The first thought that came to mind was "Wow !!! You must have rather big transactions."

According to mysqlperformanceblog.com's Reasons for run-away main Innodb Tablespace, these are the main issues that cause ibdata1 to grow:

• Lots of Transactional Changes
• Very Long Transactions
• Lagging Purge Thread

The undo logs inside ibdata1 will hold lots of info to support transaction isolation levels. Since you are using READ-COMMITTED, this growth can be more significant.

I have discussed this before in the DBA StackExchange

• Aug 21, 2015 : Transactional DDL workflow for MySQL
• Jun 16, 2014 : MySQL Index creation failing on table is full
• Apr 23, 2013 : How can Innodb ibdata1 file grows by 5X even with innodb_file_per_table set?
• ... and more

SUGGESTION

Since you are using MariaDB, please look into configuring the undo logs outside of the system tablespace. Please read the MariaDB docs on innodb_undo_directory and innodb_undo_tablespaces and go from there.

The first thought that came to mind was "Wow !!! You must have rather big transactions."

According to mysqlperformanceblog.com's Reasons for run-away main Innodb Tablespace, these are the main issues that cause ibdata1 to grow:

• Lots of Transactional Changes
• Very Long Transactions
• Lagging Purge Thread

The undo logs inside ibdata1 will hold lots of info to support transaction isolation levels. Since you are using READ-COMMITTED, this growth can be more significant.

I have discussed this before in the DBA StackExchange

• Aug 21, 2015 : Transactional DDL workflow for MySQL
• Jun 16, 2014 : MySQL Index creation failing on table is full
• Apr 23, 2013 : How can Innodb ibdata1 file grows by 5X even with innodb_file_per_table set?
• ... and more

SUGGESTION #1

Since you are using MariaDB, please look into configuring the undo logs outside of the system tablespace. Please read the MariaDB docs on innodb_undo_directory and innodb_undo_tablespaces and go from there.

SUGGESTION #2

You may have to mysqldump are your data and load it into a new installation of MariaDB. See my posts in How do I shrink the innodb file ibdata1 without dumping all databases? for other ideas. Either way, this will take some work !!!