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I was using 14.04 LTS on my machine. When I got the notification that I can upgrade to 16.04.1 LTS, I downloaded the iso in order to get a clean reinstall. I have / on sda1 and /home on sda2 (seperate partitions). While installing 16.04.1, I chose to format sda1 and use it as / and I chose to use sda2 as /home. I chose the same username and the same password as before. The install went fine. After the first boot, I tried to log in, but it failed. I can go to a virtual terminal and log in using my usual credentials. I can cd to /home/user/Downloads for example and all my files in the subfolders of the home directory seem to be there. Yet, when I do ls while in ~ I get the following error:

ls: relocation error: /lib/x86_64-linux-gnu/libpthread.so.0: symbol __libc_vfork, version GLIBC_PRIVATE not defined in file libc.so.6 with link time reference

When I try to do nano ~/.bashrc I simply get a segmentation error. But the bash seems to have loaded my bashrc, since it looks like my usual bash. touch test gives me the same, while doing touch test in ~/Downloads works fine.

When I boot from my installation device, I can mount the partition sda2 and read fine from it. Writing is only possible by using sudo.

Any ideas what this is all about? Also: I have never used encryption of my home directory.

[EDIT]: The dmesg tells me (after trying to log in into the graphic interface)

traps: gnome-session[3282] general protection ip:[hex numbers] sp:[more hex] error:0 in libc.so.6[even more hex]

[EDIT]: I cannot do ls while in ~, but I can do ls ~ while in / and even in /home. I'm so confused right now.

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Probably something went wrong with files ownership settings (can be checked ls -al /home/USER). You can repair it by:

sudo chown USER /home/USER/ -Rv
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  • I just did this (removing the v option speeds this process up a lot), but I didn't fix anything. My user had the same UID (1000) in the old and in the new installation. – Wauzl Aug 10 '16 at 12:55
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I feel so dumb right now. This answer is likely to be unhelpful to anyone, but it solved my problem. I had (I don't really know why) a file called libc.so.6 lying around in my home directory. I removed it via rm ~/libc.so.6 while not being in ~ and it fixed everything.

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