graph_tool_segfault_gdb_log_new.txt

graph_tool_segfault_gdb_log_new.txt (text/plain), 17.25 KB, created by Justin Keogh on 2015-01-29 10:12:26 UTC

$/usr/bin/python3.3 -c 'import graph_tool.all as gt'
Segmentation fault
$tail -n 1 /var/log/messages 
Jan 29 02:17:32 localhost kernel: [51783.768473] python3.3[4638]: segfault at 1b1b06 ip 00000000001b1b06 sp 00007fffe8be4578 error 14 in libgmp.so.10.2.0[7ff1d11e7000+79000]

$/usr/bin/gdb /usr/bin/python3.3
GNU gdb (Gentoo 9999 vanilla) 7.9.50.20150125-cvs
Copyright (C) 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-pc-linux-gnu".
Type "show configuration" for configuration details.
For bug reporting instructions, please see:
<http://bugs.gentoo.org/>.
Find the GDB manual and other documentation resources online at:
<http://www.gnu.org/software/gdb/documentation/>.
For help, type "help".
Type "apropos word" to search for commands related to "word"...
Reading symbols from /usr/bin/python3.3...Reading symbols from /usr/lib64/debug//usr/bin/python3.3.debug...done.
done.
(gdb) set args -c 'import graph_tool.all as gt'
(gdb) run
Starting program: /usr/bin/python3.3 -c 'import graph_tool.all as gt'
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".

Program received signal SIGSEGV, Segmentation fault.
0x00000000001b1b06 in ?? ()
(gdb) bt 20
#0  0x00000000001b1b06 in ?? ()
#1  0x00007fffd72489ee in PyInit_libgraph_tool_generation () at graph_generation.cc:99
#2  0x00007ffff7a7ead1 in _PyImport_LoadDynamicModule (name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so', fp=fp@entry=0x0) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/importdl.c:86
#3  0x00007ffff7a7b686 in imp_load_dynamic (self=<optimized out>, args=<optimized out>) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/import.c:1801
#4  0x00007ffff79e9a90 in PyCFunction_Call (func=func@entry=<built-in method load_dynamic of module object at remote 0x7ffff7f39b90>, arg=arg@entry=('graph_tool.generation.libgraph_tool_generation', '/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so'), kw=kw@entry={})
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/methodobject.c:81
#5  0x00007ffff7a683c3 in ext_do_call (nk=<optimized out>, na=0, flags=<optimized out>, pp_stack=0x7fffffff9788, func=<built-in method load_dynamic of module object at remote 0x7ffff7f39b90>) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:4378
#6  PyEval_EvalFrameEx (
    f=f@entry=Frame 0x555555fdd330, for file <frozen importlib._bootstrap>, line 313, in _call_with_frames_removed (f=<built-in method load_dynamic of module object at remote 0x7ffff7f39b90>, args=('graph_tool.generation.libgraph_tool_generation', '/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so'), kwds={}), throwflag=throwflag@entry=0) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:2720
#7  0x00007ffff7a6a090 in PyEval_EvalCodeEx (_co=<code at remote 0x7ffff7f41390>, globals=<optimized out>, locals=locals@entry=0x0, args=<optimized out>, argcount=argcount@entry=3, kws=0x555555c00ae8, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0)
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:3436
#8  0x00007ffff7a67c3f in fast_function (nk=0, na=3, n=3, pp_stack=0x7fffffff9980, func=<function at remote 0x7ffff7f66b00>) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:4164
#9  call_function (oparg=<optimized out>, pp_stack=0x7fffffff9980) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:4087
#10 PyEval_EvalFrameEx (
    f=f@entry=Frame 0x555555c00930, for file <frozen importlib._bootstrap>, line 1132, in load_module (self=<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, fullname='graph_tool.generation.libgraph_tool_generation', is_reload=False), throwflag=throwflag@entry=0) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:2679
#11 0x00007ffff7a6a090 in PyEval_EvalCodeEx (_co=<code at remote 0x7ffff7f56d20>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fffde801410, argcount=2, kws=kws@entry=0x7ffff7f6d068, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=0x0)
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:3436
#12 0x00007ffff79ce120 in function_call (func=<function at remote 0x7ffff7eed050>, 
    arg=(<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, 'graph_tool.generation.libgraph_tool_generation'), kw={})
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/funcobject.c:633
#13 0x00007ffff799ff68 in PyObject_Call (func=func@entry=<function at remote 0x7ffff7eed050>, 
    arg=arg@entry=(<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, 'graph_tool.generation.libgraph_tool_generation'), kw=kw@entry={})
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/abstract.c:2035
#14 0x00007ffff7a683df in ext_do_call (nk=0, na=1, flags=<optimized out>, pp_stack=0x7fffffff9c48, func=<function at remote 0x7ffff7eed050>) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:4381
#15 PyEval_EvalFrameEx (
    f=f@entry=Frame 0x7ffff03ba238, for file <frozen importlib._bootstrap>, line 508, in set_loader_wrapper (self=<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, args=('graph_tool.generation.libgraph_tool_generation',), kwargs={}), throwflag=throwflag@entry=0) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:2720
#16 0x00007ffff7a6a090 in PyEval_EvalCodeEx (_co=<code at remote 0x7ffff7f418a0>, globals=<optimized out>, locals=locals@entry=0x0, args=args@entry=0x7fffde80ac80, argcount=2, kws=kws@entry=0x7ffff7f6d068, kwcount=0, defs=0x0, defcount=0, kwdefs=0x0, closure=(<cell at remote 0x7ffff7f612f0>,))
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:3436
#17 0x00007ffff79ce120 in function_call (func=<function at remote 0x7ffff7eed0e0>, 
    arg=(<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, 'graph_tool.generation.libgraph_tool_generation'), kw={})
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/funcobject.c:633
#18 0x00007ffff799ff68 in PyObject_Call (func=func@entry=<function at remote 0x7ffff7eed0e0>, 
    arg=arg@entry=(<ExtensionFileLoader(name='graph_tool.generation.libgraph_tool_generation', path='/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so') at remote 0x7fffde8293d0>, 'graph_tool.generation.libgraph_tool_generation'), kw=kw@entry={})
    at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Objects/abstract.c:2035
#19 0x00007ffff7a683df in ext_do_call (nk=0, na=0, flags=<optimized out>, pp_stack=0x7fffffff9f08, func=<function at remote 0x7ffff7eed0e0>) at /var/tmp/portage/dev-lang/python-3.3.5-r1/work/Python-3.3.5/Python/ceval.c:4381
(More stack frames follow...)
(gdb) break graph_generation.cc:99
Breakpoint 1 at 0x7fffd72489b1: file graph_generation.cc, line 99.
(gdb) run
The program being debugged has been started already.
Start it from the beginning? (y or n) y
Starting program: /usr/bin/python3.3 -c 'import graph_tool.all as gt'
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".

Breakpoint 1, PyInit_libgraph_tool_generation () at graph_generation.cc:99
99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
(gdb) disas $pc
Dump of assembler code for function PyInit_libgraph_tool_generation():
=> 0x00007fffd72489b1 <+0>:     push   %rbp
   0x00007fffd72489b2 <+1>:     mov    %rsp,%rbp
   0x00007fffd72489b5 <+4>:     lea    -0x1030(%rsp),%rsp
   0x00007fffd72489bd <+12>:    orq    $0x0,(%rsp)
   0x00007fffd72489c2 <+17>:    lea    0x1020(%rsp),%rsp
   0x00007fffd72489ca <+25>:    mov    %fs:0x28,%rax
   0x00007fffd72489d3 <+34>:    mov    %rax,-0x8(%rbp)
   0x00007fffd72489d7 <+38>:    xor    %eax,%eax
   0x00007fffd72489d9 <+40>:    cmpb   $0x0,0x7a23a0(%rip)        # 0x7fffd79ead80 <_ZGVZ31PyInit_libgraph_tool_generationE9moduledef>
   0x00007fffd72489e0 <+47>:    jne    0x7fffd7248a44 <PyInit_libgraph_tool_generation()+147>
   0x00007fffd72489e2 <+49>:    lea    0x7a2397(%rip),%rdi        # 0x7fffd79ead80 <_ZGVZ31PyInit_libgraph_tool_generationE9moduledef>
   0x00007fffd72489e9 <+56>:    callq  0x7fffd7247b00 <__cxa_guard_acquire@plt>
   0x00007fffd72489ee <+61>:    test   %eax,%eax
   0x00007fffd72489f0 <+63>:    je     0x7fffd7248a44 <PyInit_libgraph_tool_generation()+147>
   0x00007fffd72489f2 <+65>:    mov    0x4f1fe7(%rip),%rax        # 0x7fffd773a9e0 <_ZZ31PyInit_libgraph_tool_generationE14initial_m_base>
   0x00007fffd72489f9 <+72>:    mov    %rax,0x7a22c0(%rip)        # 0x7fffd79eacc0 <_ZZ31PyInit_libgraph_tool_generationE9moduledef>
   0x00007fffd7248a00 <+79>:    mov    0x4f1fe1(%rip),%rax        # 0x7fffd773a9e8 <_ZZ31PyInit_libgraph_tool_generationE14initial_m_base+8>
   0x00007fffd7248a07 <+86>:    mov    %rax,0x7a22ba(%rip)        # 0x7fffd79eacc8 <_ZZ31PyInit_libgraph_tool_generationE9moduledef+8>
   0x00007fffd7248a0e <+93>:    mov    0x4f1fdb(%rip),%rax        # 0x7fffd773a9f0 <_ZZ31PyInit_libgraph_tool_generationE14initial_m_base+16>
   0x00007fffd7248a15 <+100>:   mov    %rax,0x7a22b4(%rip)        # 0x7fffd79eacd0 <_ZZ31PyInit_libgraph_tool_generationE9moduledef+16>
   0x00007fffd7248a1c <+107>:   mov    0x4f1fd5(%rip),%rax        # 0x7fffd773a9f8 <_ZZ31PyInit_libgraph_tool_generationE14initial_m_base+24>
   0x00007fffd7248a23 <+114>:   mov    %rax,0x7a22ae(%rip)        # 0x7fffd79eacd8 <_ZZ31PyInit_libgraph_tool_generationE9moduledef+24>
   0x00007fffd7248a2a <+121>:   mov    0x4f1fcf(%rip),%rax        # 0x7fffd773aa00 <_ZZ31PyInit_libgraph_tool_generationE14initial_m_base+32>
   0x00007fffd7248a31 <+128>:   mov    %rax,0x7a22a8(%rip)        # 0x7fffd79eace0 <_ZZ31PyInit_libgraph_tool_generationE9moduledef+32>
   0x00007fffd7248a38 <+135>:   lea    0x7a2341(%rip),%rdi        # 0x7fffd79ead80 <_ZGVZ31PyInit_libgraph_tool_generationE9moduledef>
   0x00007fffd7248a3f <+142>:   callq  0x7fffd72421a0 <__cxa_guard_release@plt>
   0x00007fffd7248a44 <+147>:   mov    0x7a118d(%rip),%rsi        # 0x7fffd79e9bd8
   0x00007fffd7248a4b <+154>:   lea    0x7a226e(%rip),%rdi        # 0x7fffd79eacc0 <_ZZ31PyInit_libgraph_tool_generationE9moduledef>
   0x00007fffd7248a52 <+161>:   callq  0x7fffd7244090 <_ZN5boost6python6detail11init_moduleER11PyModuleDefPFvvE@plt>
   0x00007fffd7248a57 <+166>:   mov    -0x8(%rbp),%rdx
   0x00007fffd7248a5b <+170>:   xor    %fs:0x28,%rdx
   0x00007fffd7248a64 <+179>:   je     0x7fffd7248a6b <PyInit_libgraph_tool_generation()+186>
   0x00007fffd7248a66 <+181>:   callq  0x7fffd7244590 <__stack_chk_fail@plt>
   0x00007fffd7248a6b <+186>:   leaveq 
   0x00007fffd7248a6c <+187>:   retq   
End of assembler dump.
(gdb) disas 0x7fffd7247b00
Dump of assembler code for function __cxa_guard_acquire@plt:
   0x00007fffd7247b00 <+0>:     jmpq   *0x7a07aa(%rip)        # 0x7fffd79e82b0 <[e-mail]>
   0x00007fffd7247b06 <+6>:     pushq  $0x85c
   0x00007fffd7247b0b <+11>:    jmpq   0x7fffd723f530
End of assembler dump.
(gdb) x/gx 0x7fffd79e82b0
0x7fffd79e82b0 <[e-mail]>:   0x00000000001b1b06
(gdb) disp/i $pc
1: x/i $pc
=> 0x7fffd72489b1 <PyInit_libgraph_tool_generation()>:  push   %rbp
(gdb) si
0x00007fffd72489b2      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489b2 <PyInit_libgraph_tool_generation()+1>:        mov    %rsp,%rbp
(gdb) si
0x00007fffd72489b5      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489b5 <PyInit_libgraph_tool_generation()+4>:        lea    -0x1030(%rsp),%rsp
(gdb) si
0x00007fffd72489bd      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489bd <PyInit_libgraph_tool_generation()+12>:       orq    $0x0,(%rsp)
(gdb) si
0x00007fffd72489c2      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489c2 <PyInit_libgraph_tool_generation()+17>:       lea    0x1020(%rsp),%rsp
(gdb) si
99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489ca <PyInit_libgraph_tool_generation()+25>:       mov    %fs:0x28,%rax
(gdb) si
0x00007fffd72489d3      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489d3 <PyInit_libgraph_tool_generation()+34>:       mov    %rax,-0x8(%rbp)
(gdb) si
0x00007fffd72489d7      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489d7 <PyInit_libgraph_tool_generation()+38>:       xor    %eax,%eax
(gdb) si
0x00007fffd72489d9      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489d9 <PyInit_libgraph_tool_generation()+40>:       cmpb   $0x0,0x7a23a0(%rip)        # 0x7fffd79ead80 <_ZGVZ31PyInit_libgraph_tool_generationE9moduledef>
(gdb) si
0x00007fffd72489e0      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489e0 <PyInit_libgraph_tool_generation()+47>:       jne    0x7fffd7248a44 <PyInit_libgraph_tool_generation()+147>
(gdb) si
0x00007fffd72489e2      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489e2 <PyInit_libgraph_tool_generation()+49>:       lea    0x7a2397(%rip),%rdi        # 0x7fffd79ead80 <_ZGVZ31PyInit_libgraph_tool_generationE9moduledef>
(gdb) 
0x00007fffd72489e9      99      BOOST_PYTHON_MODULE(libgraph_tool_generation)
1: x/i $pc
=> 0x7fffd72489e9 <PyInit_libgraph_tool_generation()+56>:       callq  0x7fffd7247b00 <__cxa_guard_acquire@plt>
(gdb) 
0x00007fffd7247b00 in __cxa_guard_acquire@plt () from /usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so
1: x/i $pc
=> 0x7fffd7247b00 <__cxa_guard_acquire@plt>:    jmpq   *0x7a07aa(%rip)        # 0x7fffd79e82b0 <[e-mail]>
(gdb) 
0x00000000001b1b06 in ?? ()
1: x/i $pc
=> 0x1b1b06:    <error: Cannot access memory at address 0x1b1b06>
(gdb) 

Program received signal SIGSEGV, Segmentation fault.
0x00000000001b1b06 in ?? ()
1: x/i $pc
=> 0x1b1b06:    <error: Cannot access memory at address 0x1b1b06>
(gdb) 

Program terminated with signal SIGSEGV, Segmentation fault.
The program no longer exists.
(gdb) quit


$LD_DEBUG="all" /usr/bin/python3.3 -c 'import graph_tool.all as gt' > ld_debug 2>&1
Segmentation fault
$tail -n 20 ld_debug 
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/libpthread.so.0 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/libdl.so.2 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/libutil.so.1 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/libz.so.1 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/lib64/librt.so.1 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/usr/lib64/libicuuc.so.52 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/usr/lib64/libicui18n.so.52 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/usr/lib64/libicudata.so.52 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/usr/lib64/libboost_thread.so.1.55.0 [0]
      4928:     symbol=_ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_;  lookup in file=/usr/lib64/libboost_system.so.1.55.0 [0]
      4928:     /usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so: error: symbol lookup error: undefined symbol: _ZNKSt3tr14hashISt6vectorISsSaISsEEEclES3_ (fatal)
      4928:     opening file=/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so [0]; direct_opencount=1
      4928:
      4928:
      4928:     add /usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so [0] to global scope
      4928:
      4928:     add /usr/lib64/libgmp.so.10 [0] to global scope
      4928:     symbol=PyInit_libgraph_tool_generation;  lookup in file=/usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so [0]
      4928:     binding file /usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so [0] to /usr/lib64/python3.3/site-packages/graph_tool/generation/libgraph_tool_generation.so [0]: normal symbol `PyInit_libgraph_tool_generation'