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You need to check on how the defaults are set on your systems. Sometimes it can be that a daemon is started with low limits (e.g., 64) and then any shells/windows that that daemon spawns inherit those low limits.
For example, see the Open MPI FAQ on this topic:
On Dec 7, 2009, at 8:45 AM, Stefan Kuhne wrote:
> Stefan Kuhne schrieb:
> > Stefan Kuhne schrieb:
> >> I'll try it on monday.
> > with:
> > user_at_head:~$ ulimit -l
> > unlimited
> > user_at_head:~$
> > it works.
> it works in ssh and FreeNX, but an Terminal on real X11 tells 64 again.
> But i need X11 for testing an MPE issue.
> Stefan Kuhne
> users mailing list