Database appears to have disappeared on a site

I went to do a pull from a flywheel local site today and got a notice that said mysql was unavailable. I clicked on the database tab and tried to load adminer and the adminer page says file not found. It’s almost like the database is gone.

I looked at the log files for SQL and see this error repeatedly when the database tries to start up.

Any ideas on how I can it back to working again? Right now I can’t push, pull, or even load the website locally.

2019-08-12T16:39:49.505123Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2019-08-12T16:39:49.505494Z 0 [Note] /usr/sbin/mysqld (mysqld 5.7.23) starting as process 1361 ...
2019-08-12T16:39:49.513794Z 0 [Note] InnoDB: PUNCH HOLE support available
2019-08-12T16:39:49.513904Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2019-08-12T16:39:49.514002Z 0 [Note] InnoDB: Uses event mutexes
2019-08-12T16:39:49.514086Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2019-08-12T16:39:49.514168Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2019-08-12T16:39:49.514250Z 0 [Note] InnoDB: Using Linux native AIO
2019-08-12T16:39:49.514785Z 0 [Note] InnoDB: Number of pools: 1
2019-08-12T16:39:49.515033Z 0 [Note] InnoDB: Using CPU crc32 instructions
2019-08-12T16:39:49.517599Z 0 [Note] InnoDB: Initializing buffer pool, total size = 32M, instances = 1, chunk size = 32M
2019-08-12T16:39:49.523084Z 0 [Note] InnoDB: Completed initialization of buffer pool
2019-08-12T16:39:49.524766Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2019-08-12T16:39:49.537881Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2019-08-12T16:39:49.538740Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 40535828
2019-08-12T16:39:49.538837Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 40535945
2019-08-12T16:39:49.538951Z 0 [ERROR] InnoDB: Ignoring the redo log due to missing MLOG_CHECKPOINT between the checkpoint 40535828 and the end 40535945.
2019-08-12T16:39:49.539047Z 0 [ERROR] InnoDB: Plugin initialization aborted with error Generic error
2019-08-12T16:39:50.141566Z 0 [ERROR] Plugin 'InnoDB' init function returned error.
2019-08-12T16:39:50.141726Z 0 [ERROR] Plugin 'InnoDB' registration as a STORAGE ENGINE failed.
2019-08-12T16:39:50.141817Z 0 [ERROR] Failed to initialize builtin plugins.
2019-08-12T16:39:50.141898Z 0 [ERROR] Aborting

2019-08-12T16:39:50.141979Z 0 [Note] Binlog end
2019-08-12T16:39:50.142102Z 0 [Note] Shutting down plugin 'CSV'
2019-08-12T16:39:50.142982Z 0 [Note] /usr/sbin/mysqld: Shutdown complete

Attaching the flywheel log file which also has an error in it.

local-by-flywheel.log (470.2 KB)

Hey @tnhsaesop

It looks like somehow the database has become corrupted. Are you able to create a new, plain WordPress site?

If you are able to create a new site, then can you try restoring the site to a new one in Local? You can use a backup of the site, or try using the files for the site by following the steps outlined in the “Restoring From Only Local Site files” section of this help doc:

I was able to restore the database from backup. Thanks.

Hunter Nelson | President & Founder

Tortoise and Hare Software