Flask/uWSGI/MariaDB running under Supervisor stops working almost daily - nginx

Question

I'm running a Flask app via uWSGI which is managed by Supervisor (and the webserver is using Nginx).
The whole setup seems to work perfectly, however, I notice that every day or two, my flask app starts throwing 500 errors (which means there is a Sqlalchemy db.commit() error) and I can't recover until I go in and reload uwsgi, after which, everything works perfectly again. To reload, I typically kill the uwsgi processes, and supervisor brings them back in and it's fine. Once I've gotten it to work by just 'touch'ing the wsgi file.
Also strangely, whenever I run supervisor with processes=1, it automatically loads TWO uwsgi instances. The first PID is the one logged as being operated by supervisor, and the other doesn't register anywhere. However, regardless of this, killing the 2nd process - it always comes back.
Below is my uwsgi startup command run by supervisor
[program:{{ app_name }}]
command=/usr/local/bin/uwsgi
--socket=/tmp/{{ app_name }}.sock
--logto={{ log_dir }}/application.log
--home={{ site_dir }}/env
--pythonpath={{ site_dir }}
--virtualenv={{ env_path }}
--wsgi-file={{ webapps_dir }}/manage.py
--callable={{ wsgi_callable }}
--max-requests=1000
--master
--processes=1
--uid={{ deployment_user }}
--gid=www-data
--chmod-socket=664
--chown-socket={{ deployment_user }}:www-data
directory={{ webapps_dir }}
autostart=true
autorestart=true
EDIT: Here is the error that's spit out from the server.
2015-03-19 15:03:38,389 ERROR: Exception on /api/v1/account/login [POST] [in /var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py:1423]
Traceback (most recent call last):
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
response = self.full_dispatch_request()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1477, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask_cors.py", line 272, in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1381, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
rv = self.dispatch_request()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask_classy.py", line 200, in proxy
response = view(**request.view_args)
File "./webportal/account/api.py", line 34, in login_user
user = auth.authenticate(username=email, password=password)
File "/var/www/website.com/server/webportal/auth.py", line 23, in authenticate
user = User.query.filter_by(email=username).first()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2367, in first
ret = list(self[0:1])
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2228, in __getitem__
return list(res)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2438, in __iter__
return self._execute_and_instances(context)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2453, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 729, in execute
return meth(self, multiparams, params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 322, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 826, in _execute_clauseelement
compiled_sql, distilled_params
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 958, in _execute_context
context)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1159, in _handle_dbapi_exception
exc_info
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 199, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 951, in _execute_context
context)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/default.py", line 436, in do_execute
cursor.execute(statement, parameters)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/MySQLdb/cursors.py", line 205, in execute
self.errorhandler(self, exc, value)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/MySQLdb/connections.py", line 36, in defaulterrorhandler
raise errorclass, errorvalue
OperationalError: (OperationalError) (2006, 'MySQL server has gone away') 'SELECT `Users`.id AS `Users_id`, `Users`.email AS `Users_email`, `Users`.password AS `Users_password`, `Users`.`emailConfirmed` AS `Users_emailConfirmed`, `Users`.`createdAtUtc` AS `Users_createdAtUtc`, `Users`.`updatedAtUtc` AS `Users_updatedAtUtc`, `Users`.`roleId` AS `Users_roleId` \nFROM `Users` \nWHERE `Users`.email = %s \n LIMIT %s' ('user#website.demo', 1)
2015-03-19 15:06:22,089 ERROR: Exception on /api/v1/account/login [POST] [in /var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py:1423]
Traceback (most recent call last):
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
response = self.full_dispatch_request()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1477, in full_dispatch_request
rv = self.handle_user_exception(e)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask_cors.py", line 272, in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1381, in handle_user_exception
reraise(exc_type, exc_value, tb)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
rv = self.dispatch_request()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/flask_classy.py", line 200, in proxy
response = view(**request.view_args)
File "./webportal/account/api.py", line 34, in login_user
user = auth.authenticate(username=email, password=password)
File "/var/www/website.com/server/webportal/auth.py", line 23, in authenticate
user = User.query.filter_by(email=username).first()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2367, in first
ret = list(self[0:1])
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2228, in __getitem__
return list(res)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2438, in __iter__
return self._execute_and_instances(context)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/orm/query.py", line 2453, in _execute_and_instances
result = conn.execute(querycontext.statement, self._params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 729, in execute
return meth(self, multiparams, params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/sql/elements.py", line 322, in _execute_on_connection
return connection._execute_clauseelement(self, multiparams, params)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 826, in _execute_clauseelement
compiled_sql, distilled_params
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 893, in _execute_context
None, None)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 1159, in _handle_dbapi_exception
exc_info
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/util/compat.py", line 199, in raise_from_cause
reraise(type(exception), exception, tb=exc_tb)
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 887, in _execute_context
conn = self._revalidate_connection()
File "/var/www/website.com/env/local/lib/python2.7/site-packages/sqlalchemy/engine/base.py", line 242, in _revalidate_connection
"Can't reconnect until invalid "
StatementError: Can't reconnect until invalid transaction is rolled back (original cause: InvalidRequestError: Can't reconnect until invalid transaction is rolled back) u'SELECT `Users`.id AS `Users_id`, `Users`.email AS `Users_email`, `Users`.password AS `Users_password`, `Users`.`emailConfirmed` AS `Users_emailConfirmed`, `Users`.`createdAtUtc` AS `Users_createdAtUtc`, `Users`.`updatedAtUtc` AS `Users_updatedAtUtc`, `Users`.`roleId` AS `Users_roleId` \nFROM `Users` \nWHERE `Users`.email = %s \n LIMIT %s' [immutabledict({})]
According to https://dev.mysql.com/doc/refman/5.0/en/gone-away.html, MySQL closes the connection after 8 hours... Once that happens, the app gets in a bit of a state.