After system upgrade (OpenSUSE Tumbleweed), akanodi crash. When running plasmashell I see how akanodi (mysqld) i running (I see parameters). I find on web there's mysql_upgrade, but I don't find parameters, which will match to this invoked by plasmashell (datadir and libdir). When searching on logs, I see there's problem with innodb, which probably isn't supported now, so I think I must ran db upgrade.

According to this uses mysql_upgrade under the hood mysqlcheck and mysql and forward the parameters to them. The difficulty could be that mysql_upgrade expects running database(server). This is why you can't find a way to specify config/datadir ...

Hmm ... Delete the database (files) and let akonadi create new one