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Segfault after Ubuntu 17.10 upgrade #15944

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khaeru opened this Issue Oct 19, 2017 · 38 comments

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khaeru commented Oct 19, 2017

Prerequisites

  • Put an X between the brackets on this line if you have done all of the following: [snip]

Description

After an upgrade to Ubuntu 17.10 "artful aardvark", and installing 1.21.1 from the official amd64 .deb, Atom will not start.

Steps to Reproduce

$ atom

Expected behavior: Atom starts.

Actual behavior: /usr/bin/atom: line 129: 9862 Segmentation fault (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

Reproduces how often: 100%

Versions

Ubuntu 17.10
https://github.com/atom/atom/releases/tag/v1.21.1

atom --version gives no output.

$ apm --version
apm  1.18.5
npm  3.10.10
node 6.9.5 x64
python 2.7.14
git 2.14.1
@laurentpayot

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laurentpayot commented Oct 20, 2017

Same here after I upgraded from Ubuntu 17.04 to 17.10.

With atom installed via atom.io debian package:

laurent@pinkmoon:~$ atom
laurent@pinkmoon:~$ /usr/bin/atom : ligne 129 : 24411 Erreur de segmentation  (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

laurent@pinkmoon:~$ atom --version
laurent@pinkmoon:~$ 

With atom installed via snap:

laurent@pinkmoon:~$ atom
Erreur de segmentation (core dumped)
laurent@pinkmoon:~$ atom --version
Gtk-Message: Failed to load module "overlay-scrollbar"
Gtk-Message: Failed to load module "overlay-scrollbar"
/usr/share/themes/Ambiance/gtk-2.0/apps/mate-panel.rc:30: error: invalid string constant "murrine-scrollbar", expected valid string constant
Atom    : 1.21.1
Electron: 1.6.15
Chrome  : 56.0.2924.87
Node    : 7.4.0
laurent@pinkmoon:~$
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laurentpayot commented Oct 20, 2017

And I can not launch atom neither with Gnome nor with Unity.
Interestingly vscode (insiders) is not working either.

This is a major bug, I can't really work anymore 😞 A quick fix/workaround would be really appreciated…

@rsese

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rsese commented Oct 20, 2017

Thanks for the reports - when you started in safe mode, was there any difference at all or did Atom crash right after starting?

I'll try to install 17.10 and test today.

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laurentpayot commented Oct 20, 2017

I didn't even know that there was a --safe option. It's quite ugly but it is working in safe mode.

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khaeru commented Oct 20, 2017

Thanks, @rsese! I did follow the instruction in the bug template to run atom --safe. Unfortunately (unlike @laurentpayot) I get the same segfault with that option.

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laurentpayot commented Oct 20, 2017

Actually, for me, now atom is working in "normal" mode too. I didn't change anything. Weird.
Either the --safe option changed something, or there is a random succession of events at startup that make it start or not.

I'm not touching anything now, I'm too glad it's working 🙄

And thanks @rsese !

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rsese commented Oct 21, 2017

Finally had a chance to install 17.10 and then installed Atom 1.21.1. I ran into the error described in #14358, but after running sudo apt --fix-broken install, that fixed things up and Atom started ok.

@khaeru did you also try temporarily resetting to factory defaults?

http://flight-manual.atom.io/hacking-atom/sections/debugging/#reset-to-factory-defaults

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khaeru commented Oct 22, 2017

@rsese yes—that was part of the "Prerequisites" in the bug template (along with --safe, as we discussed previously) so did I try that. I had been using a custom location by setting the ATOM_HOME environment variable, so I also unset that. Same symptoms.

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Puller commented Oct 22, 2017

Same here...
Really annoying. Reset to Factory settings and Safe mode do not help either!

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laurentpayot commented Oct 23, 2017

Are you guys using gnome system-monitor? It displays system informations in gnome shell status bar, such as memory usage, cpu usage, network rate etc. It may interfere with atom title display, because that's the only thing I can remember playing with between my non-working and my working atom.

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Puller commented Oct 23, 2017

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khaeru commented Oct 23, 2017

FYI, I have two computers: a laptop and a desktop; the former displays the bug, the latter does not (ie. Atom 1.21.1 works, no segfault, after Ubuntu 17.10 upgrade). I will try to diff a list of installed packages between the two systems, and inspect Atom-related files, sometime today or tomorrow to determine what might be causing this issue.

In any case, it would be lovely if there were also an atom-dbg package that could be installed to produce a human-readable stack trace when things like this happen…

PS. @laurentpayot gnome-system-monitor appears to be installed on both systems, but like @Puller I never use it.

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pcnate commented Oct 23, 2017

I am experiencing the same issue, apm --version is the same version as @khaeru . I upgraded from Ubuntu 17.04 to Ubuntu 17.10 with no errors. Running Gnome via Xorg.

Here are the things I have tried:

  • runnning atom --safe
  • removed ~/.atom
  • removed ~/.config/Atom
  • apt-get purge atom and reinstalled via acu and via PPA as in this guide
  • installed 1.22.0-beta
  • installed several previous versions as far back as 1.10.x
  • building from source and executing final result
  • removed gnome-system-monitor
  • sudo apt --fix-broken install
  • atom --clear-window-state
  • apm unlink --all

Everything results in:

[Oct23 13:13] atom[19088]: segfault at ffffffffffffe633 ip 00000000033aeacb sp 00007ffd0d7dea60 error 5 in atom[400000+49c9000]

Still searching for the magical state of: My code works, I don't know why

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pcnate commented Oct 23, 2017

I skipped the state of: My code works, I don't know why.

While rebooting to switch to the previous kernel for testing which failed to load the GUI, I discovered 4 packages from the PPA from the guide above that could be updated. After updating them, and rebooting back to the GUI, Atom works!

2017-10-23 14:08:25 upgrade libicu-dev:amd64 57.1-6 57.1-6ubuntu0.2
2017-10-23 14:08:27 upgrade icu-devtools:amd64 57.1-6 57.1-6ubuntu0.2
2017-10-23 14:08:27 upgrade libicu57:i386 57.1-6 57.1-6ubuntu0.2
2017-10-23 14:08:28 upgrade libicu57:amd64 57.1-6 57.1-6ubuntu0.2
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khaeru commented Oct 23, 2017

Hi all—this has now mysteriously fixed itself on my system, too.

  1. Noticed that I received the same upgrades to libicu57 as @pcnate (however I don't think these are from the webupd8team/atom PPA, but from Ubuntu's official repositories), as well as others to libcurl3{,-gnutls} and libmysqlclient20.
  2. Tried atom, atom --safe, atom --version etc.—same segfault.
  3. Rebooted.
  4. atom, atom --safe and atom --version now work. ¯\_(ツ)_/¯

So, @rsese, I suppose it can be closed unless it is still affecting someone else. Sorry for the spam.

P.S. for any dev who may care at a later date, the last crash of Atom at 2—unlike all others before—was caught by Ubuntu apport's tool, which displayed the message "atom crashed with SIGSEGV in __start_google_malloc()". No idea where that method appears in Atom or its dependencies.

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rsese commented Oct 24, 2017

Thanks for the update @khaeru - since we were unable to get a reproduction with the .deb from atom.io (the PPA and the snap are unofficial) on a fresh install of Ubuntu 17.10, we'll go ahead and close for now (but definitely not spam @khaeru, we appreciate the bug report). But at least we have more information in case other folks run into problems with Ubuntu 17.10, thanks to everyone who chimed in.

@rsese rsese closed this Oct 24, 2017

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snaumov commented Nov 5, 2017

hi all. Just to add my 5 cents - the same problem is happening to me after an upgrade from 17.04 to 17.10 and that's what ubuntu apport stacktrace contains

screenshot from 2017-11-05 11-50-49
screenshot from 2017-11-05 11-51-40

neither of electron based apps work now... Will try to see if I can find something else or if the issue magically disappears.

Update: it works after reboot now. As I didn't reboot for some time, probably, libgtk and it's dependencies got updated in meantime

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adamdrake commented Nov 10, 2017

I have this issue as well, and with all Electron apps (though not atom). Originally none of them worked with 17.10, then they did for a while, now they don't again. I can confirm the bug occurs with 17.10 and the latest version of Slack and VS Code. Any developments on this issue?

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laurentpayot commented Nov 10, 2017

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settel-np commented Nov 21, 2017

Issue is not solved for me, atom still crashes.
All Ubuntu updates have been applied successfully, there are no broken packages left. And I rebooted several times after upgrading, too.

Using atom 1.22.1 from atom.io under Ubuntu 17.10 (upgraded from Ubuntu 17.04).

 $ dpkg -l atom libicu-dev icu-devtools libicu57
||/ Name           Version      Architecture Description
+++-==============-============-============-=================================
ii  atom           1.22.1       amd64        A hackable text editor for the 21
ii  icu-devtools   57.1-6ubuntu amd64        Development utilities for Interna
ii  libicu-dev     57.1-6ubuntu amd64        Development files for Internation
ii  libicu57:amd64 57.1-6ubuntu amd64        International Components for Unic
ii  libicu57:i386  57.1-6ubuntu i386         International Components for Unic

 $ apm --version
apm  1.18.8
npm  3.10.10
node 6.9.5 x64
python 2.7.14
git 2.14.1


 $ atom
/usr/bin/atom: line 129: 23536 Segmentation fault      nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

 $ ls -l nohup.out 
-rw-rw-r-- 1 settel settel    0  Nov 21 18:55 nohup.out

BTW: Running atom as root (strongly discouraged! Don't try this at home!) works, the editor shows up.

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pcnate commented Nov 22, 2017

I would expect when you run it as root, then ~/.atom becomes /root/.atom instead of /home/you/.atom

Have you tried backing up then removing ~/.atom?

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settel-np commented Nov 22, 2017

I would expect when you run it as root, then ~/.atom becomes /root/.atom instead of /home/you/.atom

I use sudo -i to run it as root, so ~/.atom is still /home/USER/.atom. But it doesn't matter, Atom crashes way before it even gets to read the .atom/ folder.

Have you tried backing up then removing ~/.atom?

sure. doesn't change the outcome.

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twogood commented Nov 23, 2017

As a workaround try to set GTK2_RC_FILES environment variable to empty when you start the application.

See my blog post https://divideandconquer.se/2017/11/23/workaround-for-crashing-electronatom-applications/

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settel-np commented Nov 23, 2017

That run-as-root-solves-the-problem stuff got me searching for the differences. Some trials later, I figured out that unsetting XDG_CONFIG_DIRS makes atom run:
XDG_CONFIG_DIRS="" /usr/share/atom/atom

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settel-np commented Nov 23, 2017

@twogood hehe, you've found a similar workaround at about the same time :-)
GTK2_RC_FILES="" /usr/share/atom/atom
works for me, too

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twogood commented Nov 23, 2017

@settel-np Cool, I'll add that to my blog post! Not less strange though! Maybe it will be solved if I restart with the latest package updates... My update manager is nagging me to reboot :)

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settel-np commented Nov 23, 2017

This issue is not atom-specific, I managed to reproduce the crash with electron quick start application, too. I filed a bugreport with electron, see electron/electron#11234

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lil5 commented Mar 7, 2018

I found that if you add 10 or more sources in GTK_RC_FILES this issue happens

~ $ GTK2_RC_FILES="a:b:c:d:e:f:g:h:i" /usr/share/atom-beta/atom # runs fine
bash: cannot set terminal process group (-1): Inappropriate ioctl for device
bash: no job control in this shell
~ $ GTK2_RC_FILES="a:b:c:d:e:f:g:h:i:f" /usr/share/atom-beta/atom # issue happens
Segmentation fault

Edit:
lol already documented in electron: Segmentation fault on startup if XDG_CONFIG_DIRS (or GTK2_RC_FILES) contains too many items #11234

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lil5 commented Mar 7, 2018

In the end I installed https://github.com/atom/atom/releases/tag/v1.21.2 after an uninstall and reboot

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shemgp commented Sep 11, 2018

Upgraded to Ubuntu Cosmic and atom won't start, but atom snap does:

 shemgp  shemgp-x230t  ~  $  atom-beta 
 shemgp  shemgp-x230t  ~  $  /usr/bin/atom-beta: line 157: 30355 Segmentation fault      (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
 shemgp  shemgp-x230t  ~  $  atom-beta --safe
 shemgp  shemgp-x230t  ~  $  /usr/bin/atom-beta: line 157: 32460 Segmentation fault      (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

 shemgp  shemgp-x230t  ~  $  XDG_CONFIG_DIRS="" atom-beta
 shemgp  shemgp-x230t  ~  $  /usr/bin/atom-beta: line 157:   547 Segmentation fault      (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

 shemgp  shemgp-x230t  ~  $  atom-beta
 shemgp  shemgp-x230t  ~  $  /usr/bin/atom-beta: line 157:  1983 Segmentation fault      (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
^C
 shemgp  shemgp-x230t  ~  SIGINT  $  GTK2_RC_FILES="" atom-beta
 shemgp  shemgp-x230t  ~  $  /usr/bin/atom-beta: line 157:  3307 Segmentation fault      (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
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rsese commented Sep 12, 2018

@shemgp - I think you're running into a different issue since you're on Cosmic, see #17904 (comment).

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madeindjs commented Oct 4, 2018

Same issue for me:

$ atom
/usr/bin/atom : ligne 157 : 26264 Erreur de segmentation  (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1
$ atom -v
$ XDG_CONFIG_DIRS="" atom
/usr/bin/atom : ligne 157 : 26590 Erreur de segmentation  (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

This happens just after upgraded to Xubuntu Cosmic Cuttlefish

$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu Cosmic Cuttlefish (development branch)
Release:	18.10
Codename:	cosmic
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larp-welt commented Oct 18, 2018

And same for me:

/usr/bin/atom: Zeile 157: 19514 Speicherzugriffsfehler  (Speicherabzug geschrieben) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1

Just after the upgrade to Ubuntu 18.10.

No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 18.10
Release:        18.10
Codename:       cosmic

I've allready redownloaded Atom, reinstalled it, and removed .atom too. Atom is Version 1.31.2.

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katian commented Oct 19, 2018

And same for me:

/usr/bin/atom : ligne 157 :  6040 Erreur de segmentation  (core dumped) nohup "$ATOM_PATH" --executed-from="$(pwd)" --pid=$$ "$@" > "$ATOM_HOME/nohup.out" 2>&1> 

Just after the upgrade to Ubuntu 18.10.

I've allready redownloaded Atom, reinstalled it, and removed .atom too.

Linux 4.18.0-10-generic #11-Ubuntu SMP Thu Oct 11 15:13:55 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
$ apm --version
apm  2.1.1
npm  6.2.0
node 8.9.3 x64
atom 1.31.2
python 2.7.15+
git 2.19.1

EDIT : it work with atom-beta
sudo apt install atom-beta

Atom    : 1.32.0-beta3
Electron: 2.0.9
Chrome  : 61.0.3163.100
Node    : 8.9.3
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rsese commented Oct 19, 2018

@madeindjs @larp-welt @katian - please see #18268 (comment). As mentioned by @katian above, 1.32 which is currently in beta should work.

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thalessa commented Oct 22, 2018

Have same problem. Confirming that 1.32 beta works.

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rmilovanov commented Dec 25, 2018

Had the same problem on Fedora after upgade from Fedora 28 to 29.

I've done:
sudo dnf remove atom
Then downloaded and installed .rpm from official site.

It fixed the problem, moreover all my settings and packages stayed safe and everything works.

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daviwil commented Jan 29, 2019

Since it seems Atom 1.32.0 has resolved this issue, I'll go ahead and close it. Please feel free to comment here if you are still experiencing the issue and we'll be happy to reopen!

@daviwil daviwil closed this Jan 29, 2019

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