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papandreoos
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PostPosted: Wed Mar 06, 2019 9:27 pm    Post subject: problem with newly installed openssl Reply with quote

[EDITED at the end]

those are the packages i installed today:
Code:
Wed Mar  6 12:34:13 2019 >>> sys-kernel/linux-headers-5.0
     Wed Mar  6 21:08:54 2019 >>> dev-libs/openssl-1.1.0j-r1
     Wed Mar  6 21:09:49 2019 >>> sys-libs/e2fsprogs-libs-1.44.6


i think that before i installed those packages, i rebooted my computer and everything worked great (AKA i automatically log into gnome).
after emerging those packages (i think that e2fsprogs-libs failed to compile) i rebooted my computer and now i am not logging in automatically to gnome.
instead i have the lighdm log in and it doesn't accept my password (and it's the right password).
so i did CTRL + ALT + F2 and log in there without a problem.
then i tried to:
Code:
sudo emaint sync -a && sudo emerge -vtuND --with-bdeps=y @world && sudo emerge -c

and i get this error:
Code:
>>> Syncing repository 'gentoo' into '/usr/portage'...
/usr/bin/git fetch origin
/usr/libexec/git-core/git-remote-https: /usr/lib64/libssl.so.1.1: version `OPENSSL_1_1_1' not found (required by /usr/lib64/libcurl.so.4)
!!! git fetch error in /usr/portage
q: Updating ebuild cache for /usr/portage ...
q: Finished 36354 entries in 0.448794 seconds


i also tried to equery openssl but get this error:
Code:
equery c openssl
!!! Fatal error: /usr/portage/dev-libs/openssl/ChangeLog does not exist or is unreadable

Add '--debug' to global options for traceback.



EDIT:
i also tried to reinstall openssl but:
Code:
sudo emerge  openssl
Calculating dependencies... done!

>>> Verifying ebuild manifests

>>> Emerging (1 of 1) dev-libs/openssl-1.1.0j-r1::gentoo
Segmentation fault

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NeddySeagoon
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PostPosted: Wed Mar 06, 2019 9:45 pm    Post subject: Reply with quote

papandreoos,

Code:
Segmentation fault
something tried to access memory it doesn't own.
There will be more information in dmesg.

Put all of dmesg onto a pastebin please.
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papandreoos
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PostPosted: Wed Mar 06, 2019 10:02 pm    Post subject: Reply with quote

here it is:
https://pastebin.com/Skt0EyYP
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NeddySeagoon
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PostPosted: Wed Mar 06, 2019 10:06 pm    Post subject: Reply with quote

papandreoos,

It looks like systemd has taken over the log.
As I'm not a systemd user, I don't know how to get the log.
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papandreoos
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PostPosted: Wed Mar 06, 2019 10:12 pm    Post subject: Reply with quote

NeddySeagoon wrote:
papandreoos,

It looks like systemd has taken over the log.
As I'm not a systemd user, I don't know how to get the log.


OK thanks :-)
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papandreoos
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PostPosted: Wed Mar 06, 2019 10:46 pm    Post subject: Reply with quote

well i tried journalctl -b and maybe this log will help?
https://pastebin.com/ce5kgujh
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NeddySeagoon
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PostPosted: Wed Mar 06, 2019 10:54 pm    Post subject: Reply with quote

papandreoos,

There are no segfault messages there. If you have rebooted they will be gone.
You need to make the error happen, then post, before a reboot.
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Computer users fall into two groups:-
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papandreoos
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PostPosted: Wed Mar 06, 2019 11:02 pm    Post subject: Reply with quote

well it is strange.
i am now writing from archlinux and in the terminal i chroot to the gentoo system and from there if i am command dmesg i get this:
https://pastebin.com/95XZnJzW

it has segfaults! :-)
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papandreoos
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PostPosted: Thu Mar 07, 2019 11:15 am    Post subject: Reply with quote

well i don't know what can i do more.
i get into gentoo again (lightdm log in).
then move to termianl and then i command all the commands i gave their output in the first post here.
i did again dmesg and save it to file.
here it is:
https://pastebin.com/0BgekTHx
there are 2 segfaults i can see in the end.

i also did journalctl -b and save it to file.
here it is:
https://pastebin.com/p0VW3aPa

there you can see that NetworkManager failed to start.
i also see it in the text when linux starting.

if you need something else please tell me.
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papandreoos
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PostPosted: Thu Mar 07, 2019 7:36 pm    Post subject: Reply with quote

i also did qcheck and this is the output:
https://pastebin.com/r1j1UiTL

someone in the chat suggested this.
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NeddySeagoon
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PostPosted: Thu Mar 07, 2019 9:16 pm    Post subject: Reply with quote

papandreoos,

Code:
[ 1122.814561] emerge[4162]: segfault at b0 ip 00007f97ccf5db56 sp 00007fffb87637a0 error 4 in ld-2.28.so[7f97ccf53000+1e000]

ld-2.28.so is the dynamic linker. Its provided by glibc. If dynamic linking fails, so does almost everything else.
In fact, I'm surprised bash works to support the chroot.

You need a binary glibc to replace your broken one. There is a catch. You must not accidiently downgrade glibc.
If you want to build and install your own glibc binary, follow Fix My Gentoo

If you trust gentooexperimental.org you will find a glibc tarball there.
You can even unpick the stage3 tarball, described in Fix My Gentoo, to get a suitable tarball.

If emerge won't work to install the binary package, you will need to use the "spray files all over the filesystem" method.

I'm reluctant to suggest a reinstall as we don't understand what went wrong and a reinstall rarely fixes anything with Gentoo.
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Computer users fall into two groups:-
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papandreoos
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PostPosted: Fri Mar 08, 2019 1:36 am    Post subject: Reply with quote

thank you very much.
i decided to delete my gentoo and start over again :-)
hope i'll finish in couple of days :-D
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trixtrax
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PostPosted: Fri Mar 15, 2019 6:55 am    Post subject: Reply with quote

In the process of upgrading my system yesterday, I seem to be facing this same issue as well. What started as a need to see if recent upgrades to KDE 5.14 series would fix some glitches in the rendering of window decorations led to a dependency conflict with nodejs and nearly everything else wanting different Openssl versions. So, to satisfy Openssh 7.9_p1-r4 and nodejs 10.15.3 (Firefox 65.0.2), I eventually reluctantly installed Openssl-1.1.0j-r1. Next I tried to emerge -ND @world and all emerges since have led to segmentation faults. As an aside, I'm using a amd64/17.0/desktop/plasma profile.

After messing with things for a while noticed that dmesg was showing a similar error occuring with a seg faulting emerge (which led me here):

Code:
[1302949.747143] emerge[5222]: segfault at b0 ip 00007f1c73170868 sp 00007fff0bea8560 error 4 in ld-2.28.so[7f1c73165000+26000]
[1302949.747150] Code: 94 c1 41 c1 e1 02 81 e2 ff 7f 00 00 41 09 c1 4d 89 ae 00 04 00 00 48 8d 14 52 45 89 8e 08 04 00 00 4c 8d 04 d6 4d 85 c0 74 0f <41> 8b 70 08 b8 00 00 00 00 85 f6 4c 0f 44 c0 41 8b 7d 00 48 8b 8d


Now, it appears that my glibc is somehow borked which seems strange because collision-protect is set. Since then, emerge is broken so (again reluctantly) decided to unfurl the matching glibc - glibc-2.28-r5 onto my filesystem and yet the problem persists. As to be expected it created a couple problems that had to be fixed like the symlink from /usr/lib64 to /usr/lib and my python profile being unset.. and unfortunately after fixing those issues, the problem still persists with the same error. I'm stumped. Thoughts?
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gentooUs3r
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PostPosted: Tue Apr 09, 2019 10:00 pm    Post subject: Reply with quote

trixtrax wrote:
In the process of upgrading my system yesterday, I seem to be facing this same issue as well. What started as a need to see if recent upgrades to KDE 5.14 series would fix some glitches in the rendering of window decorations led to a dependency conflict with nodejs and nearly everything else wanting different Openssl versions. So, to satisfy Openssh 7.9_p1-r4 and nodejs 10.15.3 (Firefox 65.0.2), I eventually reluctantly installed Openssl-1.1.0j-r1. Next I tried to emerge -ND @world and all emerges since have led to segmentation faults. As an aside, I'm using a amd64/17.0/desktop/plasma profile.

After messing with things for a while noticed that dmesg was showing a similar error occuring with a seg faulting emerge (which led me here):

Code:
[1302949.747143] emerge[5222]: segfault at b0 ip 00007f1c73170868 sp 00007fff0bea8560 error 4 in ld-2.28.so[7f1c73165000+26000]
[1302949.747150] Code: 94 c1 41 c1 e1 02 81 e2 ff 7f 00 00 41 09 c1 4d 89 ae 00 04 00 00 48 8d 14 52 45 89 8e 08 04 00 00 4c 8d 04 d6 4d 85 c0 74 0f <41> 8b 70 08 b8 00 00 00 00 85 f6 4c 0f 44 c0 41 8b 7d 00 48 8b 8d


Now, it appears that my glibc is somehow borked which seems strange because collision-protect is set. Since then, emerge is broken so (again reluctantly) decided to unfurl the matching glibc - glibc-2.28-r5 onto my filesystem and yet the problem persists. As to be expected it created a couple problems that had to be fixed like the symlink from /usr/lib64 to /usr/lib and my python profile being unset.. and unfortunately after fixing those issues, the problem still persists with the same error. I'm stumped. Thoughts?


I've encountered exactly same problem around same time. I've exactly the same segfault. Unfortunately I didn't fixed it yet. That must be some kind of bug, as we can see, some people actually have the same issue.
I'm practically still locked down with the portage immediately crashing after each start. I've also tried to untar the glibc version 2.28-r5 from external packages, but without any positive results.
In my case problem was also related to the openssl emerges, so that could be the main cause. Now I just have a 1.1.0j-r1 openssl version. Previously I've used 1.0.2q. I'm using amd64/17.0/desktop/plasma profile as well.
Do you have any solution?
Maybe someone can give us a hint how to restore portage functioning?

Thanks a lot for any help in advance.

EDIT

I've used LD_DEBUG=all setting to find out what library causes the problem - it is libssl.so.1.1

Code:
     1571:     calling init: /usr/lib64/python3.6/site-packages/portage/util/libc.cpython-36m-x86_64-linux-gnu.so
      1571:
      1571:     opening file=/usr/lib64/python3.6/site-packages/portage/util/libc.cpython-36m-x86_64-linux-gnu.so [0]; direct_opencount=1
      1571:
      1571:     symbol=PyInit_libc;  lookup in file=/usr/lib64/python3.6/site-packages/portage/util/libc.cpython-36m-x86_64-linux-gnu.so [0]
      1571:     binding file /usr/lib64/python3.6/site-packages/portage/util/libc.cpython-36m-x86_64-linux-gnu.so [0] to /usr/lib64/python3.6/site-packages/portage/util/libc.cpython-36m-x86_64-linux-gnu.so [0]: normal symbol `PyInit_libc'
      1571:     symbol=_exit;  lookup in file=/usr/bin/python3.6 [0]
      1571:     symbol=_exit;  lookup in file=/usr/lib64/libpython3.6m.so.1.0 [0]
      1571:     symbol=_exit;  lookup in file=/lib64/libpthread.so.0 [0]
      1571:     symbol=_exit;  lookup in file=/lib64/libc.so.6 [0]
      1571:     binding file /usr/lib64/libpython3.6m.so.1.0 [0] to /lib64/libc.so.6 [0]: normal symbol `_exit' [GLIBC_2.2.5]
      1561:     symbol=_PyEval_SignalReceived;  lookup in file=/usr/bin/python3.6 [0]
      1561:     symbol=_PyEval_SignalReceived;  lookup in file=/usr/lib64/libpython3.6m.so.1.0 [0]
      1561:     binding file /usr/lib64/libpython3.6m.so.1.0 [0] to /usr/lib64/libpython3.6m.so.1.0 [0]: normal symbol `_PyEval_SignalReceived'
      1561:     symbol=_Py_write_noraise;  lookup in file=/usr/bin/python3.6 [0]
      1561:     symbol=_Py_write_noraise;  lookup in file=/usr/lib64/libpython3.6m.so.1.0 [0]
      1561:     binding file /usr/lib64/libpython3.6m.so.1.0 [0] to /usr/lib64/libpython3.6m.so.1.0 [0]: normal symbol `_Py_write_noraise'
      1561:     symbol=_Py_bytes_contains;  lookup in file=/usr/bin/python3.6 [0]
      1561:     symbol=_Py_bytes_contains;  lookup in file=/usr/lib64/libpython3.6m.so.1.0 [0]
      1561:     binding file /usr/lib64/libpython3.6m.so.1.0 [0] to /usr/lib64/libpython3.6m.so.1.0 [0]: normal symbol `_Py_bytes_contains'
      1561:     object=/lib64/libc.so.6 [0]
      1561:      scope 0: /usr/bin/python3.6 /usr/lib64/libpython3.6m.so.1.0 /lib64/libpthread.so.0 /lib64/libc.so.6 /lib64/libdl.so.2 /lib64/libutil.so.1 /lib64/libm.so.6 /lib64/ld-linux-x86-64.so.2
      1561:
      1561:
      1561:     relocation processing: /usr/lib64/libssl.so.1.1
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wrc1944
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PostPosted: Thu Apr 11, 2019 2:00 am    Post subject: Reply with quote

NeddySeagoon wrote:
Quote:
It looks like systemd has taken over the log.
As I'm not a systemd user, I don't know how to get the log.

This is indeed a historic post on the Gentoo Forum!

I never thought I'd see the day there was something NeddySeagoon didn't know!

I'm stunned! 8O 8O 8O
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gentooUs3r
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PostPosted: Sat Apr 13, 2019 11:33 am    Post subject: Reply with quote

wrc1944 wrote:
NeddySeagoon wrote:
Quote:
It looks like systemd has taken over the log.
As I'm not a systemd user, I don't know how to get the log.

This is indeed a historic post on the Gentoo Forum!

I never thought I'd see the day there was something NeddySeagoon didn't know!

I'm stunned! 8O 8O 8O

Yeah, yeah, thanks for help.

I've managed to find a solution, not a pretty one, I'm afraid, but at least working for some time now.
There must be some kind of a bug in the openssl 1.1.0j-r1 package. Extracting package from the URL mentioned before - http://packages.gentooexperimental.org/packages/, didn't fixed anything.
I've manually extracted the previous version of the openssl (1.0.2r). I've also changed symlinks:
Code:

/usr/lib64/libssl.so -> libssl.so.1.0.0
/usr/lib64/libcrypto.so -> libcrypto.so.1.0.0

Emerge was moving on, but still crashing (again segfault) with python 3.6 using the libssl.so.1.1 from the openssl 1.1.0j-r1 package (ignoring the symlink). I've replaced that file with the one provided by the 1.0.2 openssl version.
Since then I was able to run emerge without a segfault. I've unmasked and emerged the openssl 1.1.1b-r2, which is not bugged. I've also removed the remaining openssl 1.0.0 files later.
Emerge world seems to be finally working great and system went back to normal.
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