mysql - After upgrading to MariaDB 5.5 connections are being dropped after a period of inactivity -

we have upgraded our database server mysql 5.1 mariadb 5.5 (5.5.40-mariadb-1~wheezy-log).

after upgrade, long running processes mysql connection si being dropped. common scenario processes is:

1. connect mysql
2. run queries
3. do heavy lifting without connecting mysql @ least 1 minute
4. try query against original connection
5. exception giving 2600 error - mysql server has gone away

this happen in php cli scripts (php 5.3), in ruby application (redmine 2.5.1). not happening mysql 5.1 , there no changes on applications side, should not app-related.

the %timeout% variables in mariadb are:

+----------------------------+----------+ | variable_name              | value    | +----------------------------+----------+ | connect_timeout            | 5        | | deadlock_timeout_long      | 50000000 | | deadlock_timeout_short     | 10000    | | delayed_insert_timeout     | 300      | | innodb_lock_wait_timeout   | 50       | | innodb_rollback_on_timeout | off      | | interactive_timeout        | 28800    | | lock_wait_timeout          | 31536000 | | net_read_timeout           | 30       | | net_write_timeout          | 60       | | slave_net_timeout          | 3600     | | thread_pool_idle_timeout   | 60       | | wait_timeout               | 28800    | +----------------------------+----------+ 

we not using thread pooling:

+---------------------------+---------------------------+ | variable_name             | value                     | +---------------------------+---------------------------+ | thread_cache_size         | 128                       | | thread_concurrency        | 10                        | | thread_handling           | one-thread-per-connection | | thread_pool_idle_timeout  | 60                        | | thread_pool_max_threads   | 500                       | | thread_pool_oversubscribe | 3                         | | thread_pool_size          | 12                        | | thread_pool_stall_limit   | 500                       | | thread_stack              | 294912                    | +---------------------------+---------------------------+ 

when thing happens, there event logged in syslog, everytime looking same:

dec 16 13:00:14 db01 mysqld: 141216 13:00:14 [warning] aborted connection 9202885 db: 'some_db_name' user: 'user' host: 'app' (unknown error) 

besides that, there weird root account disconnection messages:

dec 16 13:05:02 db01 mysqld: 141216 13:05:02 [warning] aborted connection 9225621 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) dec 16 13:10:00 db01 mysqld: 141216 13:10:00 [warning] aborted connection 9218291 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) dec 16 13:10:12 db01 mysqld: 141216 13:10:12 [warning] aborted connection 9232561 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) dec 16 13:17:01 db01 /usr/sbin/cron[41343]: (root) cmd (   cd / && run-parts --report /etc/cron.hourly) dec 16 13:20:02 db01 mysqld: 141216 13:20:02 [warning] aborted connection 9248777 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) dec 16 13:20:02 db01 mysqld: 141216 13:20:02 [warning] aborted connection 9248788 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) dec 16 13:20:12 db01 mysqld: 141216 13:20:12 [warning] aborted connection 9248798 db: 'unconnected' user: 'root' host: 'localhost' (unknown error) 

out of settings there any, should changed fix weird server has gone away errors?

in end have found out db not cause of exceptions dropping, drops appearing in other unrelated systems.