Error Code: 2006. MySQL server has gone away (MYSQL Workbench 6.36)

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I'm having issues where the server will always have this 2006 error. I have changed the settings in the preferences and also in the cnf file(max_packet size). Every morning when I check the server it will show the 2006 error. I will have to go to the home page of workbench and manually double click the local host then the connection will be okay(connected).I have attached the cnf lines and the mysql workbench images. Please help. Thanks.

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    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.

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

[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_size         = 16M


max_allowed_packet      = 256M
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        = 200
table_cache            = 64
thread_concurrency     = 10

 * Query Cache Configuration

query_cache_limit       = 5M
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
log_slow_queries       = /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
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