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I have a weird problem on my notebook. When I want to login to the system (for example on tty1), immediately after I put in my username I get a Permission Denied error, even with root!

I booted a liveCD and checked /etc/{passwd,shadow}, but both are accessible by root and the users are still in there. What could be the problem? How do I fix it?

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You get it before it even asks you for a password? – Michael Mrozek Nov 11 '11 at 15:20
sounds like a pam error. check /etc/pam.d/system-auth – Sirex Nov 11 '11 at 15:58
Is /etc/shadow world-readable? What does pwck say after you booted from the live-cd and chroot your disk-environment? – Nils Nov 11 '11 at 21:34
What distribution are you running? Did it work before? Have you enabled any security feature (e.g. SELinux), upgraded your system, modified some configuration, or done anything else that might impact authentication recently? Do any messages from the time you tried to log in appear under /var/log? (specifically /var/log/auth.log, I think, but the path depends on your distribution). – Gilles Nov 11 '11 at 22:50
Where did you work on before this happened? What could have caused this? – glglgl Nov 12 '11 at 9:41
up vote 1 down vote accepted

It is definitely PAM error as mentioned in comments. I also had same issue, I just downloaded latest PAM source from the link below and compiled as instructed in the webpage. http://www.linuxfromscratch.org/blfs/view/svn/postlfs/linux-pam.html

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Which distribution are you using? On Fedora/Centos/Redhat selinux is enforced by default. Maybe your pam files are not labelled correctly. In the grub console, edit the boot line and add "selinux=0" to check if it makes a difference.

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