Thanks a lot Michael! Creating the index solved this problem. Before the index, it took about 90 mins to dump everything in the mysql. After the index creation: 60s for the initial config dump and another 40s for the rest of the dumping. By the way, if this info might help you: I switched to Icinga 2 years ago and was on nagios before, since 2007 (and all nagios&icinga logs are kept since then).
Regards, Christophe Disclaimer: http://www.minfin.fgov.be/disclaimer.htm
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