$ python
Python 2.7.5 (default, Oct 14 2013, 09:13:45)
[GCC 4.7.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
from graph_tool.all import *
Segmentation fault
I am on Sabayon Linux 64bit, alll ./configure options met including
optionals.
attachment.html (475 Bytes)
This is not very useful information. Please provide a gdb backtrace, the
compiler version you are using, as well as Boost, the options you passed
to the configure script, the contents of the config.log file, etc.
Best,
Tiago
Included confg.log and config.status
let me know if theres anything.
attachment.html (797 Bytes)
config.log (86.9 KB)
config.status (76.8 KB)
It would be useful to have a gdb backtrace of the segfault as well.
1 . Boost version : dev-libs/boost-1.52.0-r6
2 . I just directly did ./configure make install
3. import graph_tool
g = graph_tool.Graph() # <== Works fine
I did attached config.log and config.status , in separated email, not sure
why it didn't show up here.
attachment.html (1.46 KB)
config.log (86.9 KB)
config.status (76.8 KB)
I am not too familiar to C(++) , need to dump core first to generate GDB
Backtrace?
attachment.html (781 Bytes)
I am not too familiar to C(++) , need to dump core first to generate GDB Backtrace?
No, you just run python from gdb:
$ gdb python
(gdb) run
Python 3.3.4 (default, Mar 16 2014, 22:38:15)
[GCC 4.8.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from graph_tool.all import *
When it segfaults you run:
(gdb) bt
Which gives you the backtrace.
Best,
Tiago
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(a)entry=0x7fffebd57228) at Objects/object.c:278
#2 0x00007ffff79f5fb9 in PyObject_CallFinalizerFromDealloc
(self=self(a)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(a)entry=0x71ab98,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2412
#5 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=0x7ffff7e52c90,
globals=<optimized out>, locals=<optimized out>, args=args(a)entry=0x0,
argcount=argcount(a)entry=0, kws=kws(a)entry=0x0,
kwcount=kwcount(a)entry=0, defs=defs(a)entry=0x0, defcount=defcount(a)entry=0,
kwdefs=kwdefs(a)entry=0x0, closure=closure(a)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
, flags=<optimized out>, pp_stack=0x7fffffffd4e8, func=0x7ffff7fb9788)
at Python/ceval.c:4548
#9 PyEval_EvalFrameEx (f=f(a)entry=0x7ffff7e20048,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2869
#10 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=_co(a)entry=0x7ffff7f5d810,
globals=<optimized out>, locals=locals(a)entry=0x0, args=<optimized out>,
argcount=argcount(a)entry=3,
kws=0x7ffff7e8a1f8, kwcount=kwcount(a)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(a)entry=0x7ffff7e8a048,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2829
#14 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
, 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(a)entry=0x7ffff7ee9728,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2829
#17 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
, 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(a)entry=0x7ffff7ef0c48,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2829
#20 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
, 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(a)entry=0x6df508, throwflag=throwflag(a)entry=0) at
Python/ceval.c:2829
#23 0x00007ffff7a67c78 in fast_function (nk=<optimized out>, na=<optimized
, 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(a)entry=0x7ffff7f2f828,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2829
#26 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=0x7ffff7f84420,
globals=<optimized out>, locals=locals(a)entry=0x0,
args=args(a)entry=0x7ffff7e30be0, argcount=2, kws=kws(a)entry=0x0,
kwcount=kwcount(a)entry=0, defs=defs(a)entry=0x0, defcount=defcount(a)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(a)entry=0x7ffff7f16598,
arg=arg(a)entry=0x7ffff7e30bc8, kw=kw(a)entry=0x0) at Objects/abstract.c:2067
#29 0x00007ffff79b5223 in _PyObject_CallMethodIdObjArgs
(callable=0x7ffff7f16598, name=name(a)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(a)entry=0x7ffff7fb93c8,
arg=arg(a)entry=0x7ffff7f4c938, kw=0x0) at Objects/abstract.c:2067
#33 0x00007ffff7a5f857 in PyEval_CallObjectWithKeywords
(func=func(a)entry=0x7ffff7fb93c8, arg=arg(a)entry=0x7ffff7f4c938,
kw=kw(a)entry=0x0) at Python/ceval.c:4104
#34 0x00007ffff7a62a3d in PyEval_EvalFrameEx (f=f(a)entry=0x7ffff7fa0d88,
throwflag=throwflag(a)entry=0) at Python/ceval.c:2469
#35 0x00007ffff7a68c8e in PyEval_EvalCodeEx (_co=_co(a)entry=0x7ffff7e1fc00,
globals=globals(a)entry=0x7ffff7f2c2c8, locals=locals(a)entry=0x7ffff7f2c2c8,
args=args(a)entry=0x0,
argcount=argcount(a)entry=0, kws=kws(a)entry=0x0, kwcount=kwcount(a)entry=0,
defs=defs(a)entry=0x0, defcount=defcount(a)entry=0, kwdefs=kwdefs(a)entry=0x0,
closure=closure(a)entry=0x0)
at Python/ceval.c:3578
#36 0x00007ffff7a68d5b in PyEval_EvalCode (co=co(a)entry=0x7ffff7e1fc00,
globals=globals(a)entry=0x7ffff7f2c2c8, locals=locals(a)entry=0x7ffff7f2c2c8) at
Python/ceval.c:773
#37 0x00007ffff7a84464 in run_mod (mod=mod(a)entry=0x70ff98,
filename=filename(a)entry=0x7ffff7ee1d88, globals=0x7ffff7f2c2c8,
locals=0x7ffff7f2c2c8, flags=flags(a)entry=0x7fffffffe460,
arena=arena(a)entry=0x677f80) at Python/pythonrun.c:2175
#38 0x00007ffff7a86f37 in PyRun_InteractiveOneObject
(fp=fp(a)entry=0x7ffff77304e0 <_IO_2_1_stdin_>,
filename=filename(a)entry=0x7ffff7ee1d88, flags=flags(a)entry=0x7fffffffe460)
at Python/pythonrun.c:1441
#39 0x00007ffff7a871de in PyRun_InteractiveLoopFlags
(fp=fp(a)entry=0x7ffff77304e0 <_IO_2_1_stdin_>,
filename_str=filename_str(a)entry=0x7ffff7b08656 "<stdin>",
flags=flags(a)entry=0x7fffffffe460)
---Type <return> to continue, or q <return> to quit---
at Python/pythonrun.c:1320
#40 0x00007ffff7a8822e in PyRun_AnyFileExFlags (fp=fp(a)entry=0x7ffff77304e0
<_IO_2_1_stdin_>, filename=0x7ffff7b08656 "<stdin>",
closeit=closeit(a)entry=0, flags=flags(a)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)
Hi,
Thanks! Boost was build against 3.3. Rebuilded it with 3.4 and now have no
segfaults anymore.