MySql service won´t start [ubuntu] - mysql

Question

Today at around 6:23 UTC my Ubuntu Server 16.04 in Amazon EC2 made an automated apt update. From around this time my MySql server refuses to start.
At first he told me the apparmor config was wrong (like here: mysql wont start Ubuntu 16.04.2 x64) which i fixed.
Now when I try to start the mysql service like this:
:~$ sudo /etc/init.d/mysql start
[....] Starting mysql (via systemctl): mysql.serviceJob for mysql.service
failed because the control process exited with error code. See "systemctl
status mysql.service" and "journalctl -xe" for details.
failed!
systemctl status mysql.service :
:~$ sudo systemctl status mysql.service
● mysql.service - MySQL Community Server
Loaded: loaded (/lib/systemd/system/mysql.service; enabled; vendor preset: enabled)
Active: activating (start-post) (Result: exit-code) since Tue 2018-04-24 19:01:31 UTC; 27s ago
Process: 22818 ExecStart=/usr/sbin/mysqld (code=exited, status=1/FAILURE)
Process: 22809 ExecStartPre=/usr/share/mysql/mysql-systemd-start pre (code=exited, status=0/SUCCESS)
Main PID: 22818 (code=exited, status=1/FAILURE); : 22819 (mysql-systemd-s)
Tasks: 2
Memory: 324.0K
CPU: 287ms
CGroup: /system.slice/mysql.service
└─control
├─22819 /bin/bash /usr/share/mysql/mysql-systemd-start post
└─22903 sleep 1
Apr 24 19:01:31 ip-172-31-38-155 systemd[1]: mysql.service: Service hold-off time over, scheduling restart.
Apr 24 19:01:31 ip-172-31-38-155 systemd[1]: Stopped MySQL Community Server.
Apr 24 19:01:31 ip-172-31-38-155 systemd[1]: Starting MySQL Community Server...
Apr 24 19:01:33 ip-172-31-38-155 systemd[1]: mysql.service: Main process exited, code=exited, status=1/FAILURE
and the journalctl -ex looks like this:
journalctl -xe
-- The result is failed.
Apr 24 19:05:41 ip-172-31-38-155 systemd[1]: mysql.service: Unit entered failed state.
Apr 24 19:05:41 ip-172-31-38-155 systemd[1]: mysql.service: Failed with result 'exit-code'.
Apr 24 19:05:41 ip-172-31-38-155 systemd[1]: mysql.service: Service hold-off time over, scheduling restart.
Apr 24 19:05:41 ip-172-31-38-155 systemd[1]: Stopped MySQL Community Server.
-- Subject: Unit mysql.service has finished shutting down
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has finished shutting down.
Apr 24 19:05:41 ip-172-31-38-155 systemd[1]: Starting MySQL Community Server...
-- Subject: Unit mysql.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has begun starting up.
Apr 24 19:05:43 ip-172-31-38-155 systemd[1]: mysql.service: Main process exited, code=exited, status=1/FAILURE
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: Failed to start MySQL Community Server.
-- Subject: Unit mysql.service has failed
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has failed.
--
-- The result is failed.
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: mysql.service: Unit entered failed state.
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: mysql.service: Failed with result 'exit-code'.
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: mysql.service: Service hold-off time over, scheduling restart.
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: Stopped MySQL Community Server.
-- Subject: Unit mysql.service has finished shutting down
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has finished shutting down.
Apr 24 19:06:12 ip-172-31-38-155 systemd[1]: Starting MySQL Community Server...
-- Subject: Unit mysql.service has begun start-up
-- Defined-By: systemd
-- Support: http://lists.freedesktop.org/mailman/listinfo/systemd-devel
--
-- Unit mysql.service has begun starting up.
Apr 24 19:06:14 ip-172-31-38-155 systemd[1]: mysql.service: Main process exited, code=exited, status=1/FAILURE
While the the cat /var/log/mysql/error.log | grep ERROR prints loads of these errors:
2018-04-24T19:10:22.941983Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2018-04-24T19:10:22.942643Z 0 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
2018-04-24T19:10:22.942683Z 0 [ERROR] Aborting
The one whole cycle of the cat /var/log/error.log would look like this:
2018-04-24T19:14:01.701232Z 0 [Note] Shutting down plugin 'ngram'
2018-04-24T19:14:01.701238Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2018-04-24T19:14:01.701241Z 0 [Note] Shutting down plugin 'partition'
2018-04-24T19:14:01.701243Z 0 [Note] Shutting down plugin 'ARCHIVE'
2018-04-24T19:14:01.701246Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2018-04-24T19:14:01.701249Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-04-24T19:14:01.701251Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-04-24T19:14:01.701253Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-04-24T19:14:01.701256Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-04-24T19:14:01.701258Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-04-24T19:14:01.701260Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-04-24T19:14:01.701263Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-04-24T19:14:01.701265Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-04-24T19:14:01.701267Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-04-24T19:14:01.701270Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-04-24T19:14:01.701272Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-04-24T19:14:01.701274Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-04-24T19:14:01.701277Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-04-24T19:14:01.701279Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-04-24T19:14:01.701282Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-04-24T19:14:01.701284Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2018-04-24T19:14:01.701286Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2018-04-24T19:14:01.701289Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-04-24T19:14:01.701291Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-04-24T19:14:01.701293Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-04-24T19:14:01.701296Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-04-24T19:14:01.701298Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-04-24T19:14:01.701300Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-04-24T19:14:01.701303Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-04-24T19:14:01.701305Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-04-24T19:14:01.701307Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2018-04-24T19:14:01.701310Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-04-24T19:14:01.701312Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-04-24T19:14:01.701314Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2018-04-24T19:14:01.701317Z 0 [Note] Shutting down plugin 'InnoDB'
2018-04-24T19:14:01.701363Z 0 [Note] InnoDB: FTS optimize thread exiting.
2018-04-24T19:14:01.701444Z 0 [Note] InnoDB: Starting shutdown...
2018-04-24T19:14:01.701486Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
2018-04-24T19:14:01.701522Z 0 [Note] InnoDB: Buffer pool(s) load completed at 180424 19:14:01 (/var/lib/mysql/ib_buffer_pool was empty)
2018-04-24T19:14:01.701533Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2018-04-24T19:14:01.701632Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 180424 19:14:01
2018-04-24T19:14:03.309269Z 0 [Note] InnoDB: Shutdown completed; log sequence number 8715994
2018-04-24T19:14:03.310751Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2018-04-24T19:14:03.310767Z 0 [Note] Shutting down plugin 'MyISAM'
2018-04-24T19:14:03.310781Z 0 [Note] Shutting down plugin 'CSV'
2018-04-24T19:14:03.310794Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-04-24T19:14:03.310840Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2018-04-24T19:14:03.310844Z 0 [Note] Shutting down plugin 'MEMORY'
2018-04-24T19:14:03.310848Z 0 [Note] Shutting down plugin 'sha256_password'
2018-04-24T19:14:03.310850Z 0 [Note] Shutting down plugin 'mysql_native_password'
2018-04-24T19:14:03.310975Z 0 [Note] Shutting down plugin 'binlog'
2018-04-24T19:14:03.311078Z 0 [Note] /usr/sbin/mysqld: Shutdown complete
2018-04-24T19:14:32.669339Z 0 [Warning] Changed limits: max_open_files: 1024 (requested 5000)
2018-04-24T19:14:32.669378Z 0 [Warning] Changed limits: table_open_cache: 431 (requested 2000)
2018-04-24T19:14:32.820589Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2018-04-24T19:14:32.822172Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.22-0ubuntu0.16.04.1) starting as process 25440 ...
2018-04-24T19:14:32.826095Z 0 [Note] InnoDB: PUNCH HOLE support available
2018-04-24T19:14:32.826121Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2018-04-24T19:14:32.826125Z 0 [Note] InnoDB: Uses event mutexes
2018-04-24T19:14:32.826129Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2018-04-24T19:14:32.826133Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.8
2018-04-24T19:14:32.826136Z 0 [Note] InnoDB: Using Linux native AIO
2018-04-24T19:14:32.826367Z 0 [Note] InnoDB: Number of pools: 1
2018-04-24T19:14:32.826496Z 0 [Note] InnoDB: Using CPU crc32 instructions
2018-04-24T19:14:32.827971Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2018-04-24T19:14:32.835607Z 0 [Note] InnoDB: Completed initialization of buffer pool
2018-04-24T19:14:32.837529Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2018-04-24T19:14:32.849179Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2018-04-24T19:14:32.858128Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2018-04-24T19:14:32.858180Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2018-04-24T19:14:32.892813Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2018-04-24T19:14:32.893685Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2018-04-24T19:14:32.893696Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2018-04-24T19:14:32.893952Z 0 [Note] InnoDB: Waiting for purge to start
2018-04-24T19:14:32.944316Z 0 [Note] InnoDB: 5.7.22 started; log sequence number 8715994
2018-04-24T19:14:32.944678Z 0 [Note] Plugin 'FEDERATED' is disabled.
mysqld: Table 'mysql.plugin' doesn't exist
2018-04-24T19:14:32.944791Z 0 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2018-04-24T19:14:32.945139Z 0 [Warning] Gtid table is not ready to be used. Table 'mysql.gtid_executed' cannot be opened.
2018-04-24T19:14:32.945192Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2018-04-24T19:14:32.945201Z 0 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
2018-04-24T19:14:32.945209Z 0 [Note] - '127.0.0.1' resolves to '127.0.0.1';
2018-04-24T19:14:32.945237Z 0 [Note] Server socket created on IP: '127.0.0.1'.
2018-04-24T19:14:32.945363Z 0 [Warning] Failed to open optimizer cost constant tables
2018-04-24T19:14:32.945455Z 0 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist
2018-04-24T19:14:32.945497Z 0 [ERROR] Aborting
2018-04-24T19:14:32.945522Z 0 [Note] Binlog end
On the one hand I have seen that the the error.log tells me to run run mysql_upgrade which i cannot do because the database itself is not running.
The [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist should be fixed by an initilize command onto the service which wont work either because the service itself is not running.
I do not have a single clue what to do next. My personal best Idea for now would be to reinstall the MySql server and copy beforehand the /var/lib/mysql/mysql and the /etc/mysql directories to insert them later as a backup.
I hope anyone of you has heard something about the problem or has any kind of idea what to do. Preferably while keeping my Data.
I hope, I provided all information you need. If you need any more, just ask.
Thanks a lot in advance!