[vtkusers] vtkpython:Linux SMP:SIGSEGV upon import vtk
donna at v1.wustl.edu
donna at v1.wustl.edu
Tue Feb 25 15:23:51 EST 2003
My vtkpython seems to run fine on several flavors of uni-processor
Linux, but a user running SuSE Linux 7.1 (i386) 2.2.18-SMP #1 SMP is
crashing with SIGSEGV.
My build environment was as follows:
Red Hat Linux release 6.1 (Cartman) Kernel 2.2.12-20 uni-processor
gcc-3.0.4
Python 2.1.3
vtk 4.1.1, 1.1358 vintage 2002/10/05 (without parallel)
I can start vtkpython, but when I import vtk, I crash:
gdb vtkpython
GNU gdb 5.3
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This GDB was configured as "i686-pc-linux-gnu"...
(gdb) run
Starting program: /home/donna/SUREfit.occipital/bin/vtkpython
[New Thread 1024 (LWP 2038)]
vtk version 4.1.1, vtk source $Revision: 1.1358 $, $Date: 2002/10/05
02:45:03 $ (GMT)
Python 2.1.3 (#1, Jan 21 2003, 14:10:19)
[GCC 3.0.4] on linux2
Type "copyright", "credits" or "license" for more information.
>>> import sys
>>> import os
>>> import vtk
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 1024 (LWP 2038)]
0x4000ba79 in _dl_relocate_object () from /lib/ld-linux.so.2
(gdb) where
#0 0x4000ba79 in _dl_relocate_object () from /lib/ld-linux.so.2
#1 0x426e8fa4 in dl_open_worker () from /lib/libc.so.6
#2 0x4000d332 in _dl_catch_error () from /lib/ld-linux.so.2
#3 0x426e915e in _dl_open () from /lib/libc.so.6
#4 0x40038354 in dlopen_doit () from /lib/libdl.so.2
#5 0x4000d332 in _dl_catch_error () from /lib/ld-linux.so.2
#6 0x40038790 in _dlerror_run () from /lib/libdl.so.2
#7 0x40038393 in dlopen@@GLIBC_2.1 () from /lib/libdl.so.2
#8 0x08075b21 in _PyImport_GetDynLoadFunc (
fqname=0xbfffccc4 "libvtkCommonPython",
shortname=0xbfffccc4 "libvtkCommonPython",
pathname=0xbfffc830 "/home/donna/SUREfit/lib/libvtkCommonPython.so",
fp=0x8127890) at Python/dynload_shlib.c:90
#9 0x0806e431 in _PyImport_LoadDynamicModule (
name=0xbfffccc4 "libvtkCommonPython",
pathname=0xbfffc830 "/home/donna/SUREfit/lib/libvtkCommonPython.so",
fp=0x8127890) at Python/importdl.c:42
#10 0x0806c852 in load_module (name=0xbfffccc4 "libvtkCommonPython",
fp=0x8127890,
buf=0xbfffc830 "/home/donna/SUREfit/lib/libvtkCommonPython.so",
type=3)
at Python/import.c:1310
#11 0x0806d4e3 in import_submodule (mod=0x80cc5ac,
subname=0xbfffccc4 "libvtkCommonPython",
fullname=0xbfffccc4 "libvtkCommonPython") at Python/import.c:1829
#12 0x0806d136 in load_next (mod=0x812331c, altmod=0x80cc5ac,
p_name=0xbfffd0f0, buf=0xbfffccc0 "vtk.libvtkCommonPython",
p_buflen=0xbfffccbc) at Python/import.c:1689
#13 0x0806ccf4 in import_module_ex (name=0x0, globals=0x8123a94,
locals=0x8123a94, fromlist=0x80fcf0c) at Python/import.c:1536
#14 0x0806ce61 in PyImport_ImportModuleEx (
name=0x8127b74 "libvtkCommonPython", globals=0x8123a94,
locals=0x8123a94,
fromlist=0x80fcf0c) at Python/import.c:1577
#15 0x080a94d5 in builtin___import__ (self=0x0, args=0x80ff9b4)
at Python/bltinmodule.c:31
#16 0x0805d7c2 in call_cfunction (func=0x80e2940, arg=0x80ff9b4, kw=0x0)
at Python/ceval.c:2858
#17 0x0805d71b in call_object (func=0x80e2940, arg=0x80ff9b4, kw=0x0)
at Python/ceval.c:2820
#18 0x0805d544 in PyEval_CallObjectWithKeywords (func=0x80e2940,
arg=0x80ff9b4, kw=0x0) at Python/ceval.c:2753
#19 0x0805b8ec in eval_code2 (co=0x8127720, globals=0x8123a94,
locals=0x8123a94, args=0x0, argcount=0, kws=0x0, kwcount=0,
defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:1832
#20 0x08058db5 in PyEval_EvalCode (co=0x8127720, globals=0x8123a94,
locals=0x8123a94) at Python/ceval.c:341
#21 0x0806ba33 in PyImport_ExecCodeModuleEx (name=0xbfffdbe0
"vtk.common",
---Type <return> to continue, or q <return> to quit---
co=0x8127720,
pathname=0xbfffd2e0
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/common.pyc")
at Python/import.c:490
#22 0x0806bfab in load_source_module (name=0xbfffdbe0 "vtk.common",
pathname=0xbfffd750
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/common.py",
fp=0x80e8690) at Python/import.c:754
#23 0x0806c82d in load_module (name=0xbfffdbe0 "vtk.common",
fp=0x80e8690,
buf=0xbfffd750
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/common.py",
type=1) at Python/import.c:1301
#24 0x0806d4e3 in import_submodule (mod=0x812331c,
subname=0xbfffdbe4 "common", fullname=0xbfffdbe0 "vtk.common")
at Python/import.c:1829
#25 0x0806d0ba in load_next (mod=0x812331c, altmod=0x80cc5ac,
p_name=0xbfffe010, buf=0xbfffdbe0 "vtk.common", p_buflen=0xbfffdbdc)
at Python/import.c:1685
#26 0x0806ccf4 in import_module_ex (name=0x0, globals=0x80e8f0c,
locals=0x80e8f0c, fromlist=0x80ff2ac) at Python/import.c:1536
#27 0x0806ce61 in PyImport_ImportModuleEx (name=0x80ffec4 "common",
globals=0x80e8f0c, locals=0x80e8f0c, fromlist=0x80ff2ac)
at Python/import.c:1577
#28 0x080a94d5 in builtin___import__ (self=0x0, args=0x80f4ca4)
at Python/bltinmodule.c:31
#29 0x0805d7c2 in call_cfunction (func=0x80e2940, arg=0x80f4ca4, kw=0x0)
at Python/ceval.c:2858
#30 0x0805d71b in call_object (func=0x80e2940, arg=0x80f4ca4, kw=0x0)
at Python/ceval.c:2820
#31 0x0805d544 in PyEval_CallObjectWithKeywords (func=0x80e2940,
arg=0x80f4ca4, kw=0x0) at Python/ceval.c:2753
#32 0x0805b8ec in eval_code2 (co=0x80f4a38, globals=0x80e8f0c,
locals=0x80e8f0c, args=0x0, argcount=0, kws=0x0, kwcount=0,
defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:1832
#33 0x08058db5 in PyEval_EvalCode (co=0x80f4a38, globals=0x80e8f0c,
locals=0x80e8f0c) at Python/ceval.c:341
#34 0x0806ba33 in PyImport_ExecCodeModuleEx (name=0xbfffef70 "vtk",
co=0x80f4a38,
pathname=0xbfffe200
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/__init__.pyc")
at Python/import.c:490
#35 0x0806bfab in load_source_module (name=0xbfffef70 "vtk",
pathname=0xbfffe670
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/__init__.py",
fp=0x80e8fc8) at Python/import.c:754
#36 0x0806c82d in load_module (name=0xbfffef70 "vtk", fp=0x80e8fc8,
buf=0xbfffe670
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk/__init__.py",
type=1) at Python/import.c:1301
#37 0x0806c17f in load_package (name=0xbfffef70 "vtk",
pathname=0xbfffeae0
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk") at
Python/import.c:811
---Type <return> to continue, or q <return> to quit---
#38 0x0806c87b in load_module (name=0xbfffef70 "vtk", fp=0x0,
buf=0xbfffeae0
"/home/donna/SUREfit/lib/python2.1/site-packages/vtkpython/vtk", type=5)
at Python/import.c:1324
#39 0x0806d4e3 in import_submodule (mod=0x80cc5ac, subname=0xbfffef70
"vtk",
fullname=0xbfffef70 "vtk") at Python/import.c:1829
#40 0x0806d0ba in load_next (mod=0x80cc5ac, altmod=0x80cc5ac,
p_name=0xbffff3a0, buf=0xbfffef70 "vtk", p_buflen=0xbfffef6c)
at Python/import.c:1685
#41 0x0806ccf4 in import_module_ex (name=0x0, globals=0x80e8edc,
locals=0x80e8edc, fromlist=0x80cc5ac) at Python/import.c:1536
#42 0x0806ce61 in PyImport_ImportModuleEx (name=0x81162ac "vtk",
globals=0x80e8edc, locals=0x80e8edc, fromlist=0x80cc5ac)
at Python/import.c:1577
#43 0x080a94d5 in builtin___import__ (self=0x0, args=0x80e9f5c)
at Python/bltinmodule.c:31
#44 0x0805d7c2 in call_cfunction (func=0x80e2940, arg=0x80e9f5c, kw=0x0)
at Python/ceval.c:2858
#45 0x0805d71b in call_object (func=0x80e2940, arg=0x80e9f5c, kw=0x0)
at Python/ceval.c:2820
#46 0x0805d544 in PyEval_CallObjectWithKeywords (func=0x80e2940,
arg=0x80e9f5c, kw=0x0) at Python/ceval.c:2753
#47 0x0805b8ec in eval_code2 (co=0x80e9368, globals=0x80e8edc,
locals=0x80e8edc, args=0x0, argcount=0, kws=0x0, kwcount=0,
defs=0x0,
defcount=0, closure=0x0) at Python/ceval.c:1832
#48 0x08058db5 in PyEval_EvalCode (co=0x80e9368, globals=0x80e8edc,
locals=0x80e8edc) at Python/ceval.c:341
#49 0x0807312b in run_node (n=0x80e8f00, filename=0x80b105f "<stdin>",
globals=0x80e8edc, locals=0x80e8edc, flags=0xbffff668)
at Python/pythonrun.c:1049
#50 0x0807202c in PyRun_InteractiveOneFlags (fp=0x427006e0,
filename=0x80b105f "<stdin>", flags=0xbffff668) at
Python/pythonrun.c:571
#51 0x08071e5e in PyRun_InteractiveLoopFlags (fp=0x427006e0,
filename=0x80b105f "<stdin>", flags=0xbffff668) at
Python/pythonrun.c:511
#52 0x08071d88 in PyRun_AnyFileExFlags (fp=0x427006e0,
filename=0x80b105f "<stdin>", closeit=0, flags=0xbffff668)
at Python/pythonrun.c:474
#53 0x080557ca in Py_Main (argc=1, argv=0xbffff714) at
Modules/main.c:320
#54 0x0805525f in main (argc=1, argv=0xbffff714)
at /surface/donna/Linux/VTK/Wrapping/Python/vtkpython.cxx:36
#55 0x42611baf in __libc_start_main () from /lib/libc.so.6
(gdb) quit
A yahoo search turned up the following links, which seemed relevant, but
I'm not able to translate them into a solution:
http://www.dssd.ca/wine/Winelib-Apps-0.2.html#visual-mingw
http://www.winehq.org/Docs/winelib-user/init-problems.shtml
Also, Andy Cedelnik once explained to me:
> Anyway, the reason why vtkpython works is because when python loads
> shared libraries, on some platforms it does not initialize c++ classess
> correctly. On platforms such as windows or linux, these classes are
> initialized, while on Suns, HPs, SGIs, they are not.
>
> The trick of vtkpython is that it is actually a C++ program which is
> linked to python library. Since it is a C++ program, it does initialize
> c++ classes.
Again -- helpful, but I'm not sure what to do.
Why not use python instead of vtkpython? Well, I tried that, and I can
import the vtk libraries successfully; however, when I try to write a
vtk file, python crashes with:
Program received signal SIGABRT, Aborted.
[Switching to Thread 1024 (LWP 1002)]
0x402e1bc1 in __kill () at __kill:-1
-1 __kill: No such file or directory.
in __kill
(gdb) where
#0 0x402e1bc1 in __kill () at __kill:-1
#1 0x4002a7ac in pthread_kill () from /lib/libpthread.so.0
#2 0x4002ac96 in raise () from /lib/libpthread.so.0
#3 0x402e2fe1 in abort () from /lib/libc.so.6
#4 0x40afe8b5 in __cxxabiv1::__terminate(void (*)()) (
handler=0x8051de0 <abort>) at eh_terminate.cc:47
#5 0x40afe8a0 in std::terminate() () at eh_terminate.cc:57
#6 0x40afe790 in __cxa_throw (obj=0x8736d90, tinfo=0x40b0bf60,
dest=0x40afe340 <std::bad_cast::~bad_cast()>) at eh_throw.cc:77
#7 0x40b08d4f in std::__throw_bad_cast() () at functexcept.cc:50
#8 0x40cfac77 in std::basic_ios<char, std::char_traits<char>
>::_M_check_facet(std::locale::facet const*) () from /home/donna/SUREfit/lib/libvtkIOPython.so
#9 0x40cfaa32 in std::ostream::operator<<(long) ()
from /home/donna/SUREfit/lib/libvtkIOPython.so
#10 0x40cf9eee in std::ostream::operator<<(int) ()
from /home/donna/SUREfit/lib/libvtkIOPython.so
#11 0x40e03ea3 in vtkDataWriter::WritePoints(std::ostream*, vtkPoints*)
()
from /home/donna/SUREfit/lib/libvtkIO.so
#12 0x40e881a1 in vtkPolyDataWriter::WriteData() ()
from /home/donna/SUREfit/lib/libvtkIO.so
#13 0x40ea9204 in vtkWriter::Write() ()
from /home/donna/SUREfit/lib/libvtkIO.so
#14 0x40cf90f5 in PyVTKClass_vtkVolumeReaderNew ()
from /home/donna/SUREfit/lib/libvtkIOPython.so
I had run into this runtime problem with python on my build host, too,
which is why I switched to vtkpython on Linux.
Any ideas as to why I'm having runtime trouble linking to the vtk
libraries are appreciated.
Thanks,
Donna Hanlon
http://surefit.sourceforge.net/
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