[graph-tool] Graphtool segfaulted

Tiago de Paula Peixoto tiago at skewed.de
Sun Mar 30 20:57:50 CEST 2014


Hi,

On 03/30/2014 06:32 PM, johndoe wrote:
> Same problem for me.
>
> GCC: 4.8.2
> Boost: 1.55.0
>
> Configure: PYTHON_LDFLAGS=-lpython3.4m ./configure --enable-openmp
> --prefix=/usr --docdir="/usr/share/doc/$pkgname"
> --with-boost-python=boost_python3
>
> (See https://aur.archlinux.org/packages/py/python-graph-tool/PKGBUILD for
> buildinformation)
>
>
> Backtrace (same for python3.4 and python3.4m):
>
> gdb python3.4m
> GNU gdb (GDB) 7.7
> Copyright (C) 2014 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-unknown-linux-gnu".
> Type "show configuration" for configuration details.
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>.
> 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 python3.4m...(no debugging symbols found)...done.
> (gdb) run
> Starting program: /usr/bin/python3.4m
> warning: Could not load shared library symbols for linux-vdso.so.1.
> Do you need "set solib-search-path" or "set sysroot"?
> [Thread debugging using libthread_db enabled]
> Using host libthread_db library "/usr/lib/libthread_db.so.1".
> Python 3.4.0 (default, Mar 17 2014, 23:20:09)
> [GCC 4.8.2 20140206 (prerelease)] on linux
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import graph_tool
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x0000000000010101 in ?? ()
> (gdb) bt
> #0  0x0000000000010101 in ?? ()
> #1  0x00007ffff79f5f84 in PyObject_CallFinalizer
> (self=self at entry=0x7fffebd57228) at Objects/object.c:278
> #2  0x00007ffff79f5fb9 in PyObject_CallFinalizerFromDealloc
> (self=self at entry=0x7fffebd57228) at Objects/object.c:295
> #3  0x00007ffff7a06ebb in subtype_dealloc (self=0x7fffebd57228) at
> Objects/typeobject.c:1110
> #4  0x00007ffff7a66c95 in PyEval_EvalFrameEx (f=f at entry=0x71ab98,
> throwflag=throwflag at entry=0) at Python/ceval.c:2412
> #5  0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=0x7ffff7e52c90,
> globals=<optimized out>, locals=<optimized out>, args=args at entry=0x0,
> argcount=argcount at entry=0, kws=kws at entry=0x0,
>     kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0,
> kwdefs=kwdefs at entry=0x0, closure=closure at entry=0x0) at Python/ceval.c:3578
> #6  0x00007ffff7a68d5b in PyEval_EvalCode (co=<optimized out>,
> globals=<optimized out>, locals=<optimized out>) at Python/ceval.c:773
> #7  0x00007ffff7a5c6da in builtin_exec (self=<optimized out>,
> args=<optimized out>) at Python/bltinmodule.c:876
> #8  0x00007ffff7a676f7 in ext_do_call (nk=<optimized out>, na=<optimized
> out>, flags=<optimized out>, pp_stack=0x7fffffffd4e8, func=0x7ffff7fb9788)
> at Python/ceval.c:4548
> #9  PyEval_EvalFrameEx (f=f at entry=0x7ffff7e20048,
> throwflag=throwflag at entry=0) at Python/ceval.c:2869
> #10 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=_co at entry=0x7ffff7f5d810,
> globals=<optimized out>, locals=locals at entry=0x0, args=<optimized out>,
> argcount=argcount at entry=3,
>     kws=0x7ffff7e8a1f8, kwcount=kwcount at entry=0, defs=0x0, defcount=0,
> kwdefs=0x0, closure=0x0) at Python/ceval.c:3578
> #11 0x00007ffff7a66311 in fast_function (nk=0, na=3, n=<optimized out>,
> pp_stack=0x7fffffffd6f0, func=<optimized out>) at Python/ceval.c:4334
> #12 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd6f0) at
> Python/ceval.c:4252
> #13 PyEval_EvalFrameEx (f=f at entry=0x7ffff7e8a048,
> throwflag=throwflag at entry=0) at Python/ceval.c:2829
> #14 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
> out>, n=2, pp_stack=0x7fffffffd840, func=<optimized out>) at
> Python/ceval.c:4324
> #15 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd840) at
> Python/ceval.c:4252
> #16 PyEval_EvalFrameEx (f=f at entry=0x7ffff7ee9728,
> throwflag=throwflag at entry=0) at Python/ceval.c:2829
> #17 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
> out>, n=2, pp_stack=0x7fffffffd990, func=<optimized out>) at
> Python/ceval.c:4324
> #18 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd990) at
> Python/ceval.c:4252
> #19 PyEval_EvalFrameEx (f=f at entry=0x7ffff7ef0c48,
> throwflag=throwflag at entry=0) at Python/ceval.c:2829
> #20 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
> out>, n=1, pp_stack=0x7fffffffdae0, func=<optimized out>) at
> Python/ceval.c:4324
> #21 call_function (oparg=<optimized out>, pp_stack=0x7fffffffdae0) at
> Python/ceval.c:4252
> #22 PyEval_EvalFrameEx (f=f at entry=0x6df508, throwflag=throwflag at entry=0) at
> Python/ceval.c:2829
> #23 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
> out>, n=2, pp_stack=0x7fffffffdc30, func=<optimized out>) at
> Python/ceval.c:4324
> #24 call_function (oparg=<optimized out>, pp_stack=0x7fffffffdc30) at
> Python/ceval.c:4252
> #25 PyEval_EvalFrameEx (f=f at entry=0x7ffff7f2f828,
> throwflag=throwflag at entry=0) at Python/ceval.c:2829
> #26 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=0x7ffff7f84420,
> globals=<optimized out>, locals=locals at entry=0x0,
> args=args at entry=0x7ffff7e30be0, argcount=2, kws=kws at entry=0x0,
>     kwcount=kwcount at entry=0, defs=defs at entry=0x0, defcount=defcount at entry=0,
> kwdefs=0x0, closure=0x0) at Python/ceval.c:3578
> #27 0x00007ffff79db926 in function_call (func=0x7ffff7f16598,
> arg=0x7ffff7e30bc8, kw=0x0) at Objects/funcobject.c:632
> #28 0x00007ffff79b482c in PyObject_Call (func=func at entry=0x7ffff7f16598,
> arg=arg at entry=0x7ffff7e30bc8, kw=kw at entry=0x0) at Objects/abstract.c:2067
> #29 0x00007ffff79b5223 in _PyObject_CallMethodIdObjArgs
> (callable=0x7ffff7f16598, name=name at entry=0x7ffff7d94e20
> <PyId__find_and_load.12671>) at Objects/abstract.c:2340
> #30 0x00007ffff7a7b183 in PyImport_ImportModuleLevelObject
> (name=0x7ffff7e30b30, given_globals=<optimized out>, locals=<optimized out>,
> given_fromlist=<optimized out>, level=0)
>     at Python/import.c:1621
> #31 0x00007ffff7a5cecf in builtin___import__ (self=<optimized out>,
> args=<optimized out>, kwds=<optimized out>) at Python/bltinmodule.c:210
> #32 0x00007ffff79b482c in PyObject_Call (func=func at entry=0x7ffff7fb93c8,
> arg=arg at entry=0x7ffff7f4c938, kw=0x0) at Objects/abstract.c:2067
> #33 0x00007ffff7a5f857 in PyEval_CallObjectWithKeywords
> (func=func at entry=0x7ffff7fb93c8, arg=arg at entry=0x7ffff7f4c938,
> kw=kw at entry=0x0) at Python/ceval.c:4104
> #34 0x00007ffff7a62a3d in PyEval_EvalFrameEx (f=f at entry=0x7ffff7fa0d88,
> throwflag=throwflag at entry=0) at Python/ceval.c:2469
> #35 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=_co at entry=0x7ffff7e1fc00,
> globals=globals at entry=0x7ffff7f2c2c8, locals=locals at entry=0x7ffff7f2c2c8,
> args=args at entry=0x0,
>     argcount=argcount at entry=0, kws=kws at entry=0x0, kwcount=kwcount at entry=0,
> defs=defs at entry=0x0, defcount=defcount at entry=0, kwdefs=kwdefs at entry=0x0,
> closure=closure at entry=0x0)
>     at Python/ceval.c:3578
> #36 0x00007ffff7a68d5b in PyEval_EvalCode (co=co at entry=0x7ffff7e1fc00,
> globals=globals at entry=0x7ffff7f2c2c8, locals=locals at entry=0x7ffff7f2c2c8) at
> Python/ceval.c:773
> #37 0x00007ffff7a84464 in run_mod (mod=mod at entry=0x70ff98,
> filename=filename at entry=0x7ffff7ee1d88, globals=0x7ffff7f2c2c8,
> locals=0x7ffff7f2c2c8, flags=flags at entry=0x7fffffffe460,
>     arena=arena at entry=0x677f80) at Python/pythonrun.c:2175
> #38 0x00007ffff7a86f37 in PyRun_InteractiveOneObject
> (fp=fp at entry=0x7ffff77304e0 <_IO_2_1_stdin_>,
> filename=filename at entry=0x7ffff7ee1d88, flags=flags at entry=0x7fffffffe460)
>     at Python/pythonrun.c:1441
> #39 0x00007ffff7a871de in PyRun_InteractiveLoopFlags
> (fp=fp at entry=0x7ffff77304e0 <_IO_2_1_stdin_>,
> filename_str=filename_str at entry=0x7ffff7b08656 "<stdin>",
> flags=flags at entry=0x7fffffffe460)
> ---Type <return> to continue, or q <return> to quit---
>     at Python/pythonrun.c:1320
> #40 0x00007ffff7a8822e in PyRun_AnyFileExFlags (fp=fp at entry=0x7ffff77304e0
> <_IO_2_1_stdin_>, filename=0x7ffff7b08656 "<stdin>",
> closeit=closeit at entry=0, flags=flags at entry=0x7fffffffe460)
>     at Python/pythonrun.c:1282
> #41 0x00007ffff7a9c804 in run_file (p_cf=0x7fffffffe460, filename=0x0,
> fp=0x7ffff77304e0 <_IO_2_1_stdin_>) at Modules/main.c:319
> #42 Py_Main (argc=<optimized out>, argv=<optimized out>) at
> Modules/main.c:751
> #43 0x0000000000400af9 in main ()
> (gdb)
>

This is very strange, since the segfault does not seem to come from
anywhere within the library.

Just to check: Are you sure boost-python was built with the same Python
version you are using to build graph-tool?

Best,
Tiago

-- 
Tiago de Paula Peixoto <tiago at skewed.de>

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