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Can't create/write to file '/var/lib/mysql/is_writable' #1107

Merged
merged 1 commit into from
Aug 23, 2017
Merged

Can't create/write to file '/var/lib/mysql/is_writable' #1107

merged 1 commit into from
Aug 23, 2017

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oaattia
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@oaattia oaattia commented Aug 22, 2017

I had issue that preventing me from starting mysql container, the error was like the following

Can't create/write to file '/var/lib/mysql/is_writable'

I found that it's a problem related to the user permission, as the mysql user which is not able to access folders mounted from OSX/Windows.

Added user: 1000:50 to fix that .

@Mahmoudz Mahmoudz merged commit a1d3eeb into laradock:master Aug 23, 2017
@a-h-abid
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a-h-abid commented Aug 25, 2017 •
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This created problem on my Linode Linux server. MySQL fails to run.

mysql_1                | Initializing database
mysql_1                | mysqld: Can't create/write to file '/var/lib/mysql/is_writable' (Errcode: 13 - Permission denied)
mysql_1                | 2017-08-25T01:13:08.807456Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
mysql_1                | 2017-08-25T01:13:08.807540Z 0 [Warning] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.
mysql_1                | 2017-08-25T01:13:08.809388Z 0 [ERROR] --initialize specified but the data directory exists and is not writable. Aborting.
mysql_1                | 2017-08-25T01:13:08.809425Z 0 [ERROR] Aborting

@Mahmoudz Your Travic-ci build is also failing. Please Check.... with PHP_VERSION=71

Update: Also failing on my windows machine

mysql_1                | 2017-08-25T01:28:16.925204Z 0 [Note] Basedir set to /usr/
mysql_1                | 2017-08-25T01:28:16.925369Z 0 [Warning] The syntax '--symbolic-links/-s' is deprecated and will be removed in a future release
mysql_1                | 2017-08-25T01:28:16.925411Z 0 [Warning] 'NO_ZERO_DATE', 'NO_ZERO_IN_DATE' and 'ERROR_FOR_DIVISION_BY_ZERO' sql modes should be used with strict mode. They will be merged with strict mode in a future release.
mysql_1                | 2017-08-25T01:28:16.926222Z 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
mysql_1                | 2017-08-25T01:28:16.926261Z 0 [Note] /usr/sbin/mysqld (mysqld 8.0.2-dmr) starting as process 1 ...
mysql_1                | 2017-08-25T01:28:16.935030Z 0 [Note] InnoDB: Using Linux native AIO
mysql_1                | 2017-08-25T01:28:16.935701Z 0 [Note] Plugin 'FEDERATED' is disabled.
mysql_1                | 2017-08-25T01:28:16.952638Z 1 [Note] InnoDB: PUNCH HOLE support available
mysql_1                | 2017-08-25T01:28:16.953023Z 1 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
mysql_1                | 2017-08-25T01:28:16.953041Z 1 [Note] InnoDB: Uses event mutexes
mysql_1                | 2017-08-25T01:28:16.953046Z 1 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
mysql_1                | 2017-08-25T01:28:16.953051Z 1 [Note] InnoDB: Compressed tables use zlib 1.2.3
mysql_1                | 2017-08-25T01:28:16.954955Z 1 [Note] InnoDB: Number of pools: 1
mysql_1                | 2017-08-25T01:28:16.957142Z 1 [Note] InnoDB: Using CPU crc32 instructions
mysql_1                | 2017-08-25T01:28:16.958837Z 1 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
mysql_1                | libnuma: Warning: /sys not mounted or invalid. Assuming one node: No such file or directory
mysql_1                | mbind: Operation not permitted
mysql_1                | mbind: Operation not permitted
mysql_1                | 2017-08-25T01:28:16.970143Z 1 [Note] InnoDB: Completed initialization of buffer pool
mysql_1                | 2017-08-25T01:28:16.971139Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
mysql_1                | 2017-08-25T01:28:17.062997Z 1 [Note] InnoDB: Using 'tablespaces.open.1' max LSN: 1222603668
mysql_1                | 2017-08-25T01:28:17.071286Z 1 [Note] InnoDB: Applying a batch of 0 redo log records ...
mysql_1                | 2017-08-25T01:28:17.071315Z 1 [Note] InnoDB: Apply batch completed!
mysql_1                | 2017-08-25T01:28:17.158631Z 1 [Note] InnoDB: Opened 2 existing undo tablespaces.
mysql_1                | 2017-08-25T01:28:17.609140Z 1 [Note] InnoDB: Creating shared tablespace for temporary tables
mysql_1                | 2017-08-25T01:28:17.610421Z 1 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
mysql_1                | 2017-08-25T01:28:17.694400Z 1 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
mysql_1                | 2017-08-25T01:28:17.704186Z 1 [Note] InnoDB: Created 128 and tracked 128 new rollback segment(s) in the temporary tablespace. 128 are now active.
mysql_1                | 2017-08-25T01:28:17.705262Z 1 [Note] InnoDB: 8.0.2 started; log sequence number 1222619483
mysql_1                | 2017-08-25T01:28:21.477270Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool
mysql_1                | 2017-08-25T01:28:21.491939Z 1 [Note] Found data dictionary with version 1
mysql_1                | 2017-08-25T01:28:21.533506Z 0 [Note] InnoDB: Buffer pool(s) load completed at 170825  7:28:21
mysql_1                | 2017-08-25T01:28:21.549173Z 0 [Note] Found ca.pem, server-cert.pem and server-key.pem in data directory. Trying to enable SSL support using them.
mysql_1                | 2017-08-25T01:28:21.567152Z 0 [Warning] CA certificate ca.pem is self signed.
mysql_1                | 2017-08-25T01:28:21.571707Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
mysql_1                | 2017-08-25T01:28:21.571819Z 0 [Note] IPv6 is available.
mysql_1                | 2017-08-25T01:28:21.571918Z 0 [Note]   - '::' resolves to '::';
mysql_1                | 2017-08-25T01:28:21.571995Z 0 [Note] Server socket created on IP: '::'.
mysql_1                | 2017-08-25T01:28:21.588177Z 0 [ERROR] Table 'mysql.component' doesn't exist
mysql_1                | 2017-08-25T01:28:21.588636Z 0 [ERROR] The mysql.component table is missing or has an incorrect definition.
mysql_1                | 2017-08-25T01:28:21.659359Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.user]
mysql_1                | 2017-08-25T01:28:21.659476Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.db]
mysql_1                | 2017-08-25T01:28:21.659510Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.proxies_priv]
mysql_1                | 2017-08-25T01:28:21.659527Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.tables_priv]
mysql_1                | 2017-08-25T01:28:21.659541Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.columns_priv]
mysql_1                | 2017-08-25T01:28:21.659592Z 0 [Warning] Storage engine 'MyISAM' does not support system tables. [mysql.procs_priv]
mysql_1                | 2017-08-25T01:28:21.659706Z 0 [ERROR] /usr/sbin/mysqld: Column count of mysql.user is wrong. Expected 47, found 45. The table is probably corrupted
mysql_1                | 2017-08-25T01:28:21.665375Z 0 [Warning] 'user' entry 'root@localhost' ignored in --skip-name-resolve mode.
mysql_1                | 2017-08-25T01:28:21.665465Z 0 [Warning] 'user' entry 'mysql.sys@localhost' ignored in --skip-name-resolve mode.
mysql_1                | 2017-08-25T01:28:21.665911Z 0 [Warning] 'db' entry 'sys mysql.sys@localhost' ignored in --skip-name-resolve mode.
mysql_1                | 2017-08-25T01:28:21.666346Z 0 [Warning] 'proxies_priv' entry '@ root@localhost' ignored in --skip-name-resolve mode.
mysql_1                | 2017-08-25T01:28:21.666417Z 0 [ERROR] Missing system table mysql.global_grants; please run mysql_upgrade to create it
mysql_1                | 2017-08-25T01:28:21.666723Z 0 [Warning] Could not load mysql.role_edges and mysql.default_roles tables. ACL DDLs will not work unless mysql_upgrade is executed.
mysql_1                | 2017-08-25T01:28:21.713054Z 0 [Warning] 'tables_priv' entry 'sys_config mysql.sys@localhost' ignored in --skip-name-resolve mode.
mysql_1                | 2017-08-25T01:28:21.728852Z 0 [Warning] System table 'func' is expected to be transactional.
mysql_1                | 2017-08-25T01:28:21.732497Z 0 [Note] /usr/sbin/mysqld: ready for connections. Version: '8.0.2-dmr'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  MySQL Community Server (GPL)

Removing this user:"1000:50" is working... Thou want to confirm, do I need to rebuild mysql container?? I'm using existing container before this PR.

@oaattia
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oaattia commented Aug 25, 2017

Have you tried to rebuild mysql container after adding user:1000:50 ?

@a-h-abid
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@oaattia Yes, I tried with rebuilding the container, still failing...

@muzk6
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muzk6 commented Sep 2, 2017

After I removed the line user: "1000:50" , and rebuild mysql container, it work successfully.

agebeyaw pushed a commit to agebeyaw/laradock that referenced this pull request Aug 22, 2018
@Mahmoudz
Merge pull request laradock#1107 from oaattia/master
7e9a361 
Can't create/write to file '/var/lib/mysql/is_writable'
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4 participants
@oaattia @a-h-abid @muzk6 @Mahmoudz