[EMAIL PROTECTED] mentioned :
=> Try ANALYZE after loading the referenced tables, but before loading the main 

I attached a new script for creating the load file...
Analyze didn't help, it actually took longer to load.
I set autocommit to off, and put a commit after every 100
inserts, chattr'd noatime atrribute off recursively on PGDATA, and
set fsync to off, this improved the time from 3min 51sec to 2min 37 sec
for the slow scenario.

But I was already doing all these things  in the app that 
used to take 40 minutes, but now takes four hours to load.

Any other suggestions?

Kind Regards

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