Unable to start mysql service, no errors

The issue

I have a debian server running a LAMP stack. For no reason this afternoon, my MySQL server crashed and I seem to be unable to restart it.

When I try to start it with the command service mysql start no output is given and no mysql instance is running either. The error log is also not recording anything.

What I tried

When I try to start a new instance with the mysqld command in console I just get the following message:

171113 18:44:52 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead.
171113 18:44:52 [Note] mysqld (mysqld 5.5.55-0+deb7u1) starting as process 6279 ...

But checking the running processes list with the top command shows no mysql instance running.

When checking the /var/log/mysql/error.log I get the following information:

171113 15:02:08 [Note] Plugin 'FEDERATED' is disabled.
171113 15:02:08 InnoDB: The InnoDB memory heap is disabled
171113 15:02:08 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 15:02:08 InnoDB: Compressed tables use zlib 1.2.7
171113 15:02:08 InnoDB: Using Linux native AIO
171113 15:02:08 InnoDB: Initializing buffer pool, size = 128.0M
171113 15:02:08 InnoDB: Completed initialization of buffer pool
171113 15:02:08 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 372845412514
171113 15:02:08  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 372846067858
171113 15:02:08  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 0 1 2 3 4 5 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
171113 15:02:09  InnoDB: Waiting for the background threads to start
171113 15:02:10 InnoDB: 5.5.55 started; log sequence number 372846067858
171113 15:02:10 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
171113 15:02:10 [Note]   - '127.0.0.1' resolves to '127.0.0.1';
171113 15:02:10 [Note] Server socket created on IP: '127.0.0.1'.
171113 15:02:10 [ERROR] Can't start server : Bind on unix socket: No such file or directory
171113 15:02:10 [ERROR] Do you already have another mysqld server running on socket: /var/run/mysqld/mysqld.sock ?
171113 15:02:10 [ERROR] Aborting

171113 15:02:10  InnoDB: Starting shutdown...
171113 15:02:10  InnoDB: Shutdown completed; log sequence number 372846067942
171113 15:02:10 [Note] mysqld: Shutdown complete

171113 15:05:25 [Note] Plugin 'FEDERATED' is disabled.
171113 15:05:25 InnoDB: The InnoDB memory heap is disabled
171113 15:05:25 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 15:05:25 InnoDB: Compressed tables use zlib 1.2.7
171113 15:05:25 InnoDB: Using Linux native AIO
171113 15:05:25 InnoDB: Initializing buffer pool, size = 128.0M
171113 15:05:25 InnoDB: Completed initialization of buffer pool
171113 15:05:25 InnoDB: highest supported file format is Barracuda.
171113 15:05:25  InnoDB: Waiting for the background threads to start
171113 15:05:26 InnoDB: 5.5.55 started; log sequence number 372846067942
mysqld: Too many arguments (first extra is 'stop').
Use --verbose --help to get a list of available options
171113 15:05:26 [ERROR] Aborting

171113 15:05:26  InnoDB: Starting shutdown...
171113 15:05:27  InnoDB: Shutdown completed; log sequence number 372846067942
171113 15:05:27 [Note] mysqld: Shutdown complete

171113 15:09:15 [Note] Plugin 'FEDERATED' is disabled.
171113 15:09:15 InnoDB: The InnoDB memory heap is disabled
171113 15:09:15 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 15:09:15 InnoDB: Compressed tables use zlib 1.2.7
171113 15:09:15 InnoDB: Using Linux native AIO
171113 15:09:15 InnoDB: Initializing buffer pool, size = 128.0M
171113 15:09:15 InnoDB: Completed initialization of buffer pool
171113 15:09:15 InnoDB: highest supported file format is Barracuda.
171113 15:09:15  InnoDB: Waiting for the background threads to start
171113 15:09:16 InnoDB: 5.5.55 started; log sequence number 372846067942
171113 15:09:16 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
171113 15:09:16 [Note]   - '127.0.0.1' resolves to '127.0.0.1';
171113 15:09:16 [Note] Server socket created on IP: '127.0.0.1'.
171113 15:09:16 [ERROR] Can't start server : Bind on unix socket: No such file or directory
171113 15:09:16 [ERROR] Do you already have another mysqld server running on socket: /var/run/mysqld/mysqld.sock ?
171113 15:09:16 [ERROR] Aborting

171113 15:09:16  InnoDB: Starting shutdown...
171113 15:09:17  InnoDB: Shutdown completed; log sequence number 372846067942
171113 15:09:17 [Note] mysqld: Shutdown complete

171113 15:10:04 [Note] Plugin 'FEDERATED' is disabled.
171113 15:10:04 InnoDB: The InnoDB memory heap is disabled
171113 15:10:04 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 15:10:04 InnoDB: Compressed tables use zlib 1.2.7
171113 15:10:04 InnoDB: Using Linux native AIO
171113 15:10:04 InnoDB: Initializing buffer pool, size = 128.0M
171113 15:10:04 InnoDB: Completed initialization of buffer pool
171113 15:10:04 InnoDB: highest supported file format is Barracuda.
171113 15:10:05  InnoDB: Waiting for the background threads to start
171113 15:10:06 InnoDB: 5.5.55 started; log sequence number 372846067942
171113 15:10:06 [Note] Server hostname (bind-address): '127.0.0.1'; port: 3306
171113 15:10:06 [Note]   - '127.0.0.1' resolves to '127.0.0.1';
171113 15:10:06 [Note] Server socket created on IP: '127.0.0.1'.
171113 15:10:06 [ERROR] Can't start server : Bind on unix socket: No such file or directory
171113 15:10:06 [ERROR] Do you already have another mysqld server running on socket: /var/run/mysqld/mysqld.sock ?
171113 15:10:06 [ERROR] Aborting

171113 15:10:06  InnoDB: Starting shutdown...
171113 15:10:06  InnoDB: Shutdown completed; log sequence number 372846067942
171113 15:10:06 [Note] mysqld: Shutdown complete

171113 15:10:16 [Note] Plugin 'FEDERATED' is disabled.
171113 15:10:16 InnoDB: The InnoDB memory heap is disabled
171113 15:10:16 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 15:10:16 InnoDB: Compressed tables use zlib 1.2.7
171113 15:10:16 InnoDB: Using Linux native AIO
171113 15:10:16 InnoDB: Initializing buffer pool, size = 128.0M
171113 15:10:16 InnoDB: Completed initialization of buffer pool
171113 15:10:16 InnoDB: highest supported file format is Barracuda.
171113 15:10:16  InnoDB: Waiting for the background threads to start
171113 15:10:17 InnoDB: 5.5.55 started; log sequence number 372846067942
mysqld: Too many arguments (first extra is 'stop').
Use --verbose --help to get a list of available options
171113 15:10:17 [ERROR] Aborting

171113 15:10:17  InnoDB: Starting shutdown...
171113 15:10:17  InnoDB: Shutdown completed; log sequence number 372846067942
171113 15:10:17 [Note] mysqld: Shutdown complete

171113 18:44:53 [Note] Plugin 'FEDERATED' is disabled.
171113 18:44:53 InnoDB: The InnoDB memory heap is disabled
171113 18:44:53 InnoDB: Mutexes and rw_locks use GCC atomic builtins
171113 18:44:53 InnoDB: Compressed tables use zlib 1.2.7
171113 18:44:53 InnoDB: Using Linux native AIO
171113 18:44:53 InnoDB: Initializing buffer pool, size = 128.0M
171113 18:44:53 InnoDB: Completed initialization of buffer pool
171113 18:44:53 InnoDB: highest supported file format is Barracuda.
171113 18:44:53  InnoDB: Waiting for the background threads to start
171113 18:44:54 InnoDB: 5.5.55 started; log sequence number 372846067942
mysqld: Too many arguments (first extra is 'start').
Use --verbose --help to get a list of available options
171113 18:44:54 [ERROR] Aborting

171113 18:44:54  InnoDB: Starting shutdown...
171113 18:44:55  InnoDB: Shutdown completed; log sequence number 372846067942
171113 18:44:55 [Note] mysqld: Shutdown complete

So at least the mysqld command shows an error… But I’m being none the wiser.

Short recap

• service mysql restart does nothing
• mysqld gives a console output but stops immediately and throws an error (error logs shown above)

Can anyone point me in the right direction to figure out how to:

• Restart my mysql server process through the preffered “service way”
• Avoid this from happening in the future

Edit: some progress

I have been playing around a bit and found a crude way to get it running, for now. After creating the mysqld folder at /var/run/mysqld the command mysqld works. But this feels terribly badly hacky and I have to recreate the mysqld folder in /var/run at each server reboot.

After I created the mysqld folder in /var/run I get the following output:
root@id93401-vps002:~# mysqld

171113 20:31:30 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead.
171113 20:31:30 [Note] mysqld (mysqld 5.5.55-0+deb7u1) starting as process 2048 ...

This at least keeps the site afloat for now. I am currently keeping mysql up with nohup mysqld.

My config file at /etc/mysql/my.cnf

# GNU nano 2.2.6                  File: my.cnf                                            
#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
#
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket          = /var/run/mysqld/mysqld.sock
  GNU nano 2.2.6                  File: my.cnf                                            
#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
  GNU nano 2.2.6                  File: my.cnf                                            
#
# The MySQL database server configuration file.
#
# You can copy this to one of:
# - "/etc/mysql/my.cnf" to set global options,
# - "~/.my.cnf" to set user-specific options.
#
# One can use all long options that the program supports.
# Run program with --help to get a list of available options and with
# --print-defaults to see which it would actually understand and use.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

# This will be passed to all mysql clients
# It has been reported that passwords should be enclosed with ticks/quotes
# escpecially if they contain "#" chars...
# Remember to edit /etc/mysql/debian.cnf when changing the socket location.
[client]
port            = 3306
socket          = /var/run/mysqld/mysqld.sock

# Here is entries for some specific programs
# The following values assume you have at least 32M ram

# This was formally known as [safe_mysqld]. Both versions are currently parsed.
[mysqld_safe]
socket          = /var/run/mysqld/mysqld.sock
nice            = 0

[mysqld]
#
# * Basic Settings
#
user            = mysql
pid-file        = /var/run/mysqld/mysqld.pid
socket          = /var/run/mysqld/mysqld.sock
port            = 3306
basedir         = /usr
datadir         = /var/lib/mysql
tmpdir          = /tmp
lc-messages-dir = /usr/share/mysql
skip-external-locking
#
# Instead of skip-networking the default is now to listen only on
# localhost which is more compatible and is not less secure.
bind-address            = 127.0.0.1
#
# * Fine Tuning
#
key_buffer              = 16M
max_allowed_packet      = 16M
thread_stack            = 192K
thread_cache_size       = 8
# This replaces the startup script and checks MyISAM tables if needed
# the first time they are touched                                                         myisam-recover-options  = BACKUP
#max_connections        = 100
#table_cache            = 64
#thread_concurrency     = 10
#
# * Query Cache Configuration
#
query_cache_limit       = 1M
query_cache_size        = 16M
#
# * Logging and Replication
#
# Both location gets rotated by the cronjob.
# Be aware that this log type is a performance killer.
# As of 5.1 you can enable the log at runtime!                                            #general_log_file        = /var/log/mysql/mysql.log
#general_log             = 1
#
# Error log - should be very few entries.
#
log_error = /var/log/mysql/error.log
#
# Here you can see queries with especially long duration
#slow_query_log = 1
#slow_query_log_file = /var/log/mysql/mysql-slow.log
#long_query_time = 2
#log-queries-not-using-indexes
#
# The following can be used as easy to replay backup logs or for replication.
# note: if you are setting up a replication slave, see README.Debian about                #       other settings you may need to change.
#server-id              = 1
#log_bin                        = /var/log/mysql/mysql-bin.log
expire_logs_days        = 10
max_binlog_size         = 100M
#binlog_do_db           = include_database_name
#binlog_ignore_db       = include_database_name
#
# * InnoDB
#
# InnoDB is enabled by default with a 10MB datafile in /var/lib/mysql/.
# Read the manual for more InnoDB related options. There are many!
#
# * Security Features
#                                                                                         # Read the manual, too, if you want chroot!
# chroot = /var/lib/mysql/
#
#
# For generating SSL certificates I recommend the OpenSSL GUI "tinyca".
#
# ssl-ca=/etc/mysql/cacert.pem
# ssl-cert=/etc/mysql/server-cert.pem
# ssl-key=/etc/mysql/server-key.pem



[mysqldump]
quick
quote-names
max_allowed_packet      = 16M                                                             
[mysql]
#no-auto-rehash # faster start of mysql but no tab completition

[isamchk]
key_buffer              = 16M

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/