Mariadb check tables on startup

As already stated, the filesystem is the problem. However, there may be some tuning that would help.

If innodb_file_per_table has been ON, then there are 2*12 files in each database directory. Turning that OFF would lead to fewer files (but not fewer directories). This might help some.

SHOW VARIABLES LIKE 'table%';
SHOW VARIABLES LIKE 'innodb%files';
SHOW VARIABLES LIKE 'open%';
SHOW GLOBAL STATUS LIKE 'Opened%';
SHOW GLOBAL STATUS LIKE 'Uptime%';
SHOW GLOBAL STATUS LIKE 'Table%';

There is some info that can be gathered from those outputs.

Or, give me (1) amount of RAM, (2) SHOW VARIABLES;, and (3) SHOW GLOBAL STATUS;. I will run a number of checks to see if the table_open_cache is too small, and other things.

Use https://github.com/alestic/ec2-consistent-snapshot of your EBS volume using --mysql-master-status-file FILE option.

Create a new volume from that snapshot and attach to new instance or another instance you can use to copy to a remote location if needed.. The db server will only be locked for a couple seconds. I just performed this operation on a server with a 2TB server with millions of tables.

Start the slave db with data files from other server reset the slave and change your master with the correct log position.