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[EP-tech] indexer stalls

Hi all!
I've a big problem with the eprints indexer (Eprint 3.1.2). I was looking for a high load problem in our server and discovered that, even with no http requests or other process running, the load was above 1.
The indexer was also at Ss state, so sleeping and log (with an increased log level) showed it was not doing any operation in the past days. Then I shut down the indexer and the high load disappeared.
I think the problem could be my eprint__rindex which has 33 millions rows and eprint__index has 3 million rows. So I think what happens is that mysql issue some kernel calls, because I can see that, when the log stops to be updated with new operations), the wa (i/o waiting) is above 50% for a lot of time.
Then the indexer stop doing indexing and load is high (above 2 or 3) with an high wa (I/O).
Now I've stopped the indexer and running it as the webserver user (www-data) with --once and --notdeamon and stopping it when stalling. Then I run it again and so on (the index_queue has still 4000 rows to process). 

Any idea on how to solve this problem?
Question: which part of Eprints now is responsible to add an entry in the index_queue table?