MySQL Bugs: #90881: mysql won't start

Bug #90881	mysql won't start
Submitted:	16 May 2018 5:24	Modified:	20 Jun 2018 9:25
Reporter:	Sandra Gutierrez	Email Updates:
Status:	Duplicate	Impact on me:	None
Category:	MySQL Server	Severity:	S1 (Critical)
Version:	8	OS:	FreeBSD (11.1)
Assigned to:		CPU Architecture:	Other (AMD64)

Description:
2018-05-16T04:58:33.6NZ mysqld_safe Logging to '/var/log/mysql/mysql-error.log'.
2018-05-16T04:58:33.6NZ mysqld_safe Starting mysqld daemon with databases from /var/db/mysql
2018-05-16T04:58:33.475367Z 0 [Warning] [MY-010140] [Server] Could not increase number of max_open_files to more than 28467 (request: 32929)
2018-05-16T04:58:33.475883Z 0 [Warning] [MY-010142] [Server] Changed limits: table_open_cache: 14153 (requested 16384)
2018-05-16T04:58:33.866629Z 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.
2018-05-16T04:58:33.866753Z 0 [Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
2018-05-16T04:58:33.866835Z 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.
2018-05-16T04:58:33.866906Z 0 [Warning] [MY-011070] [Server] 'Disabling symbolic links using --skip-symbolic-links (or equivalent) is the default. Consider not using this option as it' is deprecated and will be removed in a future release.
2018-05-16T04:58:33.872337Z 0 [System] [MY-010116] [Server] /usr/local/libexec/mysqld (mysqld 8.0.11) starting as process 26539
 100
2018-05-16T04:58:36.856143Z 1 [ERROR] [MY-012097] [InnoDB] InnoDB: Table flags are 28363cd in the data dictionary but the flags in file   are 20![FATAL]Table flags are 4800 in the data dictionary but the flags in file mysql.ibd  are 800!
2018-05-16T04:58:36.857605Z 1 [ERROR] [MY-000000] [InnoDB] InnoDB: Assertion failure: ut0ut.cc:675
InnoDB: thread 34475362304
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/8.0/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
04:58:36 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=8388608
read_buffer_size=131072
max_used_connections=0
max_threads=151
thread_count=1
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 67779 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x806e7e000
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 7fffdfdfcf48 thread_stack 0x46000
0x1cb51ce <_Z19my_print_stacktracePhm+0x2e> at /usr/local/libexec/mysqld
0xdfefc2 <handle_fatal_signal+0x2c2> at /usr/local/libexec/mysqld
0x8063b6926 <pthread_sigmask+0x536> at /lib/libthr.so.3
0x8063b5ecf <pthread_getspecific+0xe5f> at /lib/libthr.so.3

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (0): is an invalid pointer
Connection ID (thread ID): 1
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
2018-05-16T04:58:36.6NZ mysqld_safe mysqld from pid file /var/db/mysql/xxxx.pid ended

How to repeat:
attempting to start server

Looks like duplicate of: https://bugs.mysql.com/bug.php?id=87837

2017-09-22T09:04:19.107270Z 1 [ERROR] [FATAL] InnoDB: Table flags are 0x4800 in the data dictionary but the flags in file mysql.ibd are 0x800!

Your server install is an upgrade?

I tried to upgrade, but failed.
So I did a new install. But I have not been able to get it going yet. With the new database files I am getting:

InnoDB: thread 34475362304
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/8.0/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
16:27:17 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=268435456
read_buffer_size=131072
max_used_connections=0
max_threads=151
thread_count=1
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 321731 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x806e7d000
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 7fffdfdfcf48 thread_stack 0x46000
0x1cb51ce <_Z19my_print_stacktracePhm+0x2e> at /usr/local/libexec/mysqld
0xdfefc2 <handle_fatal_signal+0x2c2> at /usr/local/libexec/mysqld
0x8063b6926 <pthread_sigmask+0x536> at /lib/libthr.so.3
0x8063b5ecf <pthread_getspecific+0xe5f> at /lib/libthr.so.3

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (0): is an invalid pointer
Connection ID (thread ID): 1
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
2018-05-16T16:27:17.6NZ mysqld_safe mysqld from pid file /var/db/mysql/xxx.pid ended

Sorry for the poor formatting.

Almost forgot, I also added:
innodb_force_recovery = 1

to my config file

I got the same error after an upgrade of MySQL 8 on FreeBSD 11.1:

        mysql80-server: 8.0.2_3 -> 8.0.11
        mysql80-client: 8.0.2_3 -> 8.0.11

Regards,
Ian.

Non repeatable test case and the error message looks the same as bug already pointed? https://bugs.mysql.com/bug.php?id=87837.