サーバーがつながらない。mysqlにつながらない

ある日突然、運営中のwebサービスに繋がらなくなった。
正確にいうと、webサービスには繋がっているが、mysql にアクセスできない。

参考になりそうなページ:https://totutotu.hatenablog.com/entry/2015/12/07/173936
サイトにアクセスしたときに表示された PHP のエラーメッセージ
-----------------------------------------------------------
Warning: mysql_set_charset(): No such file or directory in /var/www/libs/~~~~

Warning: mysql_set_charset(): A link to the server could not be established in /var/www/~~~~~
ConnectError!DB Error: connect failed
-----------------------------------------------------------
前回と同じエラー。
サーバーを再起動したら mysql に繋がらなくなった。

mysqld の状態を確認
-----------------------------------------------------------
service mysqld status
mysqld は停止していますがサブシステムがロックされています
-----------------------------------------------------------
(↑これはrootでない状態で確認した)

サーバーのerror_log
-----------------------------------------------------------
[Sun Sep 12 11:30:15 2021] [error] server reached MaxClients setting, consider raising the MaxClients setting
-----------------------------------------------------------

システムのログを調べる
-----------------------------------------------------------
cat /var/log/messages
-----------------------------------------------------------
サーバー再起動後だったため再起動前の情報が見えなかったので不明

ターミナルから mysqld のログを調べる
-----------------------------------------------------------
cat /var/log/mysqld.log
-----------------------------------------------------------

 
怪しいそうな部分だけ抜粋
-------------------------------------------------------------------------
2021-09-12 10:14:41 1623 [Note] - '::' resolves to '::';
2021-09-12 10:14:41 1623 [Note] Server socket created on IP: '::'.
2021-09-12 10:14:41 1623 [Note] Event Scheduler: Loaded 0 events
2021-09-12 10:14:41 1623 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:32:49 3983 [Note] Plugin 'FEDERATED' is disabled. ← おそらく起動開始がここ。disabled = 無効
2021-09-12 11:32:49 3983 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:32:49 3983 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:32:49 3983 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:32:49 3983 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:32:49 3983 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:32:49 3983 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:32:49 3983 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:32:49 3983 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:32:49 3983 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:32:50 3983 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:32:50 3983 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069557708 in the ib_logfiles!
2021-09-12 11:32:50 3983 [Note] InnoDB: Database was not shutdown normally!
2021-09-12 11:32:50 3983 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:32:50 3983 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:32:50 3983 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:32:50 3983 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:32:50 3983 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:32:50 3983 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:32:50 3983 [Note] InnoDB: 5.6.36 started; log sequence number 209069557708
2021-09-12 11:32:50 3983 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:32:50 3983 [Note] IPv6 is available.
2021-09-12 11:32:50 3983 [Note] - '::' resolves to '::';
2021-09-12 11:32:50 3983 [Note] Server socket created on IP: '::'.
2021-09-12 11:32:50 3983 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:32:50 3983 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:06 4025 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:06 4025 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:06 4025 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:06 4025 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:06 4025 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:06 4025 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:06 4025 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:06 4025 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:06 4025 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:07 4025 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:07 4025 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:07 4025 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069557927 in the ib_logfiles!
2021-09-12 11:33:07 4025 [Note] InnoDB: Database was not shutdown normally!
2021-09-12 11:33:07 4025 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:07 4025 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:07 4025 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:07 4025 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:33:07 4025 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:07 4025 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:07 4025 [Note] InnoDB: 5.6.36 started; log sequence number 209069557927
2021-09-12 11:33:07 4025 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:07 4025 [Note] IPv6 is available.
2021-09-12 11:33:07 4025 [Note] - '::' resolves to '::';
2021-09-12 11:33:07 4025 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:07 4025 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:07 4025 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:12 4068 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:12 4068 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:12 4068 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:12 4068 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:12 4068 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:12 4068 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:12 4068 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:12 4068 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:12 4068 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:12 4068 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:12 4068 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:12 4068 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069557937 in the ib_logfiles!
2021-09-12 11:33:12 4068 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:33:12 4068 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:12 4068 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:13 4068 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:13 4068 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:33:13 4068 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:13 4068 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:13 4068 [Note] InnoDB: 5.6.36 started; log sequence number 209069557937
2021-09-12 11:33:13 4068 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:13 4068 [Note] IPv6 is available.
2021-09-12 11:33:13 4068 [Note] - '::' resolves to '::';
2021-09-12 11:33:13 4068 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:13 4068 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:13 4068 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:17 4110 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:17 4110 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:17 4110 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:17 4110 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:17 4110 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:17 4110 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:17 4110 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:17 4110 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:17 4110 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:17 4110 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:17 4110 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:17 4110 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069557937
2021-09-12 11:33:17 4110 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:33:17 4110 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:17 4110 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:18 4110 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:18 4110 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069557947
2021-09-12 11:33:18 4110 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:18 4110 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:18 4110 [Note] InnoDB: 5.6.36 started; log sequence number 209069557947
2021-09-12 11:33:19 4110 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:19 4110 [Note] IPv6 is available.
2021-09-12 11:33:19 4110 [Note] - '::' resolves to '::';
2021-09-12 11:33:19 4110 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:19 4110 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:19 4110 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:22 4152 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:22 4152 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:22 4152 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:22 4152 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:22 4152 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:22 4152 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:22 4152 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:23 4152 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:23 4152 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:23 4152 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:23 4152 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:23 4152 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069557957 in the ib_logfiles!
2021-09-12 11:33:23 4152 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:33:23 4152 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:23 4152 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:23 4152 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:23 4152 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:33:24 4152 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:24 4152 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:24 4152 [Note] InnoDB: 5.6.36 started; log sequence number 209069557957
2021-09-12 11:33:24 4152 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:24 4152 [Note] IPv6 is available.
2021-09-12 11:33:24 4152 [Note] - '::' resolves to '::';
2021-09-12 11:33:24 4152 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:24 4152 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:24 4152 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:28 4201 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:28 4201 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:28 4201 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:28 4201 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:28 4201 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:28 4201 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:28 4201 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:28 4201 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:28 4201 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:28 4201 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:28 4201 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:28 4201 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069557957
2021-09-12 11:33:28 4201 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:33:28 4201 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:28 4201 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:28 4201 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:28 4201 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069558157
2021-09-12 11:33:29 4201 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
2021-09-12 11:33:29 4201 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:29 4201 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:29 4201 [Note] InnoDB: 5.6.36 started; log sequence number 209069558157
2021-09-12 11:33:29 4201 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:29 4201 [Note] IPv6 is available.
2021-09-12 11:33:29 4201 [Note] - '::' resolves to '::';
2021-09-12 11:33:29 4201 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:29 4201 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:29 4201 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:33:37 4265 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:33:37 4265 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:33:37 4265 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:33:37 4265 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:33:37 4265 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:33:37 4265 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:33:37 4265 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:33:37 4265 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:33:37 4265 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:33:37 4265 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:33:37 4265 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:33:37 4265 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069558563 in the ib_logfiles!
2021-09-12 11:33:37 4265 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:33:37 4265 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:33:37 4265 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:33:37 4265 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:33:37 4265 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:33:38 4265 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:33:38 4265 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:33:38 4265 [Note] InnoDB: 5.6.36 started; log sequence number 209069558563
2021-09-12 11:33:38 4265 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:33:38 4265 [Note] IPv6 is available.
2021-09-12 11:33:38 4265 [Note] - '::' resolves to '::';
2021-09-12 11:33:38 4265 [Note] Server socket created on IP: '::'.
2021-09-12 11:33:38 4265 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:33:38 4265 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:14 4355 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:14 4355 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:14 4355 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:14 4355 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:14 4355 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:14 4355 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:14 4355 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:14 4355 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:14 4355 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:14 4355 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:14 4355 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:14 4355 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069568015 in the ib_logfiles!
2021-09-12 11:36:14 4355 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:14 4355 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:14 4355 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:14 4355 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:14 4355 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:36:14 4355 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:14 4355 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:14 4355 [Note] InnoDB: 5.6.36 started; log sequence number 209069568015
2021-09-12 11:36:14 4355 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:14 4355 [Note] IPv6 is available.
2021-09-12 11:36:14 4355 [Note] - '::' resolves to '::';
2021-09-12 11:36:14 4355 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:14 4355 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:14 4355 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:21 4404 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:21 4404 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:21 4404 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:21 4404 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:21 4404 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:21 4404 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:21 4404 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:21 4404 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:21 4404 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:21 4404 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:21 4404 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:21 4404 [Note] InnoDB: The log sequence numbers 209069373861 and 209069373861 in ibdata files do not match the log sequence number 209069568235 in the ib_logfiles!
2021-09-12 11:36:21 4404 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:21 4404 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:21 4404 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:21 4404 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:21 4404 [Note] InnoDB: from the doublewrite buffer...
2021-09-12 11:36:21 4404 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:21 4404 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:21 4404 [Note] InnoDB: 5.6.36 started; log sequence number 209069568235
2021-09-12 11:36:21 4404 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:21 4404 [Note] IPv6 is available.
2021-09-12 11:36:21 4404 [Note] - '::' resolves to '::';
2021-09-12 11:36:21 4404 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:21 4404 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:21 4404 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:25 4449 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:25 4449 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:25 4449 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:25 4449 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:25 4449 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:25 4449 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:25 4449 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:25 4449 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:25 4449 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:25 4449 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:25 4449 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:25 4449 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568235
2021-09-12 11:36:25 4449 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:25 4449 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:25 4449 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:25 4449 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:25 4449 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568440
2021-09-12 11:36:25 4449 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
2021-09-12 11:36:26 4449 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:26 4449 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:26 4449 [Note] InnoDB: 5.6.36 started; log sequence number 209069568440
2021-09-12 11:36:26 4449 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:26 4449 [Note] IPv6 is available.
2021-09-12 11:36:26 4449 [Note] - '::' resolves to '::';
2021-09-12 11:36:26 4449 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:26 4449 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:26 4449 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:28 4503 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:28 4503 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:28 4503 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:28 4503 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:28 4503 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:28 4503 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:28 4503 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:28 4503 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:28 4503 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:28 4503 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:28 4503 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:28 4503 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568235
2021-09-12 11:36:28 4503 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:28 4503 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:28 4503 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:28 4503 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:28 4503 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568450
2021-09-12 11:36:28 4503 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
2021-09-12 11:36:29 4503 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:29 4503 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:29 4503 [Note] InnoDB: 5.6.36 started; log sequence number 209069568450
2021-09-12 11:36:29 4503 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:29 4503 [Note] IPv6 is available.
2021-09-12 11:36:29 4503 [Note] - '::' resolves to '::';
2021-09-12 11:36:29 4503 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:29 4503 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:29 4503 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:32 4551 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:32 4551 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:32 4551 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:32 4551 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:32 4551 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:32 4551 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:32 4551 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:32 4551 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:32 4551 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:32 4551 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:32 4551 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:32 4551 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568450
2021-09-12 11:36:32 4551 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:32 4551 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:32 4551 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:32 4551 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:32 4551 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568460
2021-09-12 11:36:32 4551 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:32 4551 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:32 4551 [Note] InnoDB: 5.6.36 started; log sequence number 209069568460
2021-09-12 11:36:32 4551 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:32 4551 [Note] IPv6 is available.
2021-09-12 11:36:32 4551 [Note] - '::' resolves to '::';
2021-09-12 11:36:32 4551 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:32 4551 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:32 4551 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:35 4601 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:35 4601 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:35 4601 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:35 4601 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:35 4601 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:35 4601 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:35 4601 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:35 4601 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:35 4601 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:35 4601 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:35 4601 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:35 4601 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568460
2021-09-12 11:36:35 4601 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:35 4601 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:35 4601 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:35 4601 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:35 4601 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568470
2021-09-12 11:36:36 4601 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:36 4601 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:36 4601 [Note] InnoDB: 5.6.36 started; log sequence number 209069568470
2021-09-12 11:36:36 4601 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:36 4601 [Note] IPv6 is available.
2021-09-12 11:36:36 4601 [Note] - '::' resolves to '::';
2021-09-12 11:36:36 4601 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:36 4601 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:36 4601 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:39 4641 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:39 4641 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:39 4641 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:39 4641 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:39 4641 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:39 4641 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:39 4641 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:39 4641 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:39 4641 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:39 4641 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:39 4641 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:39 4641 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568470
2021-09-12 11:36:39 4641 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:39 4641 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:39 4641 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:39 4641 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:39 4641 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568480
2021-09-12 11:36:39 4641 [Note] InnoDB: 128 rollback segment(s) are active.
2021-09-12 11:36:39 4641 [Note] InnoDB: Waiting for purge to start
2021-09-12 11:36:39 4641 [Note] InnoDB: 5.6.36 started; log sequence number 209069568480
2021-09-12 11:36:39 4641 [Note] Server hostname (bind-address): '*'; port: 3306
2021-09-12 11:36:39 4641 [Note] IPv6 is available.
2021-09-12 11:36:39 4641 [Note] - '::' resolves to '::';
2021-09-12 11:36:39 4641 [Note] Server socket created on IP: '::'.
2021-09-12 11:36:39 4641 [Note] Event Scheduler: Loaded 0 events
2021-09-12 11:36:39 4641 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.6.36' socket: '/var/lib/mysql/mysql.sock' port: 3306 MySQL Community Server (GPL)

2021-09-12 11:36:42 4689 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 11:36:42 4689 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:36:42 4689 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:36:42 4689 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 11:36:42 4689 [Note] InnoDB: Memory barrier is not used
2021-09-12 11:36:42 4689 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 11:36:42 4689 [Note] InnoDB: Using Linux native AIO
2021-09-12 11:36:42 4689 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 11:36:42 4689 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2021-09-12 11:36:42 4689 [Note] InnoDB: Completed initialization of buffer pool
2021-09-12 11:36:42 4689 [Note] InnoDB: Highest supported file format is Barracuda.
2021-09-12 11:36:42 4689 [Note] InnoDB: Log scan progressed past the checkpoint lsn 209069568470
2021-09-12 11:36:42 4689 [Note] InnoDB: InnoDB: Database was not shutdown normally!
2021-09-12 11:36:42 4689 [Note] InnoDB: Starting crash recovery.
2021-09-12 11:36:42 4689 [Note] InnoDB: Reading tablespace information from the .ibd files...
2021-09-12 11:36:42 4689 [Note] InnoDB: Restoring possible half-written data pages
2021-09-12 11:36:42 4689 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 209069568490 ← この後に mysqld が停止してログ無しみたい

2021-09-12 11:47:07 1622 [Note] Plugin 'FEDERATED' is disabled. ←サーバー手動再起動後
2021-09-12 11:47:07 1622 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 11:47:07 1622 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 11:47:07 1622 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
-------------------------------------------------------------------------
「InnoDB: Database was not shutdown normally!」というログが短時間のうちに複数あり、再起動を繰り返しているのが分かる。
これ以前を解析していけばシャットダウンの原因が分かるはず。

もう少しログをさかのぼったらこんな記述も見つけた。これも mysql が停止したタイミングもログと思われる
-------------------------------------------------------------------------
2021-09-12 09:01:57 1810 [Note] Plugin 'FEDERATED' is disabled.
2021-09-12 09:01:57 1810 [Note] InnoDB: Using atomics to ref count buffer pool pages
2021-09-12 09:01:57 1810 [Note] InnoDB: The InnoDB memory heap is disabled
2021-09-12 09:01:57 1810 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2021-09-12 09:01:57 1810 [Note] InnoDB: Memory barrier is not used
2021-09-12 09:01:57 1810 [Note] InnoDB: Compressed tables use zlib 1.2.3
2021-09-12 09:01:57 1810 [Note] InnoDB: Using Linux native AIO
2021-09-12 09:01:57 1810 [Note] InnoDB: Using CPU crc32 instructions
2021-09-12 09:01:57 1810 [Note] InnoDB: Initializing buffer pool, size = 128.0M
InnoDB: mmap(137363456 bytes) failed; errno 12
2021-09-12 09:01:57 1810 [ERROR] InnoDB: Cannot allocate memory for the buffer pool
2021-09-12 09:01:57 1810 [ERROR] Plugin 'InnoDB' init function returned error.
2021-09-12 09:01:57 1810 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2021-09-12 09:01:57 1810 [ERROR] Unknown/unsupported storage engine: InnoDB
2021-09-12 09:01:57 1810 [ERROR] Aborting

2021-09-12 09:01:57 1810 [Note] Binlog end
2021-09-12 09:01:57 1810 [Note] Shutting down plugin 'partition'
2021-09-12 09:01:57 1810 [Note] Shutting down plugin 'ARCHIVE'
2021-09-12 09:01:57 1810 [Note] Shutting down plugin 'BLACKHOLE'
2021-09-12 09:01:57 1810 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
-------------------------------------------------------------------------

短い時間で解決策を調べたけど不明。

とりあえずバッファプールへのメモリ割り当てを上げておく。
参考ページ:https://tech.librastudio.co.jp/entry/index.php/2018/05/22/post-1891/

現状を確認。128Mであることが分かる
--------------------------------------------------------
mysql> SHOW VARIABLES LIKE 'innodb_buffer_pool_size';
+-------------------------+-----------+
| Variable_name | Value |
+-------------------------+-----------+
| innodb_buffer_pool_size | 134217728 |
+-------------------------+-----------+
--------------------------------------------------------

my.cnf を編集(my.conf でない)
--------------------------------------------------------
vi my.cnf
--------------------------------------------------------

--------------------------------------------------------
[mysqld]
...
innodb_buffer_pool_size=512M
--------------------------------------------------------

mysql を再起動
--------------------------------------------------------
/etc/init.d/mysqld restart
--------------------------------------------------------

変更できていることを確認
--------------------------------------------------------
mysql> SHOW VARIABLES LIKE 'innodb_buffer_pool_size';
+-------------------------+-----------+
| Variable_name | Value |
+-------------------------+-----------+
| innodb_buffer_pool_size | 536870912 |
+-------------------------+-----------+
--------------------------------------------------------

ここも後で見る
MySQLパフォーマンスチューニング -my.cnfの見直し-