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mysql version 8.0.11 and Symfony 4 error “MySQL server has gone away”

I' m using Symfony 4 and Mysql version is 8.0.11 and using a user instead of a root login and when i try to use the command php bin/console make:migration i get this error:

php bin/console make:migration

In AbstractMySQLDriver.php line 126:
An exception occurred in driver: SQLSTATE[HY000] [2006] MySQL server has gone away

In PDOConnection.php line 50:
SQLSTATE[HY000] [2006] MySQL server has gone away

In PDOConnection.php line 46:
SQLSTATE[HY000] [2006] MySQL server has gone away

In PDOConnection.php line 46:
PDO::__construct(): Unexpected server respose while doing caching_sha2 auth: 109


Then i tried to search online and i found out that something went wrong with the MySQL variables wait_timeout and max_allowed_packet and had to change those variables on the file /etc/mysql/my.cnf, the problem is when i go edit that file i only find this:

wait_timeout

max_allowed_packet

/etc/mysql/my.cnf

# Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License, version 2.0,
# as published by the Free Software Foundation.
#
# This program is also distributed with certain software (including
# but not limited to OpenSSL) that is licensed under separate terms,
# as designated in a particular file or component or in included license
# documentation. The authors of MySQL hereby grant you an additional
# permission to link the program and your derivative works with the
# separately licensed software that they have included with MySQL.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License, version 2.0, for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
#
# The MySQL Server configuration file.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html
# * 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/
!includedir /etc/mysql/mysql.conf.d/


so then i tried to see a thread called "Why is /etc/mysql/my.cnf EMPTY?" and a user said to use one of these paths:

/etc/mysql/conf.d/
/etc/mysql/mysql.conf.d/
/etc/mysql/mysql.conf.d/mysqld.cnf


and so i tried...
/etc/mysql/conf.d/:

/etc/mysql/conf.d/

## Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License, version 2.0,
# as published by the Free Software Foundation.
#
# This program is also distributed with certain software (including
# but not limited to OpenSSL) that is licensed under separate terms,
# as designated in a particular file or component or in included license
# documentation. The authors of MySQL hereby grant you an additional
# permission to link the program and your derivative works with the
# separately licensed software that they have included with MySQL.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License, version 2.0, for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

#
# The MySQL Client configuration file.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

[mysql]


in the file /etc/mysql/mysql.conf.d/:

/etc/mysql/mysql.conf.d/

# Copyright (c) 2014, 2017, Oracle and/or its affiliates. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License, version 2.0,
# as published by the Free Software Foundation.
#
# This program is also distributed with certain software (including
# but not limited to OpenSSL) that is licensed under separate terms,
# as designated in a particular file or component or in included license
# documentation. The authors of MySQL hereby grant you an additional
# permission to link the program and your derivative works with the
# separately licensed software that they have included with MySQL.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License, version 2.0, for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

#
# The MySQL Server configuration file.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

[mysqld]
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
datadir = /var/lib/mysql
log-error = /var/log/mysql/error.log


and in the file /etc/mysql/mysql.conf.d/mysqld.cnf:

/etc/mysql/mysql.conf.d/mysqld.cnf

# Copyright (c) 2014, 2017, Oracle and/or its affiliates. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License, version 2.0,
# as published by the Free Software Foundation.
#
# This program is also distributed with certain software (including
# but not limited to OpenSSL) that is licensed under separate terms,
# as designated in a particular file or component or in included license
# documentation. The authors of MySQL hereby grant you an additional
# permission to link the program and your derivative works with the
# separately licensed software that they have included with MySQL.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License, version 2.0, for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA

#
# The MySQL Server configuration file.
#
# For explanations see
# http://dev.mysql.com/doc/mysql/en/server-system-variables.html

[mysqld]
pid-file = /var/run/mysqld/mysqld.pid
socket = /var/run/mysqld/mysqld.sock
datadir = /var/lib/mysql
log-error = /var/log/mysql/error.log


and in any of these files i failed to find the MySQL variables wait_timeout and max_allowed_packet, so thanks in advance if someone could help me with this problem. :)

wait_timeout

max_allowed_packet

P.S:(i already runned this command php bin/console make:migration several times before this error and also created databases and went fine so its seems to not be an installation problem).

php bin/console make:migration

Update: it seems successfully changed the two variables wait_timeout and max_allowed_packet globally by adding to the three files the following

wait_timeout

max_allowed_packet

max_allowed_packet=1024M
wait_timeout=3000000


and then using this command sudo service mysql restart
giving me this:

sudo service mysql restart

mysql> SHOW global VARIABLES LIKE "wait_timeout";
+---------------+---------+
| Variable_name | Value |
+---------------+---------+
| wait_timeout | 3000000 |
+---------------+---------+
1 row in set (0,00 sec)

mysql> SHOW VARIABLES like 'max_allowed_packet';
+--------------------+------------+
| Variable_name | Value |
+--------------------+------------+
| max_allowed_packet | 1073741824 |
+--------------------+------------+
1 row in set (0,00 sec)


but still when i tried using this command php bin/console make:migration it gave me the same error has mentioned above this post, also tried to change the wait_timeout variable to 300 by the same method and it gave me the same result. :(

php bin/console make:migration

wait_timeout

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