package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to install/upgrade: Exceeded 5 min timeout

Bug #1901830 reported by suraj
88
This bug affects 20 people
Affects Status Importance Assigned to Milestone
mysql-8.0 (Ubuntu)
Confirmed
Undecided
Unassigned

Bug Description

mysql server running issue

ProblemType: Package
DistroRelease: Ubuntu 20.04
Package: mysql-server-8.0 8.0.22-0ubuntu0.20.04.2
ProcVersionSignature: Ubuntu 5.4.0-52.57-generic 5.4.65
Uname: Linux 5.4.0-52-generic x86_64
ApportVersion: 2.20.11-0ubuntu27.10
AptOrdering:
 mysql-client-8.0:amd64: Install
 libevent-pthreads-2.1-7:amd64: Install
 mysql-server-8.0:amd64: Install
 mysql-server-core-8.0:amd64: Install
 NULL: ConfigurePending
Architecture: amd64
CasperMD5CheckResult: skip
Date: Wed Oct 28 11:10:00 2020
ErrorMessage: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1
InstallationDate: Installed on 2019-06-01 (515 days ago)
InstallationMedia: Ubuntu 18.04.2 LTS "Bionic Beaver" - Release amd64 (20190210)
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
ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-5.4.0-52-generic root=UUID=34674da7-99d1-4d89-b45c-e63b0530dc54 ro quiet splash vt.handoff=7
Python3Details: /usr/bin/python3.8, Python 3.8.5, python3-minimal, 3.8.2-0ubuntu2
PythonDetails: /usr/bin/python3.8, Python 3.8.5, python-is-python2, 2.7.17-4
RelatedPackageVersions:
 dpkg 1.19.7ubuntu3
 apt 2.0.2ubuntu0.1
SourcePackage: mysql-8.0
Title: package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1
UpgradeStatus: Upgraded to focal on 2020-07-21 (98 days ago)
modified.conffile..etc.init.mysql.conf: [modified]
mtime.conffile..etc.init.mysql.conf: 2020-10-18T11:59:17.625913

Revision history for this message
suraj (singhsuraj) wrote :
tags: removed: need-duplicate-check
Revision history for this message
suraj (singhsuraj) wrote :

no comment

Revision history for this message
Launchpad Janitor (janitor) wrote :

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

Changed in mysql-8.0 (Ubuntu):
status: New → Confirmed
Revision history for this message
Paride Legovini (paride) wrote :

Hello suraj and thanks for this bug report. The problem is that the "server upgrade" operation took too long and exceeded the 5min timeout currently in place:

2020-10-28T05:32:22.777181Z 4 [System] [MY-013381] [Server] Server upgrade from '80021' to '80022' started.
2020-10-28T05:38:34.718235Z 4 [System] [MY-013381] [Server] Server upgrade from '80021' to '80022' completed.

This is the same error as LP: #1901708 and LP: #1882527. We thought that this could a somehow corner case caused by very large databases, but the latest comments to LP: #1901708 do not support this hypothesis.

Just to collect one more data point: do you have a very large mysql database? Or: was the system load *very* high during the upgrade? Any other clue on why the "server upgrade" operation took so long? (This doesn't take away the fact that the package should handle even huge database cleanly, so we do have a bug here, but we need to constrain the problem in order to work on it effectively.)

Thanks,

Paride

Revision history for this message
suraj (singhsuraj) wrote : Re: [Bug 1901830] Re: package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1
Download full text (4.0 KiB)

Hello paride legovini
I am using ubuntu as my primary operating system in Lenovo ideapad 100
system with 8 gm ram i3 processor.
I think 8 GB ram is enough for run a linux operating system with gnome
desktop environment. And i am using MySQL server with lampp for web
application development purpose. That means it's not even large database
issues.
That's from my side will be glad to give further information if needed or
officials want to run several tests on my pc for further information
gethering.

Best regards
Suraj Singh
India

On Thu, 29 Oct, 2020, 8:20 PM Paride Legovini, <email address hidden>
wrote:

> Hello suraj and thanks for this bug report. The problem is that the
> "server upgrade" operation took too long and exceeded the 5min timeout
> currently in place:
>
> 2020-10-28T05:32:22.777181Z 4 [System] [MY-013381] [Server] Server upgrade
> from '80021' to '80022' started.
> 2020-10-28T05:38:34.718235Z 4 [System] [MY-013381] [Server] Server upgrade
> from '80021' to '80022' completed.
>
> This is the same error as LP: #1901708 and LP: #1882527. We thought that
> this could a somehow corner case caused by very large databases, but the
> latest comments to LP: #1901708 do not support this hypothesis.
>
> Just to collect one more data point: do you have a very large mysql
> database? Or: was the system load *very* high during the upgrade? Any
> other clue on why the "server upgrade" operation took so long? (This
> doesn't take away the fact that the package should handle even huge
> database cleanly, so we do have a bug here, but we need to constrain the
> problem in order to work on it effectively.)
>
> Thanks,
>
> Paride
>
> --
> You received this bug notification because you are subscribed to the bug
> report.
> https://bugs.launchpad.net/bugs/1901830
>
> Title:
> package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to
> install/upgrade: installed mysql-server-8.0 package post-installation
> script subprocess returned error exit status 1
>
> Status in mysql-8.0 package in Ubuntu:
> Confirmed
>
> Bug description:
> mysql server running issue
>
> ProblemType: Package
> DistroRelease: Ubuntu 20.04
> Package: mysql-server-8.0 8.0.22-0ubuntu0.20.04.2
> ProcVersionSignature: Ubuntu 5.4.0-52.57-generic 5.4.65
> Uname: Linux 5.4.0-52-generic x86_64
> ApportVersion: 2.20.11-0ubuntu27.10
> AptOrdering:
> mysql-client-8.0:amd64: Install
> libevent-pthreads-2.1-7:amd64: Install
> mysql-server-8.0:amd64: Install
> mysql-server-core-8.0:amd64: Install
> NULL: ConfigurePending
> Architecture: amd64
> CasperMD5CheckResult: skip
> Date: Wed Oct 28 11:10:00 2020
> ErrorMessage: installed mysql-server-8.0 package post-installation
> script subprocess returned error exit status 1
> InstallationDate: Installed on 2019-06-01 (515 days ago)
> InstallationMedia: Ubuntu 18.04.2 LTS "Bionic Beaver" - Release amd64
> (20190210)
> 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
> ProcCmdline: BOOT_IMAGE=/boot/vmlinuz-5.4.0-52-generic
> root=UUID=34674d...

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Revision history for this message
xaaaaaan (xaaaaaan) wrote : Re: package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to install/upgrade: installed mysql-server-8.0 package post-installation script subprocess returned error exit status 1

Hello,

Same issue here.

Here is my mysql error log :
2020-10-31T09:59:34.121013Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-10-31T09:59:41.886417Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.22-0ubuntu0.20.04.2) (Ubuntu).
2020-10-31T09:59:45.998648Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.22-0ubuntu0.20.04.2) starting as process 23556
2020-10-31T09:59:46.023570Z 1 [System] [MY-013576] [InnoDB] InnoDB initialization has started.
2020-10-31T10:02:19.183591Z 1 [System] [MY-013577] [InnoDB] InnoDB initialization has ended.
2020-10-31T10:02:32.911095Z 0 [System] [MY-011323] [Server] X Plugin ready for connections. Bind-address: '::' port: 33060, socket: /var/run/mysqld/mysqlx.sock
2020-10-31T10:02:32.925302Z 4 [System] [MY-013381] [Server] Server upgrade from '80021' to '80022' started.
2020-10-31T10:04:31.291449Z 4 [ERROR] [MY-013178] [Server] Execution of server-side SQL statement '-- Copyright (c) 2015, 2019, Oracle and/or its affiliates. All rights reserved. -- -- This program is free software; you can redistribute it and/or modify -- it under the terms of the GNU General Public License as published by -- the Free Software Foundation; version 2 of the License. -- -- This program is distributed in the hope that it will be useful, -- but WITHOUT ANY WARRANTY; without even the implied warranty of -- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -- GNU General Public License for more details. -- -- You should have received a copy of the GNU General Public License -- along with this program; if not, write to the Free Software -- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA -- NOTE: This needs to be replicated within the sys_config_clean.inc file INSERT IGNORE INTO sys.sys_config (variable, value) VALUES ('statement_truncate_len', 64), ('statement_performance_analyzer.limit', 100), ('statement_performance_analyzer.view', NULL), ('diagnostics.allow_i_s_tables', 'OFF'), ('diagnostics.include_raw', 'OFF'), ('ps_thread_trx_info.max_length', 65535); ' failed with error code = 1436, error message = 'Thread stack overrun: 11968 bytes used of a 131072 byte stack, and 160000 bytes needed. Use 'mysqld --thread_stack=#' to specify a bigger stack.'.
2020-10-31T10:04:31.502119Z 0 [ERROR] [MY-013380] [Server] Failed to upgrade server.
2020-10-31T10:04:31.502698Z 0 [ERROR] [MY-010119] [Server] Aborting
2020-10-31T10:04:39.602176Z 0 [System] [MY-010910] [Server] /usr/sbin/mysqld: Shutdown complete (mysqld 8.0.22-0ubuntu0.20.04.2) (Ubuntu).
2020-10-31T10:04:44.082547Z 0 [System] [MY-010116] [Server] /usr/sbin/mysqld (mysqld 8.0.22-0ubuntu0.20.04.2) starting as process 23616

Revision history for this message
xaaaaaan (xaaaaaan) wrote :

Well, reply to myself, I changed my my.cnf from thread_stack = 128K to thread_stack = 256K and it solved my problem.
Not really sure this is the same issue as first post.

Revision history for this message
Sergio Durigan Junior (sergiodj) wrote :

@xaaaaaan, this seems like a different problem (by looking at the logs).

@suraj, would you happen to know if the system load was high during the upgrade process for some reason?

Bryce Harrington (bryce)
summary: package mysql-server-8.0 8.0.22-0ubuntu0.20.04.2 failed to
- install/upgrade: installed mysql-server-8.0 package post-installation
- script subprocess returned error exit status 1
+ install/upgrade: Exceeded 5 min timeout
Revision history for this message
Bryce Harrington (bryce) wrote :

May be same thing going on as:
   https://bugs.launchpad.net/ubuntu/+source/mysql-8.0/+bug/1957013/comments/3
   total RAM covered: 4014M
   Memory: 3862760K/4087216K
   CPU0: Intel(R) Core(TM) i5-3210M CPU @ 2.50GHz

From suraj's comment #5 maybe it is worth examining if a resource-limited system will cause an otherwise ordinary lamp setup to have long mysql shutdown cycles?

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