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Indeed, the results obtained by adding session optional pam_systemd.so to /etc/pam.d/lsf were not positive, as you stated.
Let me explain better the use case for which we need to set up the environment correctly: Vnc sessions are used as virtual desktops by users. There is a need for the user to login as if he using a 'traditional desktop', hence the need for the dbus configuration to be correctly valued.
Currently we are using a template that launches a script that does an SSH and then launches the Vnc session in which the application is executed.
When the LSF service starts a job on behalf the user it does not perform an OS login, so pam_login() is not called, and that pam_systemd is not invoked to /run/user/$uid is not created.
Changing LSF to perform a login() would fundamentally change an established architecture, and is not something we would do.
As previously discussed, you could add
session optional pam_systemd.so
to /etc/pam.d/lsf, but it may result in some other unexpected behaviour as login() has not been called, and not tty would be associated with the session, so may have other issues. Furthermore, you could not use LSF's own cgroup support at the same time.