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I finally managed to find a workaround. If I added

 --ulimit nofile=1024

to my "docker run" command the loading of nodes and nodelets is very fast. Without this the value given by "ulimit -Hn" is above 1000000 (probably the maximum value). It seems to be a race condition or so that gives this high value. The value should really be the one you have in the shell were you start the docker container. If it is correct behaviour to be slow if this values is high I do not know.