No meu sistema, /etc/security/limits.conf faz parte do pacote libpam-modules:amd64 :
$ dpkg -S /etc/security/limits.conf
libpam-modules:amd64: /etc/security/limits.conf
e tenho os seguintes pacotes instalados:
$ dpkg -l libpam\*| grep -Ev '^un'
Desired=Unknown/Install/Remove/Purge/Hold
| Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)
||/ Name Version Architecture Description
+++-==========================-======================-============-==========================================================
ii libpam-cgfs 2.0.8-0ubuntu1~16.04.2 amd64 PAM module for managing cgroups for LXC
ii libpam-gnome-keyring:amd64 3.18.3-0ubuntu2 amd64 PAM module to unlock the GNOME keyring upon login
ii libpam-modules:amd64 1.1.8-3.2ubuntu2 amd64 Pluggable Authentication Modules for PAM
ii libpam-modules-bin 1.1.8-3.2ubuntu2 amd64 Pluggable Authentication Modules for PAM - helper binaries
ii libpam-runtime 1.1.8-3.2ubuntu2 all Runtime support for the PAM library
ii libpam-systemd:amd64 229-4ubuntu21.2 amd64 system and service manager - PAM module
ii libpam0g:amd64 1.1.8-3.2ubuntu2 amd64 Pluggable Authentication Modules library
Então, eu reinstalaria o libpam-modules:amd64 :
sudo apt-get install --reinstall libpam-modules:amd64
Como meu sistema pode ser diferente do seu, devo dizer YMMV .