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take note that qjackctl is a GUI from-end to JACK and the problems in your case are pretty well known although exclusive to Linux (fwiw. qjackctl also runs on macosx and windows ere those settings don't apply ever) and there are some distro cases that some system settings are in fact provided at JACK packages installation time, not necessarily when qjackctl is.

the information you request may be found in too many sites, being the following just an example:

• jakjaudio.org Wiki: Troubleshooting Problems starting in realtime mode - Operation not permitted
  https://github.com/jackaudio/jackaudio.github.com/wiki/Troubleshooting
• linuxaudio.org Wiki: System Configuration - limits.conf / audio.conf
  http://wiki.linuxaudio.org/wiki/system_configuration#limitsconfaudioconf

hth.
cheers