My actual problem is that python sqlite3 module throws database disk image malformed.
Now there must be a million possible reasons for that. However, I can provide a number of clues:

I am using python multiprocessing to spawn a number of workers that all read (not write) from this DB
The problem definitely has to do with multiple processes accessing the DB, which fails on the remote setup but not on the local one. If I use only one worker on the remote setup, it works
The same 6GB database works perfectly well on my local machine. I copied it with git and later again with scp to remote. There the same script with the copy of the original DB gives the error
Now if I do PRAGMA integrity_check on the remote, it returns ok after a while - even after the problem occurred
Here are the versions (OS are both Ubuntu):

local:  sqlite3.version >>> 2.6.0, sqlite3.sqlite_version >>> 3.22.0
remote: sqlite3.version >>> 2.6.0, sqlite3.sqlite_version >>> 3.28.0


Do you have some ideas how to allow for save "parallel" SELECT?
The problem was for the following reason (and it had happened to me before):
Using multiprocessing with sqlite3, make sure to create a separate connection for each worker!
Apparently this causes problems with some setups and sometimes doesn't.
SQLITE3 / Python - Database disk image malformed but integrity_check ok