Wordpress Server Crashes, Ubuntu 16.04.3 LTS, access denied error


I have a website that crashes probably weekly. I checked the error logs and it looks like it’s an access issue. Still new to ubuntu, linux, and back-end work, so any help would be much appreciated.

Box: No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 16.04.3 LTS Release: 16.04 Codename: xenial

tail -40 /var/log/mysql/error.log

Error Log: 2019-05-13T11:54:50.669077Z 2 [Note] Access denied for user ‘root’@‘localhost’ (using password: NO) 2019-05-18T18:04:41.576981Z 0 [Warning] Changed limits: max_open_files: 1024 (requested 5000) 2019-05-18T18:04:41.589442Z 0 [Warning] Changed limits: table_open_cache: 431 (requested 2000) 2019-05-18T18:04:43.872335Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details). 2019-05-18T18:04:43.900979Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.25-0ubuntu0.16.04.2) starting as process 1442 … 2019-05-18T18:04:43.954087Z 0 [Note] InnoDB: PUNCH HOLE support available 2019-05-18T18:04:43.954139Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins 2019-05-18T18:04:43.954147Z 0 [Note] InnoDB: Uses event mutexes 2019-05-18T18:04:43.954214Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier 2019-05-18T18:04:43.954227Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.8 2019-05-18T18:04:43.954234Z 0 [Note] InnoDB: Using Linux native AIO 2019-05-18T18:04:43.956877Z 0 [Note] InnoDB: Number of pools: 1 2019-05-18T18:04:43.959548Z 0 [Note] InnoDB: Using CPU crc32 instructions 2019-05-18T18:04:44.005443Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M 2019-05-18T18:04:44.138851Z 0 [Note] InnoDB: Completed initialization of buffer pool 2019-05-18T18:04:44.179508Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority(). 2019-05-18T18:04:44.212889Z 0 [Note] InnoDB: Highest supported file format is Barracuda. 2019-05-18T18:04:44.221553Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 2995825286 2019-05-18T18:04:44.221593Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 2995825295 2019-05-18T18:04:44.221604Z 0 [Note] InnoDB: Database was not shutdown normally! 2019-05-18T18:04:44.221619Z 0 [Note] InnoDB: Starting crash recovery. 2019-05-18T18:04:44.414438Z 0 [Note] InnoDB: Removed temporary tablespace data file: “ibtmp1” 2019-05-18T18:04:44.414488Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables 2019-05-18T18:04:44.414690Z 0 [Note] InnoDB: Setting file ‘./ibtmp1’ size to 12 MB. Physically writing the file full; Please wait … 2019-05-18T18:04:44.506934Z 0 [Note] InnoDB: File ‘./ibtmp1’ size is now 12 MB. 2019-05-18T18:04:44.508474Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active. 2019-05-18T18:04:44.508491Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active. 2019-05-18T18:04:44.510921Z 0 [Note] InnoDB: Waiting for purge to start 2019-05-18T18:04:44.561531Z 0 [Note] InnoDB: 5.7.25 started; log sequence number 2995825295 2019-05-18T18:04:44.563157Z 0 [Note] InnoDB: Loading buffer pool(s) from /var/lib/mysql/ib_buffer_pool 2019-05-18T18:04:44.563684Z 0 [Note] Plugin ‘FEDERATED’ is disabled. 2019-05-18T18:04:44.616975Z 0 [Note] InnoDB: Buffer pool(s) load completed at 190518 18:04:44 2019-05-18T18:04:44.624628Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key 2019-05-18T18:04:44.624659Z 0 [Note] Server hostname (bind-address): ‘’; port: 3306 2019-05-18T18:04:44.624694Z 0 [Note] - ‘’ resolves to ‘’; 2019-05-18T18:04:44.624757Z 0 [Note] Server socket created on IP: ‘’. 2019-05-18T18:04:44.694594Z 0 [Note] Event Scheduler: Loaded 0 events 2019-05-18T18:04:44.696204Z 0 [Note] /usr/sbin/mysqld: ready for connections. Version: ‘5.7.25-0ubuntu0.16.04.2’ socket: ‘/var/run/mysqld/mysqld.sock’ port: 3306 (Ubuntu) 2019-05-18T18:04:45.031568Z 2 [Note] Access denied for user ‘root’@‘localhost’ (using password: NO)

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I believe that your server is running out of RAM and your MySQL is being killed because of that. But I don’t think that MySQL is the core problem.

What you could do is check your system logs first:

dmesg | less

Then if you are using PHP and Apache, make sure to adjust the PHP memory usage so that it is not too high.

Also I would strongly suggest checking your Apache access logs for that period of time when the MySQL was killed and see if there is any spike in your traffic or maybe any malicious requests.

Another thing that you could also do is to add some extra RAM to your server.

Hope that this helps! Regards, Bobby