Arch Linux

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Calibre core dump when closed

I'm using 64 bit kernel - 4.4.1-2

Calibre (calibre2.50.1-1) starts up and I can use it as usual, but when I close it, there is a segmentation fault.
Exactly the same thing when I use another program from the calibre package ebook-viewer.
I haven't noticed any other programs causing issues yet.

Anyone have the same problem or know why it's causing a segfault?

FlowIt

Member

Registered: 2014-10-25

Posts: 243

Re: Calibre core dump when closed

a) Did you use pacman -Syu to update your system? Partial updates are not supported and can cause such problems.
b) Run calibre from command line and post the output.

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

Yes everything is up to date.
The only response :

[1]    10982 segmentation fault (core dumped)  calibre

Plus it  creates a new 300-400 MB file core.10982 in my home folder.

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: Calibre core dump when closed

I get those errors sometimes too, but it's never caused an issue.

(calibre-git 2.51.0.r65.ge7976ae-1, not that it matters since I've been seeing it for a long time.)

Last edited by eschwartz (2016-02-21 02:02:34)

---

Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

I get those errors sometimes too, but it's never caused an issue.

(calibre-git 2.51.0.r65.ge7976ae-1, not that it matters since I've been seeing it for a long time.)

Yes but I don't want to have to keep cleaning out 300+MB file is my home directory. It's a sign that something's wrong and Id like to find out what.

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,729

Re: Calibre core dump when closed

so open the coredump with gdb and see if you can get a backtrace

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: Calibre core dump when closed

Well, it's not the only thing that occasionally segfaults, if I take a look at coredumpctl.

And given that they are all automatically stored in /var/lib/systemd/coredump/ and cleaned up after three days, I am not inclined to care overmuch.
If they are being stored in your home directory, then perhaps you have changed the default behavior for core dumps.

Or go investigate why it is happening -- if your question is "has anyone investigated yet", then the answer is probably "no", or they would've done something. And commiserating is not very useful...

Last edited by eschwartz (2016-02-21 05:06:39)

---

Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

so open the coredump with gdb and see if you can get a backtrace

Thanks for the suggestion.

gdb core core.22346
...
(gdb) backtrace

#0  0x00007f99ef11b992 in ?? ()
#1  0x0000000000000001 in ?? ()
#2  0x00007f99ef6d44d8 in ?? ()
#3  0x00007f99d4000070 in ?? ()
#4  0x00007f99d4000900 in ?? ()
#5  0x00007f99d9451698 in ?? ()
#6  0x00007f99d4000020 in ?? ()
#7  0x0000000000000020 in ?? ()
#8  0x000000000001ba10 in ?? ()
#9  0x0000000000000800 in ?? ()
#10 0x0000000000000004 in ?? ()
#11 0x00007f99d4000020 in ?? ()
#12 0x00007f99ef11d6c0 in ?? ()
#13 0x00000000ffffffff in ?? ()
#14 0x0000000000000050 in ?? ()
#15 0x00000000000007f0 in ?? ()
#16 0x00007f99ef86f4e0 in ?? ()
#17 0x00007f99eba46a50 in ?? ()
#18 0x00007f99ebc5e618 in ?? ()
#19 0x00007f99eba46a30 in ?? ()
#20 0x00007f99e6d5e628 in ?? ()
#21 0x00007f99d4000900 in ?? ()
#22 0x0000000000000000 in ?? ()

I'm already out of my depth - I've never used gdb before.

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

I've noticed some more core dumps in my home folder. The latest was due to firefox.

$ firefox --version
Mozilla Firefox 44.0.2

$ gdb /usr/bin/firefox core.26455
...
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f51fa577c39 in raise () from /usr/lib/libpthread.so.0
[Current thread is 1 (Thread 0x7f517ccff700 (LWP 29102))]
(gdb) bt
#0  0x00007f51fa577c39 in raise () from /usr/lib/libpthread.so.0
#1  0x00007f51eab54fe4 in ?? () from /usr/lib/firefox/libxul.so
#2  0x00007f51eafb5673 in ?? () from /usr/lib/firefox/libxul.so
#3  <signal handler called>
#4  0x00007f51eba6e587 in ?? () from /usr/lib/firefox/libxul.so
#5  0x00007f51e7ddfd7b in ?? () from /usr/lib/libnspr4.so
#6  0x00007f51fa56e4a4 in start_thread () from /usr/lib/libpthread.so.0
#7  0x00007f51f9811dcd in clone () from /usr/lib/libc.so.6

Could that mean that some library used by calibre and firefox is causing the segfaults? Calibre is consistently dumping and firefox intermittently.

This thread about firefox 43 suggests GTK3 and mesa have caused problems.

I've no idea how to get any further.

eschwartz

Fellow

Registered: 2014-08-08

Posts: 4,097

Re: Calibre core dump when closed

Segfaults sometimes happen. I would worry more about it if I actually noticed my programs dying on me (rather than when the program exits), but as it is I am blissfully ignorant since the dumps don't appear in  my home folder.

Last edited by eschwartz (2016-02-21 15:20:56)

---

Managing AUR repos The Right Way -- aurpublish (now a standalone tool)

Scimmia

Fellow

Registered: 2012-09-01

Posts: 13,729

Re: Calibre core dump when closed

That needs to be something like `gdb /usr/bin/calibre <coredump>`

Last edited by Scimmia (2016-02-21 15:22:08)

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

Core was generated by `python2 /usr/bin/calibre'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f561ca22930 in ?? ()
[Current thread is 1 (LWP 32028)]
(gdb) bt
#0  0x00007f561ca22930 in ?? ()
#1  0x00007f5631ad5b52 in ?? ()
#2  0x000055ae3991a460 in ?? ()
#3  0x48bafb16c6b69e00 in ?? ()
#4  0x000055ae39912020 in ?? ()
#5  0x00007ffd4fe1e670 in ?? ()
#6  0x0000000000000000 in ?? ()

I guess since calibre is a python program it doesn't give much useful information.

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

More core dumps after closing down the machine.

$ for i in core.*; do file $i; done
core.1491: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from 'emacs --daemon'
core.840: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from '/usr/bin/kactivitymanagerd'
core.852: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from '/usr/bin/kactivitymanagerd'
core.912: ELF 64-bit LSB core file x86-64, version 1 (SYSV), SVR4-style, from '/usr/bin/kactivitymanagerd start-daemon'

emacs backtrace

$gdb emacs core.1491 
...
Core was generated by `emacs --daemon'.
Program terminated with signal SIGABRT, Aborted.
#0  0x00007fca9ac95c39 in raise () from /usr/lib/libpthread.so.0
[Current thread is 1 (Thread 0x7fcaa144aa00 (LWP 1491))]
(gdb) bt
#0  0x00007fca9ac95c39 in raise () from /usr/lib/libpthread.so.0
#1  0x00000000004e99e6 in ?? ()
#2  0x00000000005032f3 in ?? ()
#3  0x000000000055d921 in ?? ()
#4  0x000000000055d939 in ?? ()
#5  0x000000000055d967 in ?? ()
#6  0x000000000052e5b4 in ?? ()
#7  0x0000000000530678 in ?? ()
#8  0x00000000005181cb in ?? ()
#9  0x000000000051961e in ?? ()
#10 0x000000000051eed5 in ?? ()
#11 0x00000000004e97d2 in ?? ()
#12 0x00000000004e99b7 in ?? ()
#13 0x00000000005032f3 in ?? ()
#14 0x000000000055d921 in ?? ()
#15 0x000000000055d939 in ?? ()
#16 0x000000000055d967 in ?? ()
#17 0x000000000052e5b4 in ?? ()
#18 0x0000000000530678 in ?? ()
#19 0x00000000005181cb in ?? ()
#20 0x000000000051961e in ?? ()
#21 0x000000000051eed5 in ?? ()
#22 0x00000000004e97d2 in ?? ()
#23 0x00000000004bd60b in ?? ()
#24 0x00000000004bd6ed in ?? ()
#25 0x00007fca9df4791e in _XIOError () from /usr/lib/libX11.so.6
#26 0x00007fca9df4525d in _XEventsQueued () from /usr/lib/libX11.so.6
#27 0x00007fca9df36b87 in XPending () from /usr/lib/libX11.so.6
#28 0x00007fca9f741f1e in ?? () from /usr/lib/libgdk-3.so.0
#29 0x00007fca9e6b354d in g_main_context_prepare () from /usr/lib/libglib-2.0.so.0
#30 0x00007fca9e6b3eeb in ?? () from /usr/lib/libglib-2.0.so.0
#31 0x00007fca9e6b4077 in g_main_context_pending () from /usr/lib/libglib-2.0.so.0
#32 0x00007fca9fbc71fd in gtk_events_pending () from /usr/lib/libgtk-3.so.0
...
about 800 lines of #num hexaddress in ?? () ending with
..
#866 0x00007fca9a901610 in __libc_start_main () from /usr/lib/libc.so.6
#867 0x0000000000418cf9 in ?? ()

kactivitymanagerd

$ gdb kactivitymanagerd core.912
...
Core was generated by `/usr/bin/kactivitymanagerd start-daemon'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f28e1d75d15 in QMutex::lock() () from /usr/lib/libQt5Core.so.5
[Current thread is 1 (Thread 0x7f28bf3ee700 (LWP 13396))]
(gdb) bt
#0  0x00007f28e1d75d15 in QMutex::lock() () from /usr/lib/libQt5Core.so.5
#1  0x00007f28cd3f77a0 in ?? () from /usr/lib/qt/plugins/kactivitymanagerd/1/kactivitymanagerd_plugin_sqlite.so
#2  0x00007f28e1d7db8e in ?? () from /usr/lib/libQt5Core.so.5
#3  0x00007f28e06eb4a4 in start_thread () from /usr/lib/libpthread.so.0
#4  0x00007f28e169adcd in __libc_ifunc_impl_list () from /usr/lib/libc.so.6
#5  0x0000000000000000 in ?? ()

kactivitymanagerd (again)

$ gdb kactivitymanagerd core.852   
...
Core was generated by `/usr/bin/kactivitymanagerd'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f49144c8930 in ?? ()
[Current thread is 1 (Thread 0x7f4923f48800 (LWP 852))]
(gdb) bt
#0  0x00007f49144c8930 in ?? ()
#1  0x00007f49225f8b52 in QInternal::activateCallbacks(QInternal::Callback, void**) () from /usr/lib/libQt5Core.so.5
#2  0x00007f49227f0b18 in QCoreApplication::notifyInternal(QObject*, QEvent*) () from /usr/lib/libQt5Core.so.5
#3  0x00007f4922826f67 in QObjectPrivate::setParent_helper(QObject*) () from /usr/lib/libQt5Core.so.5
#4  0x00007f4922827604 in QObject::~QObject() () from /usr/lib/libQt5Core.so.5
#5  0x00007f492282bdd9 in QSocketNotifier::~QSocketNotifier() () from /usr/lib/libQt5Core.so.5
#6  0x00007f492400a8ef in ?? () from /usr/lib/libQt5DBus.so.5
#7  0x00007f49204f55d3 in _dbus_watch_list_remove_watch () from /usr/lib/libdbus-1.so.3
#8  0x00007f49204f3a6e in ?? () from /usr/lib/libdbus-1.so.3
#9  0x00007f49204f3ae9 in ?? () from /usr/lib/libdbus-1.so.3
#10 0x00007f49204f28ab in ?? () from /usr/lib/libdbus-1.so.3
#11 0x00007f49204dd482 in ?? () from /usr/lib/libdbus-1.so.3
#12 0x00007f4924005f62 in ?? () from /usr/lib/libQt5DBus.so.5
#13 0x00007f4923ffd363 in ?? () from /usr/lib/libQt5DBus.so.5
#14 0x00007f4923ffd3e9 in ?? () from /usr/lib/libQt5DBus.so.5
#15 0x00007f4921e79f88 in __run_exit_handlers () from /usr/lib/libc.so.6
#16 0x00007f4921e79fd5 in exit () from /usr/lib/libc.so.6
#17 0x000000000041034e in main ()

I don't know how to investigate further.

Can anyone offer any help?

Since both emacs and firefox complained about libpthread owned by glibc (which was updated just before these dump files started appearing.) I'm going to downgrade glibc to see whether helps in the short term.

bhrgunatha

Member

Registered: 2009-12-16

Posts: 103

Re: Calibre core dump when closed

Core was generated by `python2 /usr/bin/calibre'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f561ca22930 in ?? ()
[Current thread is 1 (LWP 32028)]
(gdb) bt
#0  0x00007f561ca22930 in ?? ()
#1  0x00007f5631ad5b52 in ?? ()
#2  0x000055ae3991a460 in ?? ()
#3  0x48bafb16c6b69e00 in ?? ()
#4  0x000055ae39912020 in ?? ()
#5  0x00007ffd4fe1e670 in ?? ()
#6  0x0000000000000000 in ?? ()

I guess since calibre is a python program it doesn't give much useful information.

Uh - that was dumb.

$ gdb python2 core.2311
...
Core was generated by `python2 /usr/bin/calibre'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0  0x00007f68c5a2a930 in ?? ()
[Current thread is 1 (Thread 0x7f68e6ef6700 (LWP 2311))]
(gdb) bt
#0  0x00007f68c5a2a930 in ?? ()
#1  0x00007f68daaaeb52 in QInternal::activateCallbacks(QInternal::Callback, void**) () from /usr/lib/libQt5Core.so.5
#2  0x00007f68daca6b18 in QCoreApplication::notifyInternal(QObject*, QEvent*) () from /usr/lib/libQt5Core.so.5
#3  0x00007f68dacdcf67 in QObjectPrivate::setParent_helper(QObject*) () from /usr/lib/libQt5Core.so.5
#4  0x00007f68dacdd604 in QObject::~QObject() () from /usr/lib/libQt5Core.so.5
#5  0x00007f68dace1dd9 in QSocketNotifier::~QSocketNotifier() () from /usr/lib/libQt5Core.so.5
#6  0x00007f68d4d378ef in ?? () from /usr/lib/libQt5DBus.so.5
#7  0x00007f68dece35d3 in _dbus_watch_list_remove_watch () from /usr/lib/libdbus-1.so.3
#8  0x00007f68dece1a6e in ?? () from /usr/lib/libdbus-1.so.3
#9  0x00007f68dece1ae9 in ?? () from /usr/lib/libdbus-1.so.3
#10 0x00007f68dece08ab in ?? () from /usr/lib/libdbus-1.so.3
#11 0x00007f68deccb482 in ?? () from /usr/lib/libdbus-1.so.3
#12 0x00007f68d4d32f62 in ?? () from /usr/lib/libQt5DBus.so.5
#13 0x00007f68d4d2a363 in ?? () from /usr/lib/libQt5DBus.so.5
#14 0x00007f68d4d2a3e9 in ?? () from /usr/lib/libQt5DBus.so.5
#15 0x00007f68e63b8f88 in __run_exit_handlers () from /usr/lib/libc.so.6
#16 0x00007f68e63b8fd5 in exit () from /usr/lib/libc.so.6
#17 0x00007f68e6a53bc6 in Py_Exit () from /usr/lib/libpython2.7.so.1.0
#18 0x00007f68e6a53d12 in handle_system_exit.part () from /usr/lib/libpython2.7.so.1.0
#19 0x00007f68e6a53f85 in PyErr_PrintEx () from /usr/lib/libpython2.7.so.1.0
#20 0x00007f68e6a54c04 in PyRun_SimpleFileExFlags () from /usr/lib/libpython2.7.so.1.0
#21 0x00007f68e6a67b05 in Py_Main () from /usr/lib/libpython2.7.so.1.0
#22 0x00007f68e63a3610 in __libc_start_main () from /usr/lib/libc.so.6
#23 0x0000564006e3d859 in _start ()

From my pacman.log

[2016-01-18 12:23] [ALPM] upgraded qt5-base (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-xmlpatterns (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-declarative (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-location (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-multimedia (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-sensors (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-webchannel (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-webkit (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-script (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-quick1 (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-quickcontrols (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-svg (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-translations (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-tools (5.5.1-8 -> 5.5.1-9)
[2016-01-18 12:23] [ALPM] upgraded qt5-x11extras (5.5.1-8 -> 5.5.1-9)

I'm going to try downgrading my qt5 packages back to 5.5.1.8 to see if that stops this problem.