Bug#981378: paraview: segfaults at startup via libvtkCommonCore-pv5.9.so
Drew Parsons
dparsons at debian.org
Sat Jan 30 10:42:55 GMT 2021
Package: paraview
Version: 5.9.0-1
Severity: grave
Justification: renders package unusable
Thanks for packaging the new paraview release. The latest version of
python-meshio should be able to run with it.
paraview is segfaulting (SIGBABRT) at start up though,
$ paraview
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
double free or corruption (out)
Loguru caught a signal: SIGABRT
gdb points the finger at libvtkCommonCore-pv5.9.so.1, or possibly via
vtkCommonCore (VTK's version, not paraview's)
$ gdb paraview
(gdb) run
Starting program: /usr/bin/paraview
...
[New Thread 0x7fffb63ff700 (LWP 219883)]
double free or corruption (out)
Thread 1 "paraview" received signal SIGABRT, Aborted.
__GI_raise (sig=sig at entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
50 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory.
(gdb) bt
#0 __GI_raise (sig=sig at entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
#1 0x00007ffff7e2a537 in __GI_abort () at abort.c:79
#2 0x00007ffff7e83768 in __libc_message (action=action at entry=do_abort, fmt=fmt at entry=0x7ffff7f91e31 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#3 0x00007ffff7e8aa5a in malloc_printerr (str=str at entry=0x7ffff7f94210 "double free or corruption (out)") at malloc.c:5347
#4 0x00007ffff7e8c088 in _int_free (av=0x7ffff7fc3b80 <main_arena>, p=0x55555627d1a0, have_lock=<optimized out>) at malloc.c:4314
#5 0x00007ffff5c51ee3 in () at /usr/bin/../lib/x86_64-linux-gnu/libvtkCommonCore-pv5.9.so.1
#6 0x00007ffff5c5138d in vtkInformationKeyLookup::RegisterKey(vtkInformationKey*, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) () at /usr/bin/../lib/x86_64-linux-gnu/libvtkCommonCore-pv5.9.so.1
#7 0x00007ffff5c50791 in vtkInformationKey::vtkInformationKey(char const*, char const*) () at /usr/bin/../lib/x86_64-linux-gnu/libvtkCommonCore-pv5.9.so.1
#8 0x00007ffff5c4e38f in vtkInformationInformationVectorKey::vtkInformationInformationVectorKey(char const*, char const*) () at /usr/bin/../lib/x86_64-linux-gnu/libvtkCommonCore-pv5.9.so.1
#9 0x00007fff7890108c in () at /usr/lib/python3/dist-packages/vtkmodules/../../../x86_64-linux-gnu/libvtkCommonCore-9.0.so.1
#10 0x00007ffff7fe1fb2 in call_init (l=<optimized out>, argc=argc at entry=1, argv=argv at entry=0x7fffffffe1e8, env=env at entry=0x5555559fa600) at dl-init.c:72
#11 0x00007ffff7fe20b9 in call_init (env=0x5555559fa600, argv=0x7fffffffe1e8, argc=1, l=<optimized out>) at dl-init.c:30
#12 _dl_init (main_map=0x555556827fd0, argc=1, argv=0x7fffffffe1e8, env=0x5555559fa600) at dl-init.c:119
#13 0x00007ffff7f3d2bd in __GI__dl_catch_exception (exception=<optimized out>, operate=<optimized out>, args=<optimized out>) at dl-error-skeleton.c:182
#14 0x00007ffff7fe6028 in dl_open_worker (a=a at entry=0x7fffffff5ef0) at dl-open.c:758
#15 0x00007ffff7f3d260 in __GI__dl_catch_exception (exception=0x7fffffff5ed0, operate=0x7ffff7fe5c70 <dl_open_worker>, args=0x7fffffff5ef0) at dl-error-skeleton.c:208
#16 0x00007ffff7fe58ca in _dl_open
(file=0x7fffc6d50450 "/usr/lib/python3/dist-packages/vtkmodules/vtkCommonCore.cpython-39-x86_64-linux-gnu.so", mode=-2147483646, caller_dlopen=0x7ffff34db3e0 <_PyImport_FindSharedFuncptr+368>, nsid=-2, argc=1, argv=0x7fffffff5ed0, env=0x5555559fa600) at dl-open.c:837
#17 0x00007ffff17e1258 in dlopen_doit (a=a at entry=0x7fffffff6110) at dlopen.c:66
#18 0x00007ffff7f3d260 in __GI__dl_catch_exception (exception=exception at entry=0x7fffffff60b0, operate=0x7ffff17e1200 <dlopen_doit>, args=0x7fffffff6110) at dl-error-skeleton.c:208
#19 0x00007ffff7f3d31f in __GI__dl_catch_error (objname=0x5555556eca50, errstring=0x5555556eca58, mallocedp=0x5555556eca48, operate=<optimized out>, args=<optimized out>) at dl-error-skeleton.c:227
#20 0x00007ffff17e1a65 in _dlerror_run (operate=operate at entry=0x7ffff17e1200 <dlopen_doit>, args=args at entry=0x7fffffff6110) at dlerror.c:170
#21 0x00007ffff17e12e4 in __dlopen (file=<optimized out>, mode=<optimized out>) at dlopen.c:87
#22 0x00007ffff34db3e0 in _PyImport_FindSharedFuncptr
(prefix=0x7ffff3618eab "PyInit", shortname=0x7fffc6d3f170 "vtkCommonCore", pathname=0x7fffc6d50450 "/usr/lib/python3/dist-packages/vtkmodules/vtkCommonCore.cpython-39-x86_64-linux-gnu.so", fp=0x0)
at ../Python/dynload_shlib.c:100
#23 0x00007ffff34a028a in _PyImport_LoadDynamicModuleWithSpec (fp=0x0, spec=0x7fffc6d3f970) at ../Python/importdl.c:134
#24 _imp_create_dynamic_impl (module=<optimized out>, file=<optimized out>, spec=0x7fffc6d3f970) at ../Python/import.c:2297
#25 _imp_create_dynamic (module=<optimized out>, args=<optimized out>, nargs=<optimized out>) at ../Python/clinic/import.c.h:330
#26 0x00007ffff33e8e84 in cfunction_vectorcall_FASTCALL (func=0x7fffd759fc20, args=0x7fffc6d3f1d8, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/methodobject.c:426
#27 0x00007ffff334b719 in do_call_core (kwdict=0x7fffc6d5a840, callargs=0x7fffc6d3f1c0, func=0x7fffd759fc20, tstate=0x555555840cf0) at ../Python/ceval.c:5120
#28 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3580
#29 0x00007ffff347bddc in _PyEval_EvalFrame (throwflag=0, f=0x7fffc6d73900, tstate=0x555555840cf0) at ../Include/internal/pycore_ceval.h:40
#30 _PyEval_EvalCode
(tstate=0x555555840cf0, _co=<optimized out>, globals=<optimized out>, locals=<optimized out>, args=<optimized out>, argcount=2, kwnames=0x0, kwargs=0x7fffc6d738e0, kwcount=0, kwstep=1, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0, name=0x7fffd758bb20, qualname=0x7fffd758bb20) at ../Python/ceval.c:4327
#31 0x00007ffff3398c7d in _PyFunction_Vectorcall (func=<optimized out>, stack=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at ../Objects/call.c:396
#32 0x00007ffff334e585 in _PyObject_VectorcallTstate (kwnames=0x0, nargsf=<optimized out>, args=0x7fffc6d738d0, callable=0x7fffd75a23a0, tstate=0x555555840cf0) at ../Include/cpython/abstract.h:118
#33 PyObject_Vectorcall (kwnames=0x0, nargsf=<optimized out>, args=0x7fffc6d738d0, callable=0x7fffd75a23a0) at ../Include/cpython/abstract.h:127
#34 call_function (kwnames=0x0, oparg=<optimized out>, pp_stack=<synthetic pointer>, tstate=0x555555840cf0) at ../Python/ceval.c:5072
#35 _PyEval_EvalFrameDefault (tstate=<optimized out>, f=<optimized out>, throwflag=<optimized out>) at ../Python/ceval.c:3487
#36 0x00007ffff3346033 in _PyEval_EvalFrame (throwflag=0, f=0x7fffc6d73740, tstate=0x555555840cf0) at ../Include/internal/pycore_ceval.h:40
...
So the SIGBART is coming from libvtkCommonCore-pv5.9.so.1.
But further down the stack there is also
#18 0x00007ffff7f3d260 in __GI__dl_catch_exception (exception=exception at entry=0x7fffffff60b0, operate=0x7ffff17e1200 <dlopen_doit>, args=0x7fffffff6110) at dl-error-skeleton.c:208
#19 0x00007ffff7f3d31f in __GI__dl_catch_error (objname=0x5555556eca50, errstring=0x5555556eca58, mallocedp=0x5555556eca48, operate=<optimized out>, args=<optimized out>) at dl-error-skeleton.c:227
#20 0x00007ffff17e1a65 in _dlerror_run (operate=operate at entry=0x7ffff17e1200 <dlopen_doit>, args=args at entry=0x7fffffff6110) at dlerror.c:170
#21 0x00007ffff17e12e4 in __dlopen (file=<optimized out>, mode=<optimized out>) at dlopen.c:87
#22 0x00007ffff34db3e0 in _PyImport_FindSharedFuncptr
(prefix=0x7ffff3618eab "PyInit", shortname=0x7fffc6d3f170 "vtkCommonCore", pathname=0x7fffc6d50450 "/usr/lib/python3/dist-packages/vtkmodules/vtkCommonCore.cpython-39-x86_64-linux-gnu.so", fp=0x0)
at ../Python/dynload_shlib.c:100
#23 0x00007ffff34a028a in _PyImport_LoadDynamicModuleWithSpec (fp=0x0, spec=0x7fffc6d3f970) at ../Python/importdl.c:134
i.e. some error or exception occurs with vtkmodules/vtkCommonCore.cpython-39-x86_64-linux-gnu.so
from python3-vtk9. This one would be built against VTK-9's vtk
libraries, not paraview's vtk libraries.
Likewise at #9, libvtkCommonCore-9.0.so.1 (from libvtk9) is referenced
just before libvtkCommonCore-pv5.9.so.1 (from paraview) at #8.
It makes me wonder if the
segfault occurs due to some cross-talk between the two libvtk builds?
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.10.0-2-amd64 (SMP w/8 CPU threads)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8), LANGUAGE=en_AU:en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages paraview depends on:
ii libavcodec58 7:4.3.1-8
ii libavformat58 7:4.3.1-8
ii libavutil56 7:4.3.1-8
ii libc6 2.31-9
ii libdouble-conversion3 3.1.5-6.1
ii libexpat1 2.2.10-1
ii libfreetype6 2.10.4+dfsg-1
ii libgcc-s1 10.2.1-6
ii libgdal28 3.2.1+dfsg-1
ii libgl2ps1.4 1.4.2+dfsg1-1
ii libglew2.1 2.1.0-4+b1
ii libglx0 1.3.2-1
ii libhdf5-103-1 1.10.6+repack-2
ii libjpeg62-turbo 1:2.0.5-2
ii liblz4-1 1.9.3-1
ii liblzma5 5.2.5-1.0
ii libnetcdf18 1:4.7.4-1
ii libopengl0 1.3.2-1
ii libopenmpi3 4.1.0-7
ii libpdal-base12 2.2.0+ds-1+b1
ii libpng16-16 1.6.37-3
ii libpython3.9 3.9.1-3
ii libqt5core5a 5.15.2+dfsg-3
ii libqt5gui5 5.15.2+dfsg-3
ii libqt5help5 5.15.2-3
ii libqt5network5 5.15.2+dfsg-3
ii libqt5widgets5 5.15.2+dfsg-3
ii libstdc++6 10.2.1-6
ii libswscale5 7:4.3.1-8
ii libtiff5 4.2.0-1
ii libx11-6 2:1.7.0-2
ii libxcursor1 1:1.2.0-2
ii libxml2 2.9.10+dfsg-6.3+b1
ii python3-autobahn 17.10.1+dfsg1-6
ii python3-matplotlib 3.3.3-1
ii python3-mpi4py 3.0.3-8
ii python3-six 1.15.0-2
ii python3-twisted 20.3.0-3
ii tcl [tclsh] 8.6.11
ii zlib1g 1:1.2.11.dfsg-2
Versions of packages paraview recommends:
ii mpi-default-bin 1.13
ii paraview-doc 5.9.0-1
ii python3-paraview [python3-paraview] 5.9.0-1
Versions of packages paraview suggests:
ii h5utils 1.13.1-4
ii hdf5-tools 1.10.6+repack-2
-- no debconf information
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