald (lars-tangvald) wrote on 2020-02-28:

I can only remember seeing this once before, which was someone who had accidentally gone from 5.7 to 8.0, then back again to 5.7.

Could you try running the mysqlcheck utility?
Syntax would be something like «sudo mysqlcheck IP_PHONES» I think.

Revision history for this message

Lars Tangvald (lars-tangvald) wrote on 2020-02-28:

Er, mysqlcheck only works if the server is running, so probably not very helpful.

Revision history for this message

Lars Tangvald (lars-tangvald) wrote on 2020-02-28:

Before upgrading, could you ensure mysql_upgrade has been run on the 5.7 database (this should be automatic in ubuntu packaging unless you've copied older 5.7 files into a newer 5.7 installation)?

Revision history for this message

Lars Tangvald (lars-tangvald) wrote on 2020-02-28:

One more thing to try (pre-upgrade) is to download mysql-shell from https://dev.mysql.com/downloads/shell/ and run the upgrade checker utility, which has tests for common upgrade issues (https://dev.mysql.com/doc/mysql-shell/8.0/en/mysql-shell-utilities-upgrade.html)

Revision history for this message

Launchpad Janitor (janitor) wrote on 2020-03-02:

Status changed to 'Confirmed' because the bug affects multiple users.

Changed in mysql-8.0 (Ubuntu):
status:	New → Confirmed

Revision history for this message

Andreas Hasenack (ahasenack) wrote on 2020-03-03:

#10

Setting the bug status to "incomplete" pending feedback from Lars' suggestions and requests.

Changed in mysql-8.0 (Ubuntu):
status:	Confirmed → Incomplete

Revision history for this message

Lars Tangvald (lars-tangvald) wrote on 2020-03-04:

#11

Another possible cause would be files being manually deleted from the datadir (so metadata tables believe they should still be there). Are the tables mentioned in the error log present and in use for the 5.7 packages?

Revision history for this message

tinodj (gjorgjioski) wrote on 2020-04-24:

#12

On my side, in conf, I had sql_mode containing NO_AUTO_CREATE_USER. After removing all was fine.

Revision history for this message

Christian Ehrhardt  (paelzer) wrote on 2020-12-08:

#13

Thanks for the feedback Tinodj.
I've marked two other similar cases as a dup now.

But now that it is confirmed we also happen to know that this is a variant of bug 1612517.
I'll mark it as dup and add info there about this new category.

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Ubuntumysql-8.0 package

package mysql-server-8.0 8.0.19-0ubuntu0.19.10.3 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1

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