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

Question

We have upgraded our database server from MySQL 5.1 to MariaDB 5.5 (5.5.40-MariaDB-1~wheezy-log).
After this upgrade, some long running processes mysql connection si being dropped.
Common scenario for those processes is:
Connect to MySQL
Run some queries
Do some heavy lifting without connecting to MySQL for at least one minute
Try to query against the original connection
Exception giving a 2600 error - MySQL server has gone away
This does happen in PHP CLI scripts (php 5.3), but also in a Ruby application (Redmine 2.5.1). It was not happening with MySQL 5.1 and there were no changes on the applications side, so it should not be 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 are 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 the thing happens, there is also an event logged in syslog, everytime looking the same:
Dec 16 13:00:14 DB01 mysqld: 141216 13:00:14 [Warning] Aborted connection 9202885 to db: 'some_db_name' user: 'user' host: 'app' (Unknown error)
Besides that, there are also weird root account disconnection messages:
Dec 16 13:05:02 DB01 mysqld: 141216 13:05:02 [Warning] Aborted connection 9225621 to db: 'unconnected' user: 'root' host: 'localhost' (Unknown error)
Dec 16 13:10:00 DB01 mysqld: 141216 13:10:00 [Warning] Aborted connection 9218291 to db: 'unconnected' user: 'root' host: 'localhost' (Unknown error)
Dec 16 13:10:12 DB01 mysqld: 141216 13:10:12 [Warning] Aborted connection 9232561 to 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 to db: 'unconnected' user: 'root' host: 'localhost' (Unknown error)
Dec 16 13:20:02 DB01 mysqld: 141216 13:20:02 [Warning] Aborted connection 9248788 to db: 'unconnected' user: 'root' host: 'localhost' (Unknown error)
Dec 16 13:20:12 DB01 mysqld: 141216 13:20:12 [Warning] Aborted connection 9248798 to db: 'unconnected' user: 'root' host: 'localhost' (Unknown error)
Out of those settings is there any, that should be changed to fix the weird server has gone away errors?

Answer 1

In the end we have found out that the DB is not the cause of exceptions dropping, as the drops are appearing also in other unrelated systems.