# mysql56-server won't start



## cbrace (Oct 23, 2016)

Hi all,

Over the weekend I switched over from portmaster to ports-mgmt/synth to keep the ports on my server up to date.

In the course of doing so, I seemed to have bumped mysql from version 55 to 56.

Now I can't start mysql. I'm seeing a lot of error messages like this in /var/log/httpd-error.log:

```
[Sun Oct 23 14:22:18.566597 2016] [:error] [pid 1510] [client 81.207.93.8:54568] PHP Fatal error:  Uncaught exception 'Doctrine\\DBAL\\DBALException' with message 'Failed to connect to the database: An exception occured in driver: SQLSTATE[HY000] [2002] Connection refused' in /usr/local/www/nextcloud/lib/private/DB/Connection.php:59\nStack trace:\n#0 /usr/local/www/nextcloud/3rdparty/doctrine/dbal/lib/Doctrine/DBAL/Connection.php(429): OC\\DB\\Connection->connect()\n#1 /usr/local/www/nextcloud/3rdparty/doctrine/dbal/lib/Doctrine/DBAL/Connection.php(389): Doctrine\\DBAL\\Connection->getDatabasePlatformVersion()\n#2 /usr/local/www/nextcloud/3rdparty/doctrine/dbal/lib/Doctrine/DBAL/Connection.php(328): Doctrine\\DBAL\\Connection->detectDatabasePlatform()\n#3 /usr/local/www/nextcloud/3rdparty/doctrine/dbal/lib/Doctrine/DBAL/Connection.php(621): Doctrine\\DBAL\\Connection->getDatabasePlatform()\n#4 /usr/local/www/nextcloud/lib/private/DB/Connection.php(142): Doctrine\\DBAL\\Connection->setTransactionIsolation(2)\n#5 /usr/local/www/nextcloud/3rdparty/doctrine/dbal/lib/Doctrine/DBAL/DriverManager.php(172): OC\\DB\\Connection->__const in /usr/local/www/nextcloud/lib/private/DB/Connection.php on line 59
```
I don't see /tmp/mysql.sock.

I tried running mysql_update:

```
$ mysql_upgrade --password=***************I --user=root
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Error: Failed while fetching Server version! Could be due to unauthorized access.
FATAL ERROR: Upgrade failed
```

Can someone point me in the right direction for troubleshooting?

Many thanks

```
/usr/local/etc $ grep -v ^# my.cnf | grep -v ^$
[client]
port       = 3306
socket       = /tmp/mysql.sock
[mysqld]
port       = 3306
socket       = /tmp/mysql.sock
skip-external-locking
key_buffer_size = 256M
max_allowed_packet = 1M
table_open_cache = 256
sort_buffer_size = 1M
read_buffer_size = 1M
read_rnd_buffer_size = 4M
myisam_sort_buffer_size = 64M
thread_cache_size = 8
query_cache_size= 16M
thread_concurrency = 8
tmp_table_size = 30M
table_cache = 48
server-id   = 1
[mysqldump]
quick
max_allowed_packet = 16M
[mysql]
no-auto-rehash
[myisamchk]
key_buffer_size = 128M
sort_buffer_size = 128M
read_buffer = 2M
write_buffer = 2M
[mysqlhotcopy]
interactive-timeout
server-id=1416597902
```


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## cbrace (Oct 23, 2016)

Some progress here: added "ignore-builtin-innodb" to my.cnf and now mysql server starts.

However, it seems some of my tables DO use innodb:


```
# mysql_upgrade --password=*********************** --user=root
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/tmp/mysql.sock'
Warning: Using a password on the command line interface can be insecure.
Running 'mysqlcheck' with connection arguments: '--port=3306' '--socket=/tmp/mysql.sock'
Warning: Using a password on the command line interface can be insecure.
bojana.zenphoto_admin_to_object
Error    : Unknown storage engine 'InnoDB'
error    : Corrupt
...
```


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## cbrace (Oct 23, 2016)

I re-enabled innoDB, but for some reason I also needed to delete these innoDB logfiles:

```
-rw-rw----  1 mysql  mysql    50331648 Oct 23 13:47 ib_logfile0
-rw-rw----  1 mysql  mysql    50331648 Jun 14  2015 ib_logfile0.bak
-rw-rw----  1 mysql  mysql    50331648 Oct 23 13:25 ib_logfile1
-rw-rw----  1 mysql  mysql    50331648 Jun 13  2015 ib_logfile1.bak
```
Now mysql server starts, and everything seems to be working again.

Source: https://spin.atomicobject.com/2011/05/09/mysql-failed-registration-of-innodb-as-a-storage-engine/


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