MySQL: The server quit without updating PID file

Question

Installing MySQL on OSX El Capitan. 10.11.2 via Homebrew next I want to start it:

  Nevada3:local kb1$ mysql.server start
    Starting MySQL
    .. ERROR! The server quit without updating PID file     (/usr/local/var/mysql/Nevada3.local.pid).

Next I checked the permissions:

    Nevada3:mysql kb1$ cd /usr/local/var/mysql/
    Nevada3:mysql kb1$ ls -lsa
    total 221296
    0 drwxr-xr-x   19 kb1  admin       646  9 Dec 11:40 .
    0 drwxr-xr-x    6 kb1  admin       204  9 Dec 11:36 ..
   32 -rw-r-----    1 kb1  admin     15184  9 Dec 11:40 Nevada3.local.err
    8 -rw-r-----    1 kb1  admin        56  9 Dec 11:36 auto.cnf
    8 -rw-------    1 kb1  admin      1676  9 Dec 11:36 ca-key.pem
    8 -rw-r--r--    1 kb1  admin      1071  9 Dec 11:36 ca.pem
    8 -rw-r--r--    1 kb1  admin      1079  9 Dec 11:36 client-cert.pem
    8 -rw-------    1 kb1  admin      1680  9 Dec 11:36 client-key.pem
    8 -rw-r-----    1 kb1  admin       303  9 Dec 11:40 ib_buffer_pool
    98304 -rw-r-----    1 kb1  admin  50331648  9 Dec 11:40 ib_logfile0
    98304 -rw-r-----    1 kb1  admin  50331648  9 Dec 11:36 ib_logfile1
    24576 -rw-r-----    1 kb1  admin  12582912  9 Dec 11:40 ibdata1
    0 drwxr-x---   77 kb1  admin      2618  9 Dec 11:36 mysql
    0 drwxr-x---   90 kb1  admin      3060  9 Dec 11:36 performance_schema
    8 -rw-------    1 kb1  admin      1680  9 Dec 11:36 private_key.pem
    8 -rw-r--r--    1 kb1  admin       452  9 Dec 11:36 public_key.pem
    8 -rw-r--r--    1 kb1  admin      1079  9 Dec 11:36 server-cert.pem
    8 -rw-------    1 kb1  admin      1676  9 Dec 11:36 server-key.pem
    0 drwxr-x---  108 kb1  admin      3672  9 Dec 11:36 sys
    Nevada3:mysql kb1$

But this seems right. All is my User. And not root.

This is the output of the error log:

Nevada3:mysql kb1$ tail Nevada3.local.err
2015-12-09T10:40:45.576656Z 0 [Note] InnoDB: Shutdown completed; log sequence number 2471965
2015-12-09T10:40:45.577321Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2015-12-09T10:40:45.577335Z 0 [Note] Shutting down plugin 'MEMORY'
2015-12-09T10:40:45.577341Z 0 [Note] Shutting down plugin 'CSV'
2015-12-09T10:40:45.577346Z 0 [Note] Shutting down plugin 'sha256_password'
2015-12-09T10:40:45.577350Z 0 [Note] Shutting down plugin 'mysql_native_password'
2015-12-09T10:40:45.577470Z 0 [Note] Shutting down plugin 'binlog'
2015-12-09T10:40:45.577946Z 0 [Note] /usr/local/Cellar/mysql/5.7.9/bin/mysqld: Shutdown complete

151209 11:40:45 mysqld_safe mysqld from pid file /usr/local/var/mysql/Nevada3.local.pid ended

I am totally lost. Never experienced this..

Answer 1

I had the same issue. Mysql would not start up after upgrading to 10.11.2.

Worked again after:

sudo chown -R `whoami` /usr/local/var/mysql
mv ib_logfile0 ib_logfile0.bak
mv ib_logfile1 ib_logfile1.bak
[move the .err logfile to a new location]

Not sure if all of them were needed.

Edit:

shortcut of creating the .bak files:

for i in $(ls *.err *logfile*); do mv $i{,.bak}; done

Answer 2

I just had and resolved this issue in the following manner:

• in terminal cd to the directory where the pid is attempted, in your case this is cd /usr/local/var/mysql/
• type ls to see files in this directory, there should be an err file (which is preventing the pid and thus the start)
• remove the error file, it will most likely be name the name of the pid with '.err' instead of the '.pid' extension. In your case I think it will be: rm -rf Nevada3.local.err
• mysql.server start

These steps worked for me. From my understanding, this occurs because mysql server is running durning the update, eventually causes an error creating the error file, preventing the start upon successful update. I think stoping mysql immediately before the updating will prevent this issue in the future. You would of course have to restart mysql after the update, but would not need to find and delete the .err file.