Error could not open mysql plugin table some plugins may be not loaded

I installed MariaDB on my system (Debian 9), however, upon running sudo service mysql start, I get these errors:

Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] /usr/sbin/mariadbd (mysqld 10.5.5-MariaDB-1:10.5.5+maria~stretch) starting as process 30151 ...
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Warning] Could not increase number of max_open_files to more than 16384 (request: 32184)
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Using Linux native AIO
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Uses event mutexes
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Compressed tables use zlib 1.2.8
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Number of pools: 1
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Using SSE4.2 crc32 instructions
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] mariadbd: O_TMPFILE is not supported on /tmp (disabling future attempts)
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Completed initialization of buffer pool
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] InnoDB: Invalid flags 0x4800 in ./ibdata1
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] InnoDB: Plugin initialization aborted with error Data structure corruption
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] InnoDB: Starting shutdown...
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] Plugin 'InnoDB' init function returned error.
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [Note] Plugin 'FEEDBACK' is disabled.
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] Could not open mysql.plugin table: "Table 'mysql.plugin' doesn't exist". Some plugins may be not loaded
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] Unknown/unsupported storage engine: InnoDB
Sep 22 12:32:37 bremea mariadbd[30151]: 2020-09-22 12:32:37 0 [ERROR] Aborting
Sep 22 12:32:37 bremea systemd[1]: mariadb.service: Main process exited, code=exited, status=1/FAILURE
Sep 22 12:32:37 bremea systemd[1]: Failed to start MariaDB 10.5.5 database server.

I assume this is an error with InnoDB, but I may be wrong. I tried uninstalling/reinstalling mysql but that didn’t work either. Can anyone steer me in the right direction?

Cannot find checkpoint record at LSN

When your Laragon app will get shutdown unexpected, it might cause you an issue where MySQL database will not start, and you will be redirected to log file for more details. The most common problem is “Unknown storage engine ‘Aria’”. The solution is very straight forward so don’t get stressed out. The fix is here.

As instructed by Laragon error prompt. Go to the MySQL log.

Could not open mysql.plugin table: “Unknown storage engine ‘Aria’”. Some plugins may be not loaded

The full error log in my case is placed under C:laragon.dvdatamariadb-10.6mysql.log (in default installation it would be placed under C:laragondatamysqlmysql.log ). If you wonder why is my path different it is because i do have multiple instances of laragon installed on my PC in different directory such as laragon.dv, laragon.bc, and laragon (default installation). I also install MariaDB engine instead default MySQL so keep that in mind to not get confused.
The error log would look something like this:

Cannot find checkpoint record at LSN (1,0x65548)
2021-12-15 15:03:16 0 [ERROR] mysqld: Aria recovery failed. Please run aria_chk -r on all Aria tables (*.MAI) and delete all aria_log.######## files
2021-12-15 15:03:16 0 [ERROR] Plugin 'Aria' init function returned error.
2021-12-15 15:03:16 0 [ERROR] Plugin 'Aria' registration as a STORAGE ENGINE failed.
2021-12-15 15:03:16 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2021-12-15 15:03:16 0 [Note] InnoDB: Number of pools: 1
2021-12-15 15:03:16 0 [Note] InnoDB: Using crc32 + pclmulqdq instructions
2021-12-15 15:03:16 0 [Note] InnoDB: Initializing buffer pool, total size = 134217728, chunk size = 134217728
2021-12-15 15:03:16 0 [Note] InnoDB: Completed initialization of buffer pool
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=4] log sequence number 234591275 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [Note] InnoDB: 128 rollback segments are active.
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=465] log sequence number 388269238 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=407] log sequence number 388269374 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=448] log sequence number 387834748 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=470] log sequence number 262503819 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [ERROR] InnoDB: Page [page id: space=0, page number=473] log sequence number 387808465 is in the future! Current system log sequence number 185498210.
2021-12-15 15:03:16 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 https://mariadb.com/kb/en/library/innodb-recovery-modes/ for information about forcing recovery.
2021-12-15 15:03:16 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2021-12-15 15:03:16 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2021-12-15 15:03:16 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2021-12-15 15:03:16 0 [Note] InnoDB: 10.6.3 started; log sequence number 185498198; transaction id 309973
2021-12-15 15:03:16 0 [Note] Plugin 'FEEDBACK' is disabled.
2021-12-15 15:03:16 0 [Note] InnoDB: Loading buffer pool(s) from C:laragon.dvdatamariadb-10.6ib_buffer_pool
2021-12-15 15:03:16 0 [ERROR] Could not open mysql.plugin table: "Unknown storage engine 'Aria'". Some plugins may be not loaded
2021-12-15 15:03:16 0 [ERROR] Failed to initialize plugins.
2021-12-15 15:03:16 0 [ERROR] Aborting

If you find a similar issue in your log file, you are in the right place.
This issue can occur when we shout down PC while having Laragon app started and connected to MySQL database. This will cause a crash on restart. The quick fix to the above issue is simple, to remove all files from our database folder which are prepended with a arial_log text string.

Path to below folder C:laragondatamariadb-10.6 (your path might look differently, like this: C:laragondatamysql depending on what database engine are you using.)

Now remove all files starting with text: arial_log.... Like in the example above. Done!
After that, stop and start your Laragon app. Your database should spin again!
Simple as that! If this tutorial did not solve your issue, fallow this instead: “Laragon database crashed“.

Let me know if this post helped solve your issue. Good luck!

This has to be a mariadb issue. In my compose file for my phpfpm service use:

volumes:
            - ./public:/usr/share/nginx/html

which works

inspect shows:

"Mounts": [
    {
        "Type": "bind",
        "Source": "/E/docker/01_testing/my_first_docker-compose/public",
        "Destination": "/usr/share/nginx/html",
        "Mode": "rw",
        "RW": true,
        "Propagation": "rprivate"
    }

…

"Volumes": {
    "/usr/share/nginx/html": {}
},

I can modify the files on the host side on the volume mapping everything works as expected.

when I try the same for mariadb service there are problems, for my db service:

 volumes:
            - ./data:/var/lib/mysql

but when I up the mariadb compose I get:

mysql_1 | 2017-12-12 9:53:49 139728345196416 [ERROR] InnoDB: Write to file ./ibdata1 failed at offset 0, 1048576 bytes should have been written, only 0 were written. Operating system error number 22. Check that your OS and file system support files of this size. Check also that the disk is not full or a disk quota exceeded.
mysql_1 | 2017-12-12 9:53:49 139728345196416 [ERROR] InnoDB: Error number 22 means ‘Invalid argument’
mysql_1 | 2017-12-12 9:53:49 139728345196416 [ERROR] InnoDB: Could not set the file size of
./ibdata1′. Probably out of disk space

inspecting the container shows:

"Mounts": [
    {
        "Type": "bind",
        "Source": "/E/docker/02_services/mariaDb/data",
        "Destination": "/var/lib/mysql",
        "Mode": "rw",
        "RW": true,
        "Propagation": "rprivate"
    }

…

"Volumes": {
    "/var/lib/mysql": {}
},

The service did write in to the mapped volume ./data:

Mode                LastWriteTime         Length Name
----                -------------         ------ ----
d-----       12/12/2017  10:53 AM                mysql
-a----       12/12/2017  10:53 AM          16384 aria_log.00000001
-a----       12/12/2017  10:53 AM             52 aria_log_control
-a----       12/12/2017  10:53 AM              0 ibdata1

I have also tried using docker run with -v and I get the same outcome.

Interestingly enough, as neuotq suggested if you use the docker internal volumes, then it works.

NOTE: There are two ways to run multiple instances of a MariaDB on the same server. You can use the mariadb@.service unit file to start independent instances, or you can use the mysqld_multi sections of the /etc/my.cnf file. This document applies to the former case only.

When attempting to configure multiple MariaDB instances using the mariadb@.service unit file, the instances fail to start. The same applies when a non-default MariaDB configuration file is used. A MariaDB instance configuration file was placed in /etc/my.cnf.d/mynode1.cnf.

$ sudo systemctl start mariadb@node1.service
Job for mariadb@node1.service failed because the control process exited with error code. See "systemctl status mariadb@node1.service" and "journalctl -xe" for details.

$ sudo journalctl -xe
$ sudo systemctl status mariadb@node1.service
...
Jun 06 15:08:35 sles12sp4 mysql-systemd-helper[2363]: Could not open required defaults file: /etc/mynode1.cnf
Jun 06 15:08:35 sles12sp4 mysql-systemd-helper[2363]: Fatal error in defaults handling. Program aborted

After moving /etc/my.cnf.d/mynode1.cnf to /etc/mynode1.cnf, the error log shows:

Jun 04 14:30:44 sles12sp4 mysql-systemd-helper[1179]: 2019-06-04 14:30:44 140137018382464 [Warning] Can't create test file /var/lib/mysql/node1/databases/sles12sp4.lower-test
Jun 04 14:30:44 sles12sp4 mysql-systemd-helper[1179]: 2019-06-04 14:30:44 140137018382464 [ERROR] Aborting
Jun 04 14:30:44 sles12sp4 systemd[1]: mariadb@node1.service: Main process exited, code=exited, status=1/FAILURE
Jun 04 14:30:44 sles12sp4 systemd[1]: Failed to start MySQL server - node1 instance.

$ cat /etc/mynode1.cnf
[client]
[mysqld]
port       = 3310
datadir    = /var/lib/mysql/node1/databases
pid-file   = /var/lib/mysql/node1/databases/mysqld.pid
socket     = /run/mysql/node1mysql.sock
bind-address    = 127.0.0.1
log-error       = /var/log/mysql/node1/mysqld.log
secure_file_priv = /var/lib/mysql-files
innodb_file_format=Barracuda
innodb_file_per_table=ON
server-id    = 1
sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES
[mysqld_multi]
mysqld     = /usr/bin/mysqld_safe
mysqladmin = /usr/bin/mysqladmin
log        = /var/log/mysqld_multi.log
!includedir /etc/my.cnf.d

$ sudo ls -l /var/lib | grep mysql
drwxr-x--- 1 mysql   mysql     0 Jun  4 00:55 mysql-files
drwx------ 1 mysql   root    242 Jun  6 15:08 mysql-node1

If the default single instance of MariaDB was started first, the /var/lib/mysql directory was created with the resulting errors.

$ sudo ls -l /var/lib | grep mysql
drwxr-xr-x 1 mysql   root    346 Jun  6 15:32 mysql
drwxr-x--- 1 mysql   mysql     0 Jun  4 00:55 mysql-files
drwx------ 1 mysql   root    242 Jun  6 15:08 mysql-node1

[Warning] Can't create test file /var/lib/mysql/node1/databases/sles12sp4.lower-test
[ERROR] Aborting

If you first create /var/lib/mysql/node1/databases directory and attempt to start the instance, you get system log errors.

[ERROR] mysqld: Can't create/write to file '/var/lib/mysql/node1/databases/aria_log_control' (Errcode: 13 "Permission denied")
[ERROR] mysqld: Got error 'Can't create file' when trying to use aria control file '/var/lib/mysql/node1/databases/aria_log_control'
[ERROR] InnoDB: Operating system error number 13 in a file operation.
[ERROR] InnoDB: The error means mysqld does not have the access rights to the directory.
[ERROR] InnoDB: Cannot open datafile './ibdata1'
[ERROR] InnoDB: Could not open or create the system tablespace. If you tried to add new data files to the system tablespace, and it failed here, you should now edit innodb_da
[ERROR] InnoDB: Database creation was aborted with error Cannot open a file. You may need to delete the ibdata1 file before trying to start up again.
[ERROR] Plugin 'InnoDB' init function returned error.
[ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
[ERROR] Could not open mysql.plugin table. Some plugins may be not loaded
[ERROR] Unknown/unsupported storage engine: InnoDB
[ERROR] Aborting

Engineering is aware of the issue and a PTF is available from support.

Configuration

MariaDB on SUSE only looks for instance configuration files in /etc, not /etc/my.cnf.d, so make sure your configuration files are saved in /etc. The resolution is based on the following configuration file examples.

Values included in /etc/mynode1.cnf

[mysqld]
port       = 3310
datadir    = /var/lib/mysql/node1/databases
pid-file   = /var/lib/mysql/node1/databases/mysqld.pid
socket     = /run/mysql/node1mysql.sock
log-error       = /var/log/mysql/node1/mysqld.log
secure_file_priv = /var/lib/mysql-files

Values included in /etc/mynode2.cnf

[mysqld]
port       = 3315
datadir    = /var/lib/mysql/node2/databases
pid-file   = /var/lib/mysql/node2/databases/mysqld.pid
socket     = /run/mysql/node2mysql.sock
log-error       = /var/log/mysql/node2/mysqld.log
secure_file_priv = /var/lib/mysql-files

Steps to Resolve

1. Install the updates when/if available in the update channel or apply the PTF received from support.

2. Stop all MariaDB instances:

$ sudo systemctl stop mariadb@node1.service
$ sudo systemctl stop mariadb@node2.service

3. Remove old datadirs:

$ sudo rm -rf /var/lib/mysql-node1 /var/lib/mysql/node1 /var/lib/mysql-node2 /var/lib/mysql/node2

4. Create the directories for the instances with the correct permissions:

$ sudo mkdir -p /var/lib/mysql/node1
$ sudo mkdir -p /var/lib/mysql/node2
$ sudo chown mysql:root /var/lib/mysql/node1
$ sudo chown mysql:root /var/lib/mysql/node2

5. Start the MariaDB instances:

$ sudo systemctl start mariadb@node1.service
$ sudo systemctl start mariadb@node2.service

6. Check the running services

$ sudo ss -nlp | grep mysql
u_str  LISTEN 0 80 /run/mysql/node2mysql.sock 150930  * 0       users:(("mysqld",pid=7356,fd=20))
u_str  LISTEN 0 80 /run/mysql/node1mysql.sock 150771  * 0       users:(("mysqld",pid=7211,fd=20))
tcp    LISTEN 0 80 127.0.0.1:3310                     0.0.0.0:* users:(("mysqld",pid=7211,fd=19))
tcp    LISTEN 0 80 127.0.0.1:3315                     0.0.0.0:* users:(("mysqld",pid=7356,fd=19))
$ sudo systemctl status mariadb@node1.service
$ sudo systemctl status mariadb@node2.service

In general, the directories in the path to datadir should have 755 root:root while the datadir itself is created as 700 mysql:root. For example,

If

datadir = /var/lib/mysql/node1/databases

then

/var/lib/mysql/node1 directories will have 755 root:root, and
/var/lib/mysql/node1/databases directory will have 700 mysql:root