Error: while trying to restart mysql - mysql

i am trying to restart mysql service, but the following error log is disturbing me.
help me to out from the situation...
here is the config file..
my.cnf:
[mysqld]
bind-address = 0.0.0.0
#server-id = 2
#master-host=192.168.10.110
#master-connect-retry=60
#master-user=slave
#master-password=slave
#replicate-do-db=repltest
max_connections=500
datadir=/var/lib/mysql
socket=/var/lib/mysql/mysql.sock
user=mysql
symbolic-links=0
here i attached the log file details...
log file:
2016-04-28T06:13:45.032226Z 0 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
2016-04-28T06:13:45.032454Z 0 [Note] - '0.0.0.0' resolves to '0.0.0.0';
2016-04-28T06:13:45.032669Z 0 [Note] Server socket created on IP: '0.0.0.0'.
2016-04-28T06:13:45.088670Z 0 [ERROR] Fatal error: mysql.user table is damaged. Please run mysql_upgrade.
2016-04-28T06:13:45.088806Z 0 [ERROR] Aborting
2016-04-28T06:13:45.088828Z 0 [Note] Binlog end
2016-04-28T06:13:45.088935Z 0 [Note] Shutting down plugin 'ngram'
2016-04-28T06:13:45.088951Z 0 [Note] Shutting down plugin 'partition'
2016-04-28T06:13:45.088960Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2016-04-28T06:13:45.088968Z 0 [Note] Shutting down plugin 'ARCHIVE'
2016-04-28T06:13:45.088984Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2016-04-28T06:13:45.088993Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2016-04-28T06:13:45.089001Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2016-04-28T06:13:45.089007Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2016-04-28T06:13:45.089013Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2016-04-28T06:13:45.089019Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2016-04-28T06:13:45.089025Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2016-04-28T06:13:45.089030Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2016-04-28T06:13:45.089036Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2016-04-28T06:13:45.089042Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2016-04-28T06:13:45.089048Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2016-04-28T06:13:45.089054Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2016-04-28T06:13:45.089060Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2016-04-28T06:13:45.089065Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2016-04-28T06:13:45.089071Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2016-04-28T06:13:45.089077Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2016-04-28T06:13:45.089083Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2016-04-28T06:13:45.089088Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2016-04-28T06:13:45.089094Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2016-04-28T06:13:45.089100Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2016-04-28T06:13:45.089105Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2016-04-28T06:13:45.089111Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2016-04-28T06:13:45.089117Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2016-04-28T06:13:45.089122Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2016-04-28T06:13:45.089128Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2016-04-28T06:13:45.089134Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2016-04-28T06:13:45.089140Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2016-04-28T06:13:45.089146Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2016-04-28T06:13:45.089151Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2016-04-28T06:13:45.089157Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2016-04-28T06:13:45.089163Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2016-04-28T06:13:45.089169Z 0 [Note] Shutting down plugin 'InnoDB'
2016-04-28T06:13:45.089256Z 0 [Note] InnoDB: FTS optimize thread exiting.
2016-04-28T06:13:45.089373Z 0 [Note] InnoDB: Starting shutdown...
2016-04-28T06:13:45.189628Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2016-04-28T06:13:45.189978Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 160428 11:43:45
2016-04-28T06:13:46.934177Z 0 [Note] InnoDB: Shutdown completed; log sequence number 49822303
2016-04-28T06:13:46.936105Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2016-04-28T06:13:46.936121Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2016-04-28T06:13:46.936169Z 0 [Note] Shutting down plugin 'MEMORY'
2016-04-28T06:13:46.936179Z 0 [Note] Shutting down plugin 'CSV'
2016-04-28T06:13:46.936184Z 0 [Note] Shutting down plugin 'MyISAM'
2016-04-28T06:13:46.936196Z 0 [Note] Shutting down plugin 'sha256_password'
2016-04-28T06:13:46.936200Z 0 [Note] Shutting down plugin 'mysql_native_password'
2016-04-28T06:13:46.936321Z 0 [Note] Shutting down plugin 'binlog'
2016-04-28T06:13:46.936427Z 0 [Note] /usr/sbin/mysqld: Shutdown complete
2016-04-28T06:13:46.947072Z mysqld_safe mysqld from pid file /var/run/mysqld/mysqld.pid ended


Try Updating / Upgrading Mysql.
Or Reset the mysql.user table , it is damaged.
Because the log says:
Fatal error: mysql.user table is damaged. Please run mysql_upgrade.

Related

MySQL Keeps shutting down

I am having an issue regarding my MySQL Database.
I have a program which has a mild to heavy traffic per day. It was working well before but these past few days it keeps on shutting and the server restarts it after a few seconds or worst I have to restart it manually. What I don't understand is that how and why does it keeps on shutting down. It displays this notes on MySQL logs :
2020-01-28T06:02:00.157339Z 0 [Note] Giving 0 client threads a chance to die gracefully
2020-01-28T06:02:00.157379Z 0 [Note] Shutting down slave threads
2020-01-28T06:02:00.157385Z 0 [Note] Forcefully disconnecting 0 remaining clients
2020-01-28T06:02:00.157393Z 0 [Note] Event Scheduler: Purging the queue. 0 events
2020-01-28T06:02:00.157442Z 0 [Note] Binlog end
2020-01-28T06:02:00.162900Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2020-01-28T06:02:00.162903Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2020-01-28T06:02:00.162906Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2020-01-28T06:02:00.162910Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2020-01-28T06:02:00.162913Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2020-01-28T06:02:00.162916Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2020-01-28T06:02:00.162920Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2020-01-28T06:02:00.162923Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2020-01-28T06:02:00.162927Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2020-01-28T06:02:00.162930Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2020-01-28T06:02:00.162933Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2020-01-28T06:02:00.162937Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2020-01-28T06:02:00.162940Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2020-01-28T06:02:00.162943Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2020-01-28T06:02:00.162947Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2020-01-28T06:02:00.162950Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2020-01-28T06:02:00.162954Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2020-01-28T06:02:00.162957Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2020-01-28T06:02:00.162960Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2020-01-28T06:02:00.162964Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2020-01-28T06:02:00.162967Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2020-01-28T06:02:00.162970Z 0 [Note] Shutting down plugin 'InnoDB'
2020-01-28T06:02:00.163030Z 0 [Note] InnoDB: FTS optimize thread exiting.
2020-01-28T06:02:00.163125Z 0 [Note] InnoDB: Starting shutdown...
2020-01-28T06:02:00.263407Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2020-01-28T06:02:00.264206Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 200128 6:02:00
2020-01-28T06:02:01.380815Z 0 [Note] InnoDB: Shutdown completed; log sequence number 564620850
2020-01-28T06:02:01.382628Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2020-01-28T06:02:01.382643Z 0 [Note] Shutting down plugin 'MEMORY'
2020-01-28T06:02:01.382649Z 0 [Note] Shutting down plugin 'CSV'
2020-01-28T06:02:01.382654Z 0 [Note] Shutting down plugin 'sha256_password'
2020-01-28T06:02:01.382657Z 0 [Note] Shutting down plugin 'mysql_native_password'
2020-01-28T06:02:01.382833Z 0 [Note] Shutting down plugin 'binlog'
2020-01-28T06:02:01.383206Z 0 [Note] /usr/sbin/mysqld: Shutdown complete
GLOBAL STATUS
https://drive.google.com/file/d/1S9kTDaMlNMenWMbGg_mByHQnG-eYRYap/view
GLOBAL VARIABLE
https://drive.google.com/file/d/1Inqp8xv3NYmEJY9x8_QmasNCp4VZUCbF/view
ADDED INFORMATION
Memory as of now: 563M/15.7G
Description: Ubuntu 18.04.1 LTS
MySQL Server version: 5.7.29-0ubuntu0.18.04.1 (Ubuntu)
I have tried searching around the web but unfortunately didn't find a solution. I hope someone can help me with this. If I am missing out some information that may help in resolving this, just let me know. Thank you 😊

Please send SHOW GLOBAL STATUS and SHOW GLOBAL VARIABLES values.

Webmin/Virtualmin MySQL Server Shuts Down Unexpectedly

I have a MySQL Server that shutdowns unexpectedly. I am using Ubuntu 16.04 LTS with Webmin/Virtualmin installed. I don't see any errors in the error log. I just see notes.
I have this error (/var/log/mysql/error.log):
2018-10-25T03:03:01.744292Z 0 [Note] Giving 0 client threads a chance to die gracefully
2018-10-25T03:03:01.744322Z 0 [Note] Shutting down slave threads
2018-10-25T03:03:01.744329Z 0 [Note] Forcefully disconnecting 0 remaining clients
2018-10-25T03:03:01.744336Z 0 [Note] Event Scheduler: Purging the queue. 0 events
2018-10-25T03:03:03.744997Z 0 [Note] Binlog end
2018-10-25T03:03:03.747376Z 0 [Note] Shutting down plugin 'auth_socket'
2018-10-25T03:03:03.747390Z 0 [Note] Shutting down plugin 'ngram'
2018-10-25T03:03:03.747394Z 0 [Note] Shutting down plugin 'partition'
2018-10-25T03:03:03.747398Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2018-10-25T03:03:03.747402Z 0 [Note] Shutting down plugin 'ARCHIVE'
2018-10-25T03:03:03.747405Z 0 [Note] Shutting down plugin 'MyISAM'
2018-10-25T03:03:03.747410Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2018-10-25T03:03:03.747414Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2018-10-25T03:03:03.747417Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2018-10-25T03:03:03.747420Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2018-10-25T03:03:03.747422Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2018-10-25T03:03:03.747425Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2018-10-25T03:03:03.747428Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2018-10-25T03:03:03.747431Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2018-10-25T03:03:03.747434Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2018-10-25T03:03:03.747447Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2018-10-25T03:03:03.747457Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2018-10-25T03:03:03.747460Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2018-10-25T03:03:03.747463Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2018-10-25T03:03:03.747465Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2018-10-25T03:03:03.747468Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2018-10-25T03:03:03.747470Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2018-10-25T03:03:03.747473Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2018-10-25T03:03:03.747475Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2018-10-25T03:03:03.747478Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2018-10-25T03:03:03.747480Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2018-10-25T03:03:03.747483Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2018-10-25T03:03:03.747486Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2018-10-25T03:03:03.747488Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2018-10-25T03:03:03.747491Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2018-10-25T03:03:03.747493Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2018-10-25T03:03:03.747496Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2018-10-25T03:03:03.747498Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2018-10-25T03:03:03.747505Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2018-10-25T03:03:03.747508Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2018-10-25T03:03:03.747510Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2018-10-25T03:03:03.747513Z 0 [Note] Shutting down plugin 'InnoDB'
2018-10-25T03:03:03.747596Z 0 [Note] InnoDB: FTS optimize thread exiting.
2018-10-25T03:03:03.747701Z 0 [Note] InnoDB: Starting shutdown...
2018-10-25T03:03:03.848008Z 0 [Note] InnoDB: Dumping buffer pool(s) to /var/lib/mysql/ib_buffer_pool
2018-10-25T03:03:03.848203Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 181025 11:03:03
2018-10-25T03:03:05.258944Z 0 [Note] InnoDB: Shutdown completed; log sequence number 94132723
2018-10-25T03:03:05.260534Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2018-10-25T03:03:05.260553Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2018-10-25T03:03:05.260585Z 0 [Note] Shutting down plugin 'CSV'
2018-10-25T03:03:05.260590Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2018-10-25T03:03:05.260594Z 0 [Note] Shutting down plugin 'MEMORY'
2018-10-25T03:03:05.260598Z 0 [Note] Shutting down plugin 'sha256_password'
2018-10-25T03:03:05.260601Z 0 [Note] Shutting down plugin 'mysql_native_password'
2018-10-25T03:03:05.260794Z 0 [Note] Shutting down plugin 'binlog'
2018-10-25T03:03:05.263651Z 0 [Note] /usr/sbin/mysqld: Shutdown complete
I need help on how to fix this. I've been with a few forums and research about this kind of issue but I don't have any luck finding a solution.
I have to always restart the service whenever service shuts down.

I'd almost guess its possibly some sort of resource issue - is this on some sort of virtual instance ? Check your memory and disk usage initially, I've seen a lot of virtual instances unable to allocate enough memory and MySQl just shut off like this.
If so, you can maybe squeeze a bit more use by increasing your SWAP memory allocation if you cannot add more memory.

install mysql server on linux without admin persmission

I tried to install MySQL 5.7 on a redhat server without root permission. I downloaded the source code and it compiled and installed smoothly. But when I run mysqld it always pop out error.
I followed the instruction on
http://www.martijn-onderwater.nl/2010/11/23/installing-mysql-on-linux-without-root-privileges/
and I created a my.cnf file
[mysqld]
port=3306
socket=/afs/crc.nd.edu/user/j/jlai1/MySQL/thesock
basedir=/afs/crc.nd.edu/user/j/jlai1/MySQL
datadir=data
pid-file=$HOME/MySQL/mysql.pid
user=root
[client]
port=3306
socket=$MySQL_HOME/thesock
user=root
[mysqladmin]
socket=$MySQL_HOME/thesock
user=root
when I run ./bin/mysqld --defaults-file=my.cnf --initialize, it works fine. But I got the following problem
./bin/mysqld --defaults-file=my.cnf
2017-02-24T16:04:40.098102Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-02-24T16:04:40.098259Z 0 [Note] --secure-file-priv is set to NULL. Operations related to importing and exporting data are disabled
2017-02-24T16:04:40.098302Z 0 [Note] ./bin/mysqld (mysqld 5.7.17) starting as process 1786 ...
2017-02-24T16:04:40.103470Z 0 [Warning] One can only use the --user switch if running as root
2017-02-24T16:04:40.105092Z 0 [Note] InnoDB: PUNCH HOLE support available
2017-02-24T16:04:40.105121Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-02-24T16:04:40.105128Z 0 [Note] InnoDB: Uses event mutexes
2017-02-24T16:04:40.105137Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2017-02-24T16:04:40.105143Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-02-24T16:04:40.105466Z 0 [Note] InnoDB: Number of pools: 1
2017-02-24T16:04:40.105593Z 0 [Note] InnoDB: Using CPU crc32 instructions
2017-02-24T16:04:40.106782Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2017-02-24T16:04:40.115005Z 0 [Note] InnoDB: Completed initialization of buffer pool
2017-02-24T16:04:40.117871Z 0 [Note] InnoDB: If the mysqld execution user is authorized, page cleaner thread priority can be changed. See the man page of setpriority().
2017-02-24T16:04:40.133076Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2017-02-24T16:04:40.150182Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2017-02-24T16:04:40.150804Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2017-02-24T16:04:40.279174Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2017-02-24T16:04:40.280871Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2017-02-24T16:04:40.280904Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2017-02-24T16:04:40.281963Z 0 [Note] InnoDB: Waiting for purge to start
2017-02-24T16:04:40.332115Z 0 [Note] InnoDB: 5.7.17 started; log sequence number 2534599
2017-02-24T16:04:40.332297Z 0 [Note] InnoDB: Loading buffer pool(s) from /afs/crc.nd.edu/user/j/jlai1/MySQL/data/ib_buffer_pool
2017-02-24T16:04:40.332547Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-02-24T16:04:40.337533Z 0 [Note] InnoDB: Buffer pool(s) load completed at 170224 11:04:40
2017-02-24T16:04:40.340352Z 0 [Warning] Failed to set up SSL because of the following SSL library error: SSL context is not usable without certificate and private key
2017-02-24T16:04:40.340424Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2017-02-24T16:04:40.342270Z 0 [Note] IPv6 is not available.
2017-02-24T16:04:40.342313Z 0 [Note] - '0.0.0.0' resolves to '0.0.0.0';
2017-02-24T16:04:40.342355Z 0 [Note] Server socket created on IP: '0.0.0.0'.
2017-02-24T16:04:40.344528Z 0 [ERROR] Can't start server : Bind on unix socket: Operation not permitted
2017-02-24T16:04:40.344546Z 0 [ERROR] Do you already have another mysqld server running on socket: /afs/crc.nd.edu/user/j/jlai1/MySQL/thesock ?
2017-02-24T16:04:40.344563Z 0 [ERROR] Aborting
2017-02-24T16:04:40.344584Z 0 [Note] Binlog end
2017-02-24T16:04:40.344674Z 0 [Note] Shutting down plugin 'ngram'
2017-02-24T16:04:40.344686Z 0 [Note] Shutting down plugin 'partition'
2017-02-24T16:04:40.344692Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2017-02-24T16:04:40.344699Z 0 [Note] Shutting down plugin 'ARCHIVE'
2017-02-24T16:04:40.344704Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2017-02-24T16:04:40.344805Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2017-02-24T16:04:40.344813Z 0 [Note] Shutting down plugin 'MyISAM'
2017-02-24T16:04:40.344830Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2017-02-24T16:04:40.344835Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-02-24T16:04:40.344840Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2017-02-24T16:04:40.344844Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2017-02-24T16:04:40.344849Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-02-24T16:04:40.344853Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2017-02-24T16:04:40.344858Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2017-02-24T16:04:40.344862Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2017-02-24T16:04:40.344866Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-02-24T16:04:40.344871Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2017-02-24T16:04:40.344875Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2017-02-24T16:04:40.344880Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-02-24T16:04:40.344895Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2017-02-24T16:04:40.344899Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2017-02-24T16:04:40.344904Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2017-02-24T16:04:40.344908Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-02-24T16:04:40.344913Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2017-02-24T16:04:40.344917Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2017-02-24T16:04:40.344921Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-02-24T16:04:40.344926Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2017-02-24T16:04:40.344932Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2017-02-24T16:04:40.344936Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-02-24T16:04:40.344941Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2017-02-24T16:04:40.344946Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2017-02-24T16:04:40.344951Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2017-02-24T16:04:40.344955Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-02-24T16:04:40.344960Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2017-02-24T16:04:40.344964Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2017-02-24T16:04:40.344969Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2017-02-24T16:04:40.344973Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2017-02-24T16:04:40.344978Z 0 [Note] Shutting down plugin 'InnoDB'
2017-02-24T16:04:40.345065Z 0 [Note] InnoDB: FTS optimize thread exiting.
2017-02-24T16:04:40.345135Z 0 [Note] InnoDB: Starting shutdown...
2017-02-24T16:04:40.445348Z 0 [Note] InnoDB: Dumping buffer pool(s) to /afs/crc.nd.edu/user/j/jlai1/MySQL/data/ib_buffer_pool
2017-02-24T16:04:40.447661Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 170224 11:04:40
2017-02-24T16:04:41.779942Z 0 [Note] InnoDB: Shutdown completed; log sequence number 2534618
2017-02-24T16:04:41.795993Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2017-02-24T16:04:41.796030Z 0 [Note] Shutting down plugin 'MEMORY'
2017-02-24T16:04:41.796045Z 0 [Note] Shutting down plugin 'CSV'
2017-02-24T16:04:41.796092Z 0 [Note] Shutting down plugin 'sha256_password'
2017-02-24T16:04:41.796105Z 0 [Note] Shutting down plugin 'mysql_native_password'
2017-02-24T16:04:41.796375Z 0 [Note] Shutting down plugin 'binlog'
2017-02-24T16:04:41.796973Z 0 [Note] ./bin/mysqld: Shutdown complete

The problem seems that your user dont have permission to bind a port, 3306 specifically for Mysql.

MySQL installation on Windows - and how to fix missing mysql.user?

I was using an old MySql 5.0 installation. Then decided to get newest 5.7 .zip release.
This is what I have done:
mysqld -initialize-insecure
(As I intend to use this for localhost/root usage only)
This creates some files in the root of the MySQL data directory.
However, running
mysqld --console
gives error
2017-02-03T02:52:01.076801Z 0 [ERROR] Fatal error: Can't open and lock
privilege tables: Table 'mysql.user' doesn't exis
I then intended to move over my two 5.0 databases (each in a subfolder in my old mysql 5.0 "data dir" directory.)
Possibly I could then run mysql_upgrade then?
My full error log is here:
D:\databases\MySQL-5_7(x86)\bin>mysqld --console
2017-02-03T02:52:00.227754Z 0 [Warning] TIMESTAMP with implicit
DEFAULT value is deprecated. Please use
--explicit_defaults_for_timestamp server option (see documentation for more details). 2017-02-03T02:52:00.227754Z 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. 2017-02-03T02:52:00.227754Z 0 [Warning]
'NO_AUTO_CREATE_USER' sql mode was not set.
2017-02-03T02:52:00.227754Z 0 [Note] --secure-file-priv is set to
NULL. Operations related to importing and exporting data are disabled
2017-02-03T02:52:00.227754Z 0 [Note] mysqld (mysqld 5.7.17) starting
as process 13872 ... 2017-02-03T02:52:00.235754Z 0 [Note] InnoDB:
Mutexes and rw_locks use Windows interlocked functions
2017-02-03T02:52:00.236754Z 0 [Note] InnoDB: Uses event mutexes
2017-02-03T02:52:00.236754Z 0 [Note] InnoDB: Memory barrier is not
used 2017-02-03T02:52:00.237754Z 0 [Note] InnoDB: Compressed tables
use zlib 1.2.3 2017-02-03T02:52:00.237754Z 0 [Note] InnoDB: Number of
pools: 1 2017-02-03T02:52:00.238755Z 0 [Note] InnoDB: Not using CPU
crc32 instructions 2017-02-03T02:52:00.240755Z 0 [Note] InnoDB:
Initializing buffer pool, total size = 128M, instances = 1, chunk size
= 128M 2017-02-03T02:52:00.249755Z 0 [Note] InnoDB: Completed initialization of buffer pool 2017-02-03T02:52:00.363762Z 0 [Note]
InnoDB: Highest supported file format is Barracuda.
2017-02-03T02:52:00.498769Z 0 [Note] InnoDB: Creating shared
tablespace for temporary tables 2017-02-03T02:52:00.499769Z 0 [Note]
InnoDB: Setting file '.\ibtmp1' size to 12 MB. Physically writing the
file full; Please wait ... 2017-02-03T02:52:00.745783Z 0 [Note]
InnoDB: File '.\ibtmp1' size is now 12 MB. 2017-02-03T02:52:00.933793Z
0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback
segment(s) are active. 2017-02-03T02:52:00.934792Z 0 [Note] InnoDB: 32
non-redo rollback segment(s) are active. 2017-02-03T02:52:00.936793Z 0
[Note] InnoDB: Waiting for purge to start 2017-02-03T02:52:00.988797Z
0 [Note] InnoDB: 5.7.17 started; log sequence number 1209961
2017-02-03T02:52:00.988797Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-02-03T02:52:00.990797Z 0 [Note] InnoDB: Loading buffer pool(s)
from W:\b-databases\MySql\5.0.x\data\ib_buffer_pool mysqld: Table
'mysql.plugin' doesn't exist 2017-02-03T02:52:00.991796Z 0 [ERROR]
Can't open the mysql.plugin table. Please run mysql_upgrade to create
it. 2017-02-03T02:52:00.993796Z 0 [Note] Salting uuid generator
variables, current_pid: 13872, server_start_time: 1486090320,
bytes_sent: 0, 2017-02-03T02:52:00.993796Z 0 [Note] InnoDB: Buffer
pool(s) load completed at 170203 3:52:00 2017-02-03T02:52:00.997796Z
0 [Note] Generated uuid: 'bc608dfe-e9bb-11e6-b692-00248c156225',
server_start_time: 1486104192, bytes_sent: 361844000
2017-02-03T02:52:00.997796Z 0 [Warning] No existing UUID has been
found, so we assume that this is the first time that this server has
been started. Generating a new UUID:
bc608dfe-e9bb-11e6-b692-00248c156225. 2017-02-03T02:52:01.041799Z 0
[Warning] Gtid table is not ready to be used. Table
'mysql.gtid_executed' cannot be opened. 2017-02-03T02:52:01.041799Z 0
[Warning] Failed to set up SSL because of the following SSL library
error: SSL context is not usable without certificate and private key
2017-02-03T02:52:01.043799Z 0 [Note] Server hostname (bind-address):
'*'; port: 3306 2017-02-03T02:52:01.044802Z 0 [Note] IPv6 is
available. 2017-02-03T02:52:01.045801Z 0 [Note] - '::' resolves to
'::'; 2017-02-03T02:52:01.045801Z 0 [Note] Server socket created on
IP: '::'. 2017-02-03T02:52:01.054800Z 0 [Warning] Failed to open
optimizer cost constant tables
2017-02-03T02:52:01.076801Z 0 [ERROR] Fatal error: Can't open and lock
privilege tables: Table 'mysql.user' doesn't exist
2017-02-03T02:52:01.077801Z 0 [ERROR] Aborting
2017-02-03T02:52:01.078801Z 0 [Note] Binlog end
2017-02-03T02:52:01.079801Z 0 [Note] Shutting down plugin 'ngram'
2017-02-03T02:52:01.079801Z 0 [Note] Shutting down plugin 'partition'
2017-02-03T02:52:01.080801Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2017-02-03T02:52:01.081801Z 0 [Note] Shutting down plugin 'ARCHIVE'
2017-02-03T02:52:01.081801Z 0 [Note] Shutting down plugin
'PERFORMANCE_SCHEMA' 2017-02-03T02:52:01.082801Z 0 [Note] Shutting
down plugin 'MRG_MYISAM' 2017-02-03T02:52:01.082801Z 0 [Note] Shutting
down plugin 'MyISAM' 2017-02-03T02:52:01.083801Z 0 [Note] Shutting
down plugin 'INNODB_SYS_VIRTUAL' 2017-02-03T02:52:01.083801Z 0 [Note]
Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-02-03T02:52:01.084801Z 0 [Note] Shutting down plugin
'INNODB_SYS_TABLESPACES' 2017-02-03T02:52:01.084801Z 0 [Note] Shutting
down plugin 'INNODB_SYS_FOREIGN_COLS' 2017-02-03T02:52:01.085801Z 0
[Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-02-03T02:52:01.087801Z 0 [Note] Shutting down plugin
'INNODB_SYS_FIELDS' 2017-02-03T02:52:01.088802Z 0 [Note] Shutting down
plugin 'INNODB_SYS_COLUMNS' 2017-02-03T02:52:01.089802Z 0 [Note]
Shutting down plugin 'INNODB_SYS_INDEXES' 2017-02-03T02:52:01.089802Z
0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-02-03T02:52:01.090802Z 0 [Note] Shutting down plugin
'INNODB_SYS_TABLES' 2017-02-03T02:52:01.091802Z 0 [Note] Shutting down
plugin 'INNODB_FT_INDEX_TABLE' 2017-02-03T02:52:01.091802Z 0 [Note]
Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-02-03T02:52:01.092802Z 0 [Note] Shutting down plugin
'INNODB_FT_CONFIG' 2017-02-03T02:52:01.093802Z 0 [Note] Shutting down
plugin 'INNODB_FT_BEING_DELETED' 2017-02-03T02:52:01.093802Z 0 [Note]
Shutting down plugin 'INNODB_FT_DELETED' 2017-02-03T02:52:01.094802Z 0
[Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-02-03T02:52:01.094802Z 0 [Note] Shutting down plugin
'INNODB_METRICS' 2017-02-03T02:52:01.095802Z 0 [Note] Shutting down
plugin 'INNODB_TEMP_TABLE_INFO' 2017-02-03T02:52:01.097802Z 0 [Note]
Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-02-03T02:52:01.098802Z 0 [Note] Shutting down plugin
'INNODB_BUFFER_PAGE_LRU' 2017-02-03T02:52:01.099802Z 0 [Note] Shutting
down plugin 'INNODB_BUFFER_PAGE' 2017-02-03T02:52:01.099802Z 0 [Note]
Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-02-03T02:52:01.100802Z 0 [Note] Shutting down plugin
'INNODB_CMP_PER_INDEX' 2017-02-03T02:52:01.100802Z 0 [Note] Shutting
down plugin 'INNODB_CMPMEM_RESET' 2017-02-03T02:52:01.101802Z 0 [Note]
Shutting down plugin 'INNODB_CMPMEM' 2017-02-03T02:52:01.102802Z 0
[Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-02-03T02:52:01.102802Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2017-02-03T02:52:01.103803Z 0 [Note] Shutting down plugin
'INNODB_LOCK_WAITS' 2017-02-03T02:52:01.103803Z 0 [Note] Shutting down
plugin 'INNODB_LOCKS' 2017-02-03T02:52:01.104802Z 0 [Note] Shutting
down plugin 'INNODB_TRX' 2017-02-03T02:52:01.104802Z 0 [Note] Shutting
down plugin 'InnoDB' 2017-02-03T02:52:01.105803Z 0 [Note] InnoDB: FTS
optimize thread exiting. 2017-02-03T02:52:01.107803Z 0 [Note] InnoDB:
Starting shutdown... 2017-02-03T02:52:01.209808Z 0 [Note] InnoDB:
Dumping buffer pool(s) to
W:\b-databases\MySql\5.0.x\data\ib_buffer_pool
2017-02-03T02:52:01.214809Z 0 [Note] InnoDB: Buffer pool(s) dump
completed at 170203 3:52:01 2017-02-03T02:52:02.408874Z 0 [Note]
InnoDB: Shutdown completed; log sequence number 1209980
2017-02-03T02:52:02.408874Z 0 [Note] InnoDB: Removed temporary
tablespace data file: "ibtmp1" 2017-02-03T02:52:02.409874Z 0 [Note]
Shutting down plugin 'MEMORY' 2017-02-03T02:52:02.410874Z 0 [Note]
Shutting down plugin 'CSV' 2017-02-03T02:52:02.410874Z 0 [Note]
Shutting down plugin 'sha256_password' 2017-02-03T02:52:02.411874Z 0
[Note] Shutting down plugin 'mysql_native_password'
2017-02-03T02:52:02.412874Z 0 [Note] Shutting down plugin 'binlog'
2017-02-03T02:52:02.412874Z 0 [Note] mysqld: Shutdown complete
And this is my.ini file:
[mysqld]
basedir=D:/databases/MySQL-5_7(x86)
datadir=W:/b-databases/MySql/5.0.x/data
port=3306
sql_mode=NO_ENGINE_SUBSTITUTION,STRICT_TRANS_TABLES

Somehow I got it working now - I redid what was mentioned here and this time the user tables were created as well. Not quite sure why it did not work befoe, but still deserves to be an answer:
https://dev.mysql.com/doc/refman/5.7/en/data-directory-initialization-mysqld.html

MySQL error after increasing innodb buffer pool

I increased the buffer pool for mysql innodb and I got this error.
Now mysql wouldn't even start.
This happened when I restarted my computer and mysql still had problems. I am working on OSX and can't find my my.cnf either.
$ mysqld -uroot -p
2017-01-11T11:17:14.127290Z 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2017-01-11T11:17:14.128286Z 0 [Warning] Insecure configuration for --secure-file-priv: Current value does not restrict location of generated files. Consider setting it to a valid, non-empty path.
2017-01-11T11:17:14.128917Z 0 [Note] mysqld (mysqld 5.7.13) starting as process 2014 ...
2017-01-11T11:17:14.139702Z 0 [Warning] Setting lower_case_table_names=2 because file system for /usr/local/var/mysql/ is case insensitive
2017-01-11T11:17:14.140644Z 0 [Warning] One can only use the --user switch if running as root
2017-01-11T11:17:14.148026Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2017-01-11T11:17:14.148056Z 0 [Note] InnoDB: Uses event mutexes
2017-01-11T11:17:14.148060Z 0 [Note] InnoDB: GCC builtin __atomic_thread_fence() is used for memory barrier
2017-01-11T11:17:14.148064Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2017-01-11T11:17:14.149318Z 0 [Note] InnoDB: Number of pools: 1
2017-01-11T11:17:14.150616Z 0 [Note] InnoDB: Using CPU crc32 instructions
2017-01-11T11:17:14.153003Z 0 [Note] InnoDB: Initializing buffer pool, total size = 128M, instances = 1, chunk size = 128M
2017-01-11T11:17:14.165811Z 0 [Note] InnoDB: Completed initialization of buffer pool
2017-01-11T11:17:14.187092Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2017-01-11T11:17:14.247127Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2017-01-11T11:17:14.247345Z 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2017-01-11T11:17:14.261446Z 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2017-01-11T11:17:14.262167Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2017-01-11T11:17:14.262177Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2017-01-11T11:17:14.264859Z 0 [Note] InnoDB: Waiting for purge to start
2017-01-11T11:17:14.319034Z 0 [Note] InnoDB: 5.7.13 started; log sequence number 1991037762
2017-01-11T11:17:14.319286Z 0 [Note] InnoDB: Loading buffer pool(s) from /usr/local/var/mysql/ib_buffer_pool
2017-01-11T11:17:14.320610Z 0 [Note] Plugin 'FEDERATED' is disabled.
2017-01-11T11:17:14.325376Z 0 [Warning] System table 'plugin' is expected to be transactional.
2017-01-11T11:17:14.327107Z 0 [ERROR] mysqld: unknown option '-p'
2017-01-11T11:17:14.327131Z 0 [ERROR] Aborting
2017-01-11T11:17:14.327143Z 0 [Note] Binlog end
2017-01-11T11:17:14.327361Z 0 [Note] Shutting down plugin 'ngram'
2017-01-11T11:17:14.327372Z 0 [Note] Shutting down plugin 'partition'
2017-01-11T11:17:14.327376Z 0 [Note] Shutting down plugin 'BLACKHOLE'
2017-01-11T11:17:14.327378Z 0 [Note] Shutting down plugin 'ARCHIVE'
2017-01-11T11:17:14.327380Z 0 [Note] Shutting down plugin 'PERFORMANCE_SCHEMA'
2017-01-11T11:17:14.327419Z 0 [Note] Shutting down plugin 'MRG_MYISAM'
2017-01-11T11:17:14.327425Z 0 [Note] Shutting down plugin 'MyISAM'
2017-01-11T11:17:14.327444Z 0 [Note] Shutting down plugin 'INNODB_SYS_VIRTUAL'
2017-01-11T11:17:14.327449Z 0 [Note] Shutting down plugin 'INNODB_SYS_DATAFILES'
2017-01-11T11:17:14.327453Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESPACES'
2017-01-11T11:17:14.327456Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN_COLS'
2017-01-11T11:17:14.327460Z 0 [Note] Shutting down plugin 'INNODB_SYS_FOREIGN'
2017-01-11T11:17:14.327464Z 0 [Note] Shutting down plugin 'INNODB_SYS_FIELDS'
2017-01-11T11:17:14.327467Z 0 [Note] Shutting down plugin 'INNODB_SYS_COLUMNS'
2017-01-11T11:17:14.327472Z 0 [Note] Shutting down plugin 'INNODB_SYS_INDEXES'
2017-01-11T11:17:14.327475Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLESTATS'
2017-01-11T11:17:14.327479Z 0 [Note] Shutting down plugin 'INNODB_SYS_TABLES'
2017-01-11T11:17:14.327482Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_TABLE'
2017-01-11T11:17:14.327485Z 0 [Note] Shutting down plugin 'INNODB_FT_INDEX_CACHE'
2017-01-11T11:17:14.327489Z 0 [Note] Shutting down plugin 'INNODB_FT_CONFIG'
2017-01-11T11:17:14.327493Z 0 [Note] Shutting down plugin 'INNODB_FT_BEING_DELETED'
2017-01-11T11:17:14.327496Z 0 [Note] Shutting down plugin 'INNODB_FT_DELETED'
2017-01-11T11:17:14.327500Z 0 [Note] Shutting down plugin 'INNODB_FT_DEFAULT_STOPWORD'
2017-01-11T11:17:14.327503Z 0 [Note] Shutting down plugin 'INNODB_METRICS'
2017-01-11T11:17:14.327507Z 0 [Note] Shutting down plugin 'INNODB_TEMP_TABLE_INFO'
2017-01-11T11:17:14.327510Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_POOL_STATS'
2017-01-11T11:17:14.327514Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE_LRU'
2017-01-11T11:17:14.327543Z 0 [Note] Shutting down plugin 'INNODB_BUFFER_PAGE'
2017-01-11T11:17:14.327556Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX_RESET'
2017-01-11T11:17:14.327561Z 0 [Note] Shutting down plugin 'INNODB_CMP_PER_INDEX'
2017-01-11T11:17:14.327566Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM_RESET'
2017-01-11T11:17:14.327570Z 0 [Note] Shutting down plugin 'INNODB_CMPMEM'
2017-01-11T11:17:14.327574Z 0 [Note] Shutting down plugin 'INNODB_CMP_RESET'
2017-01-11T11:17:14.327577Z 0 [Note] Shutting down plugin 'INNODB_CMP'
2017-01-11T11:17:14.327581Z 0 [Note] Shutting down plugin 'INNODB_LOCK_WAITS'
2017-01-11T11:17:14.327585Z 0 [Note] Shutting down plugin 'INNODB_LOCKS'
2017-01-11T11:17:14.327590Z 0 [Note] Shutting down plugin 'INNODB_TRX'
2017-01-11T11:17:14.327595Z 0 [Note] Shutting down plugin 'InnoDB'
2017-01-11T11:17:14.327641Z 0 [Note] InnoDB: FTS optimize thread exiting.
2017-01-11T11:17:14.327684Z 0 [Note] InnoDB: Starting shutdown...
2017-01-11T11:17:14.327773Z 0 [Note] InnoDB: Buffer pool(s) load completed at 170111 17:02:14
2017-01-11T11:17:14.327836Z 0 [Note] InnoDB: Dumping buffer pool(s) to /usr/local/var/mysql/ib_buffer_pool
2017-01-11T11:17:14.328161Z 0 [Note] InnoDB: Buffer pool(s) dump completed at 170111 17:02:14
2017-01-11T11:17:15.780219Z 0 [Note] InnoDB: Shutdown completed; log sequence number 1991037781
2017-01-11T11:17:15.781632Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2017-01-11T11:17:15.781739Z 0 [Note] Shutting down plugin 'MEMORY'
2017-01-11T11:17:15.781747Z 0 [Note] Shutting down plugin 'CSV'
2017-01-11T11:17:15.781752Z 0 [Note] Shutting down plugin 'sha256_password'
2017-01-11T11:17:15.781756Z 0 [Note] Shutting down plugin 'mysql_native_password'
2017-01-11T11:17:15.781958Z 0 [Note] Shutting down plugin 'binlog'
2017-01-11T11:17:15.782174Z 0 [Note] mysqld: Shutdown complete

Did you just upgrade? You probably failed to run mysql_upgrade.