Can't start mysql server after update on Ubuntu 16.04

Question

I have a problem using mysql on my server. After an update mysql stopped working on my system. It seems that it crashes immediatly after start so I even can't backup my databases as the service is not running. My mysql error log has the following content:

tail -70 /var/log/mysql/error.log
2017-07-27T06:56:20.080287Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080330Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=406] log sequence number 199107155900 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080336Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080432Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=208] log sequence number 199110108309 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080440Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080481Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=735] log sequence number 196716783961 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080488Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080530Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=378] log sequence number 199109175046 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080536Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080586Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=209] log sequence number 199110429878 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080598Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080641Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=342] log sequence number 199106867077 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080647Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27T06:56:20.080690Z 0 [ERROR] InnoDB: Page [page id: space=0, page number=16395] log sequence number 199094094548 is in the future! Current system log sequence number 191999990814.
2017-07-27T06:56:20.080701Z 0 [ERROR] InnoDB: Your database may be corrupt or you may have copied the InnoDB tablespace but not the InnoDB log files. Please refer to http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2017-07-27 08:56:20 0xb7343700  InnoDB: Assertion failure in thread 3073652480 in file fut0lst.ic line 85
InnoDB: Failing assertion: addr.page == FIL_NULL || addr.boffset >= FIL_PAGE_DATA
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/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
06:56:20 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=16777216
read_buffer_size=131072
max_used_connections=0
max_threads=151
thread_count=0
connection_count=0
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 75717 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x0
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 = 0 thread_stack 0x30000
/usr/sbin/mysqld(my_print_stacktrace+0x3c)[0x8a8b33c]
/usr/sbin/mysqld(handle_fatal_signal+0x426)[0x837f356]
[0xb77c0c14]
[0xb77c0c31]
/lib/i386-linux-gnu/libc.so.6(gsignal+0x39)[0xb738bea9]
/lib/i386-linux-gnu/libc.so.6(abort+0x157)[0xb738d407]
/usr/sbin/mysqld[0x8355dcf]
/usr/sbin/mysqld(_Z19trx_undo_lists_initP10trx_rseg_t+0xddc)[0x8d394dc]
/usr/sbin/mysqld[0x8d1d60f]
/usr/sbin/mysqld[0x8d203ec]
/usr/sbin/mysqld(_Z24trx_sys_init_at_db_startv+0x18cc)[0x8d2792c]
/usr/sbin/mysqld(_Z34innobase_start_or_create_for_mysqlv+0x5382)[0x8ceaa32]
/usr/sbin/mysqld[0x8b98d0e]
/usr/sbin/mysqld(_Z24ha_initialize_handlertonP13st_plugin_int+0x52)[0x83ccfd2]
/usr/sbin/mysqld[0x88611a2]
/usr/sbin/mysqld(_Z11plugin_initPiPPci+0x60f)[0x886916f]
/usr/sbin/mysqld[0x8377795]
/usr/sbin/mysqld(_Z11mysqld_mainiPPc+0x83b)[0x837906b]
/usr/sbin/mysqld(main+0x27)[0x8357917]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf7)[0xb7378637]
/usr/sbin/mysqld[0x836f4dc]
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.

It seems that there is a problem with InnoDB.

Because of that I already tried to adjust my my.conf file and added the following lines:

[mysqld]
innodb_force_recovery = 4

After trying to restart (systemctl restart mysql.service) it's still the same problem.

I also tried out to completely reinstall mysql-server but it's still the same problem.

I tried also to backup every files from /var/lib/mysql and running:

mkdir /root/backup_mysql/
mv /var/lib/mysql/* /root/backup_mysql/
dpkg --configure mysql-server-5.7

But even after that it's still the same issue.

Do you have any idea how to solve this problem?

Answer 1

The problem is associated with tablespace that MySql database engine InnoDb uses for CRUD operations.

Use

[mysqld]
innodb_force_recovery = 1

Lets the server run even if it detects a corrupt page. Tries to make SELECT * FROM tbl_name jump over corrupt index records and pages, which helps in dumping tables.

Which seems helpful for your case, for more information, refer mysql manual and the same is suggested in your error log.

If you use different values without understanding their effects, you might end up loosing your data. So be careful.

If data was not so important, you can completely remove the mysql from your system and re-install it carefully, this would work hopefully.

How to remove mysql completely?

Go to /var/lib/mysql/ something like that in your system, delete mysql folder also remove configuration file manually from /etc/mysql folder.

Update your ubuntu repository and reinstall mysql again.