My server disk is filling up, 116Gb used out of 138Gb
The sites seem to be about 15Gb however I find a file
/var/lib/mysql/ibdata1 which appears to be 92Gb
A google says that I can not delete this file or even shrink it, any wise advice
That's the main storage file for InnoDB databases... You might want to check if there's any of those on your system with excessive amount of data (maybe a log table overflowing?).
And yep, you must not simply delete that file, or your InnoDB databases will be efficiently killed. :)
It might help to export all databases to SQL dump files and re-import them. At least that can help to find out which DB is the culprit. Virtualmin's Backup feature can be used for that since it creates SQL dumps.
There's a post here in the MySQL forums about that issue:
It mirrors what locutus mentioned above though, that you may need to drop and re-add your databases.
I will look into that