Why does QGIS 3 crash on startup with Xenial?

Question

I'm trying to run QGIS 3.2.2 from the official PPA on Ubuntu 16.04 (Xenial) including the ubuntugis-unstable repo. It took me a while to get QGIS3 to install, and to make it happy about PyQt5. To do that, I had to run sudo pip3 uninstall pyqt5. Then QGIS no longer complained about PyQt5 on startup (since the APT version was being used instead), but now I get a plain ole' crash.

First symptom:

Warning: QSqlQuery::prepare: database not open
QGIS died on signal 11Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.
No thread selected
No stack.
gdb returned 0
Aborted

Running as root:

Warning: QSqlQuery::prepare: database not open
QGIS died on signal 11[New LWP 16241]
[New LWP 16244]
[New LWP 16245]
[New LWP 16247]
[New LWP 16248]
[New LWP 16249]
[New LWP 16250]
[New LWP 16251]
[New LWP 16252]
[New LWP 16253]
[New LWP 16254]
[New LWP 16255]
[New LWP 16256]
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
0x00007fcf358fa0cb in __GI___waitpid (pid=16257, stat_loc=0x7ffd33e146ec, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
29  ../sysdeps/unix/sysv/linux/waitpid.c: No such file or directory.
[Current thread is 1 (Thread 0x7fcf14af0340 (LWP 16238))]
#0  0x00007fcf358fa0cb in __GI___waitpid (pid=16257, stat_loc=0x7ffd33e146ec, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:29
        resultvar = 18446744073709551104
        sc_cancel_oldtype = 0
#1  0x000055854b0ca2da in ?? ()
No symbol table info available.
#2  <signal handler called>
No locals.
#3  0x00007fceb19eb560 in PyType_IsSubtype () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#4  0x00007fceb13cfdf1 in vp_convertor () from /usr/local/lib/python3.5/dist-packages/sip.so
No symbol table info available.
#5  0x00007fceb13d0675 in sip_api_convert_to_void_ptr () from /usr/local/lib/python3.5/dist-packages/sip.so
No symbol table info available.
#6  0x00007fceb10d210d in ?? () from /usr/lib/python3/dist-packages/PyQt5/QtCore.cpython-35m-x86_64-linux-gnu.so
No symbol table info available.
#7  0x00007fceb10138f4 in PyInit_QtCore () from /usr/lib/python3/dist-packages/PyQt5/QtCore.cpython-35m-x86_64-linux-gnu.so
No symbol table info available.
#8  0x00007fceb1b4e011 in _PyImport_LoadDynamicModuleWithSpec () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#9  0x00007fceb1b51917 in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#10 0x00007fceb1a0c039 in PyCFunction_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#11 0x00007fceb1b1986e in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#12 0x00007fceb1ba8cac in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#13 0x00007fceb1b16f39 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#14 0x00007fceb1b18639 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#15 0x00007fceb1b18639 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#16 0x00007fceb1b18639 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#17 0x00007fceb1b18639 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#18 0x00007fceb1ba8cac in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#19 0x00007fceb1ba8d83 in PyEval_EvalCodeEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#20 0x00007fceb1a30ad8 in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#21 0x00007fceb1ae554e in PyObject_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#22 0x00007fceb1ad2fdf in _PyObject_CallMethodIdObjArgs () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#23 0x00007fceb1b4f954 in PyImport_ImportModuleLevelObject () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#24 0x00007fceb1b1c6b8 in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#25 0x00007fceb1a0c059 in PyCFunction_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#26 0x00007fceb1b1986e in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#27 0x00007fceb1ba8cac in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#28 0x00007fceb1b16f39 in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#29 0x00007fceb1ba8cac in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#30 0x00007fceb1ba8d83 in PyEval_EvalCodeEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#31 0x00007fceb1a30ad8 in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#32 0x00007fceb1ae554e in PyObject_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#33 0x00007fceb1ad2fdf in _PyObject_CallMethodIdObjArgs () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#34 0x00007fceb1b4f765 in PyImport_ImportModuleLevelObject () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#35 0x00007fceb1b1c6b8 in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#36 0x00007fceb1a0c059 in PyCFunction_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#37 0x00007fceb1ae554e in PyObject_Call () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#38 0x00007fceb1ba7937 in PyEval_CallObjectWithKeywords () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#39 0x00007fceb1b1203d in PyEval_EvalFrameEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#40 0x00007fceb1ba8cac in ?? () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#41 0x00007fceb1ba8d83 in PyEval_EvalCodeEx () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#42 0x00007fceb1b109cb in PyEval_EvalCode () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#43 0x00007fceb1b2de6f in PyRun_StringFlags () from /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0
No symbol table info available.
#44 0x00007fceb1fe7728 in ?? () from /usr/lib/libqgispython.so.3.2.2
No symbol table info available.
#45 0x00007fceb1fe9aa6 in ?? () from /usr/lib/libqgispython.so.3.2.2
No symbol table info available.
#46 0x00007fceb1fed6c8 in ?? () from /usr/lib/libqgispython.so.3.2.2
No symbol table info available.
#47 0x00007fceb1feea71 in ?? () from /usr/lib/libqgispython.so.3.2.2
No symbol table info available.
#48 0x00007fcf382f6e51 in QgisApp::loadPythonSupport() () from /usr/lib/libqgis_app.so.3.2.2
No symbol table info available.
#49 0x00007fcf382fb7dd in QgisApp::QgisApp(QSplashScreen*, bool, bool, QString const&, QString const&, QWidget*, QFlags<Qt::WindowType>) () from /usr/lib/libqgis_app.so.3.2.2
No symbol table info available.
#50 0x000055854b0c5d56 in ?? ()
No symbol table info available.
#51 0x00007fcf3584e830 in __libc_start_main (main=0x55854b0c4040, argc=1, argv=0x7ffd33e19158, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7ffd33e19148) at ../csu/libc-start.c:291
        result = <optimized out>
        unwind_buf = {cancel_jmp_buf = {{jmp_buf = {0, -8625621155720158750, 94030978129120, 140725473874256, 0, 0, -2541346749737033246, -2531200757466357278}, mask_was_saved = 0}}, priv = {pad = {0x0, 0x0, 0x7ffd33e19168, 0x7fcf38e9c168}, data = {prev = 0x0, cleanup = 0x0, canceltype = 870420840}}}
        not_first_call = <optimized out>
#52 0x000055854b0c9d09 in _start ()
No symbol table info available.
gdb returned 0
Aborted

score 3 · Answer 1 · answered Sep 12 '18 at 18:56

3

Turns out that, in addition to the incompatibility of PyQt5 from PyPI, there's also an incompatibility with a newer version of the sip library. I had to run sudo pip3 uninstall sip (to use the APT version instead) and that enabled QGIS to start. In general, it seems that QGIS is rather vulnerable to version discrepancies from the PyPI versions of its libraries if they're installed at the OS level.

answered Sep 12 '18 at 18:56

Ethan T

157
5

2

Updating python modules externally is a kind of heart transplantation for QGIS: Don't do it unless you know what you are doing. – AndreJ Sep 13 '18 at 07:25
@AndreJ Yep. Agreed. Relevant xkcd. – Ethan T Sep 13 '18 at 18:26

score -3 · Answer 2 · answered Sep 12 '18 at 20:09

-3

As per the instructions in the link below, you will only be able to run QGIS 3.x on Ubuntu / Debian version 18.x

Installing latest QGIS version on Ubuntu?

For Ubuntu 16, you'll have to stick with version 2.18

answered Sep 12 '18 at 20:09

DPSSpatial_BoycottingGISSE

18,790
4
66
110

I've got it running just fine on Xenial right now. I was able to get it working with the steps at this answer, plus the fixes I detail here. – Ethan T Sep 12 '18 at 20:10
I try to stay away from repos with the world 'unstable' in them!! – DPSSpatial_BoycottingGISSE Sep 12 '18 at 21:24
1

@DPSSpatial as I told you some time ago, QGIS 3 does run on my Ubuntu 16/ Linux Mint 18 with the ubuntugis ppa. Only some of the new 3D function may not work. Please update your linked answer as it is not correct for now. – AndreJ Sep 13 '18 at 07:21
@AndreJ I'm still confused by your answer in the linked answer, and I still stand by the fact that using an 'unstable' repository isn't the best solution for running software. – DPSSpatial_BoycottingGISSE Sep 13 '18 at 15:36

Why does QGIS 3 crash on startup with Xenial?

2 Answers2