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Re: Periodic* test crashes

To: yade-dev@xxxxxxxxxxxxxxxxxxx
From: Anton Gladky <gladky.anton@xxxxxxxxx>
Date: Mon, 11 Jan 2010 16:53:58 +0100
In-reply-to: <4B4B4842.8080104@hmg.inpg.fr>
For example:

./../bin/yade-currentMono periodic-simple-shear.py

Welcome to Yade bzr1955
TCP python prompt on localhost:9001, auth cookie `syeckd'
TCP info provider on localhost:21001
Running script periodic-simple-shear.py
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-W1MtAh/tmp-0'
GNU gdb (GDB) 7.0-ubuntu
Copyright (C) 2009 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-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
[Thread debugging using libthread_db enabled]
[New Thread 0x7fbaad6fd910 (LWP 22015)]
[New Thread 0x7fbaadefe910 (LWP 22014)]
[New Thread 0x7fbaaf620910 (LWP 22013)]
[New Thread 0x7fbab0dab910 (LWP 22012)]
[New Thread 0x7fbab15ac910 (LWP 22011)]
[New Thread 0x7fbab2237910 (LWP 22010)]
0x00007fbaca42b8f1 in nanosleep () from /lib/libpthread.so.0
No symbol "info" in current context.

Thread 7 (Thread 0x7fbab2237910 (LWP 22010)):
#0  0x00007fbac98e4412 in select () from /lib/libc.so.6
#1  0x00007fbab2313b20 in ?? () from /usr/lib/libtcl8.5.so.0
#2  0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#3  0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#4  0x0000000000000000 in ?? ()

Thread 6 (Thread 0x7fbab15ac910 (LWP 22011)):
#0  0x00007fbac98e4412 in select () from /lib/libc.so.6
#1  0x00000000004ef733 in select_select (self=<value optimized out>,
args=<value optimized out>) at ../Modules/selectmodule.c:278
#2  0x00000000004a290d in call_function (f=0x1e25720, throwflag=<value
optimized out>) at ../Python/ceval.c:3706
#3  PyEval_EvalFrameEx (f=0x1e25720, throwflag=<value optimized out>) at
../Python/ceval.c:2389
#4  0x00000000004a40e0 in PyEval_EvalCodeEx (co=0x1dd45d0, globals=<value
optimized out>, locals=<value optimized out>, args=0x2, argcount=<value
optimized out>, kws=<value optimized out>, kwcount=0, defs=0x1dd8268,
defcount=1, closure=0x0) at ../Python/ceval.c:2968
#5  0x000000000052be30 in function_call (func=0x1dd9320, arg=0x1da2950,
kw=0x0) at ../Objects/funcobject.c:524
#6  0x000000000041d6e7 in PyObject_Call (func=0x1dd9320, arg=0x7fbab15abaa0,
kw=0x7fbab15aba20) at ../Objects/abstract.c:2492
#7  0x00000000004254ff in instancemethod_call (func=0x1dd9320,
arg=0x1da2950, kw=0x0) at ../Objects/classobject.c:2579
#8  0x000000000041d6e7 in PyObject_Call (func=0x1207190, arg=0x7fbab15abaa0,
kw=0x7fbab15aba20) at ../Objects/abstract.c:2492
#9  0x000000000049c623 in PyEval_CallObjectWithKeywords (func=0x1207190,
arg=0x7fbaca7eb050, kw=0x7fbab15aba20) at ../Python/ceval.c:3575
#10 0x00000000004d0bed in t_bootstrap (boot_raw=0x1cc1bd0) at
../Modules/threadmodule.c:425
#11 0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#12 0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#13 0x0000000000000000 in ?? ()

Thread 5 (Thread 0x7fbab0dab910 (LWP 22012)):
#0  0x00007fbac98e4412 in select () from /lib/libc.so.6
#1  0x00000000004ef733 in select_select (self=<value optimized out>,
args=<value optimized out>) at ../Modules/selectmodule.c:278
#2  0x00000000004a290d in call_function (f=0x1d88020, throwflag=<value
optimized out>) at ../Python/ceval.c:3706
#3  PyEval_EvalFrameEx (f=0x1d88020, throwflag=<value optimized out>) at
../Python/ceval.c:2389
#4  0x00000000004a40e0 in PyEval_EvalCodeEx (co=0x1dd45d0, globals=<value
optimized out>, locals=<value optimized out>, args=0x2, argcount=<value
optimized out>, kws=<value optimized out>, kwcount=0, defs=0x1dd8268,
defcount=1, closure=0x0) at ../Python/ceval.c:2968
#5  0x000000000052be30 in function_call (func=0x1dd9320, arg=0x108f2d0,
kw=0x0) at ../Objects/funcobject.c:524
#6  0x000000000041d6e7 in PyObject_Call (func=0x1dd9320, arg=0x7fbab0daaaa0,
kw=0x7fbab0daaa20) at ../Objects/abstract.c:2492
#7  0x00000000004254ff in instancemethod_call (func=0x1dd9320,
arg=0x108f2d0, kw=0x0) at ../Objects/classobject.c:2579
#8  0x000000000041d6e7 in PyObject_Call (func=0x1dc0a00, arg=0x7fbab0daaaa0,
kw=0x7fbab0daaa20) at ../Objects/abstract.c:2492
#9  0x000000000049c623 in PyEval_CallObjectWithKeywords (func=0x1dc0a00,
arg=0x7fbaca7eb050, kw=0x7fbab0daaa20) at ../Python/ceval.c:3575
#10 0x00000000004d0bed in t_bootstrap (boot_raw=0x1e26100) at
../Modules/threadmodule.c:425
#11 0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#12 0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#13 0x0000000000000000 in ?? ()

Thread 4 (Thread 0x7fbaaf620910 (LWP 22013)):
#0  0x00007fbac98df3c3 in *__GI___poll (fds=<value optimized out>,
nfds=<value optimized out>, timeout=-1) at
../sysdeps/unix/sysv/linux/poll.c:87
#1  0x00007fbaba2ed29a in ?? () from /usr/lib/libxcb.so.1
#2  0x00007fbaba2eec2c in xcb_wait_for_reply () from /usr/lib/libxcb.so.1
#3  0x00007fbac22dcf23 in _XReply () from /usr/lib/libX11.so.6
#4  0x00007fbac2ab7db8 in ?? () from /usr/lib/libGL.so.1
#5  0x00007fbac2ab9259 in ?? () from /usr/lib/libGL.so.1
#6  0x00007fbac6bcb8a2 in QGLContext::makeCurrent() () from
/usr/lib/libqt-mt.so.3
#7  0x00007fbac6bc8cf4 in QGLWidget::glDraw() () from /usr/lib/libqt-mt.so.3
#8  0x00007fbab8605469 in YadeQtMainWindow::redrawAll (this=<value optimized
out>, force=true) at gui/qt3/YadeQtMainWindow.cpp:104
#9  0x00007fbab860103c in SimulationController::timerEvent (this=0x1ed9840)
at gui/qt3/SimulationController.cpp:295
#10 0x00007fbac6999102 in QObject::event(QEvent*) () from
/usr/lib/libqt-mt.so.3
#11 0x00007fbac69ccd93 in QWidget::event(QEvent*) () from
/usr/lib/libqt-mt.so.3
#12 0x00007fbac693a785 in QApplication::internalNotify(QObject*, QEvent*) ()
from /usr/lib/libqt-mt.so.3
#13 0x00007fbac693b52e in QApplication::notify(QObject*, QEvent*) () from
/usr/lib/libqt-mt.so.3
#14 0x00007fbac6931094 in QEventLoop::activateTimers() () from
/usr/lib/libqt-mt.so.3
#15 0x00007fbac68ec009 in QEventLoop::processEvents(unsigned int) () from
/usr/lib/libqt-mt.so.3
#16 0x00007fbac69515c1 in QEventLoop::enterLoop() () from
/usr/lib/libqt-mt.so.3
#17 0x00007fbac6951472 in QEventLoop::exec() () from /usr/lib/libqt-mt.so.3
#18 0x00007fbac85a6f93 in thread_proxy () from
/usr/lib/libboost_thread-mt.so.1.38.0
#19 0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#20 0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#21 0x0000000000000000 in ?? ()

Thread 3 (Thread 0x7fbaadefe910 (LWP 22014)):
#0  0x00007fbac98afb4d in __libc_waitpid (pid=22016, stat_loc=<value
optimized out>, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:41
#1  0x00007fbac984d1f9 in do_system (line=<value optimized out>) at
../sysdeps/posix/system.c:149
#2  0x00007fbac984d530 in __libc_system (line=<value optimized out>) at
../sysdeps/posix/system.c:190
#3  0x00007fbac8e7c4a2 in crashHandler (sig=11) at core/main/pyboot.cpp:43
#4  <signal handler called>
#5  0x00000000004b5b0d in PyImport_GetModuleDict (name=0x543028 "__main__")
at ../Python/import.c:361
#6  PyImport_AddModule (name=0x543028 "__main__") at ../Python/import.c:600
#7  0x00000000004c2d68 in PyRun_SimpleStringFlags (command=0x21105d8
"triaxDone()", flags=0x0) at ../Python/pythonrun.c:953
#8  0x00007fbab8a95765 in PeriTriaxController::action (this=0x2110410) at
/home/gladk/dem/yade/currentMono/yade/pkg/dem/Engine/GlobalEngine/PeriIsoCompressor.cpp:251
#9  0x00007fbac44d7c8e in Scene::moveToNextTimeStep (this=0xe54520) at
/home/gladk/dem/yade/currentMono/yade/core/Scene.cpp:90
#10 0x00007fbac44dd78c in SimulationFlow::singleAction (this=0xdf94a0) at
/home/gladk/dem/yade/currentMono/yade/core/SimulationFlow.cpp:18
#11 0x00007fbac44d8371 in ThreadWorker::callSingleAction (this=0xdf94a0) at
/home/gladk/dem/yade/currentMono/yade/core/ThreadWorker.cpp:71
#12 0x00007fbac44e2a51 in ThreadRunner::call (this=0xe58240) at
/home/gladk/dem/yade/currentMono/yade/core/ThreadRunner.cpp:53
#13 0x00007fbac44e2aeb in ThreadRunner::run (this=0xe58240) at
/home/gladk/dem/yade/currentMono/yade/core/ThreadRunner.cpp:27
#14 0x00007fbac451ae14 in boost::function0<void>::operator() (this=<value
optimized out>) at /usr/include/boost/function/function_template.hpp:989
#15 0x00007fbac85a6f93 in thread_proxy () from
/usr/lib/libboost_thread-mt.so.1.38.0
#16 0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#17 0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#18 0x0000000000000000 in ?? ()

Thread 2 (Thread 0x7fbaad6fd910 (LWP 22015)):
#0  0x00007fbac49edf76 in ?? () from /usr/lib/libgomp.so.1
#1  0x00007fbac49ec9d6 in ?? () from /usr/lib/libgomp.so.1
#2  0x00007fbaca423a04 in start_thread (arg=<value optimized out>) at
pthread_create.c:300
#3  0x00007fbac98eb80d in clone () at
../sysdeps/unix/sysv/linux/x86_64/clone.S:112
#4  0x0000000000000000 in ?? ()

Thread 1 (Thread 0x7fbaca82b6f0 (LWP 22009)):
#0  0x00007fbaca42b8f1 in nanosleep () from /lib/libpthread.so.0
#1  0x00007fbab7d61ecb in pyOmega::wait (this=0x7fbaca691640) at
py/yadeWrapper/yadeWrapper.cpp:380
#2  0x00007fbab7d62c90 in
invoke<boost::python::detail::caller_arity::impl::operator()::result_converter,
void (pyOmega::*)(), boost::python::detail::caller_arity<1u>::impl<F,
Policies, Sig>::operator()(PyObject*, PyObject*) [with F = void
(pyOmega::*)(), Policies = boost::python::default_call_policies, Sig =
boost::mpl::vector2<void, pyOmega&>]::c_t0> (this=0xe7dd70, args=<value
optimized out>, kw=<value optimized out>) at
/usr/include/boost/python/detail/invoke.hpp:94
#3  boost::python::detail::caller_arity<1u>::impl<void (pyOmega::*)(),
boost::python::default_call_policies, boost::mpl::vector2<void, pyOmega&>
>::operator() (this=0xe7dd70, args=<value optimized out>, kw=<value
optimized out>) at /usr/include/boost/python/detail/caller.hpp:223
#4
boost::python::objects::caller_py_function_impl<boost::python::detail::caller<void
(pyOmega::*)(), boost::python::default_call_policies,
boost::mpl::vector2<void, pyOmega&> > >::operator() (this=0xe7dd70,
args=<value optimized out>, kw=<value optimized out>) at
/usr/include/boost/python/object/py_function.hpp:38
#5  0x00007fbac7322fce in boost::python::objects::function::call(_object*,
_object*) const () from /usr/lib/libboost_python-mt-py26.so.1.38.0
#6  0x00007fbac73231b8 in ?? () from
/usr/lib/libboost_python-mt-py26.so.1.38.0
#7  0x00007fbac732afb4 in boost::function0<void>::operator()() const () from
/usr/lib/libboost_python-mt-py26.so.1.38.0
#8  0x00007fbac732a7b8 in
boost::python::handle_exception_impl(boost::function0<void>) () from
/usr/lib/libboost_python-mt-py26.so.1.38.0
#9  0x00007fbac731fe2b in ?? () from
/usr/lib/libboost_python-mt-py26.so.1.38.0
#10 0x000000000041d6e7 in PyObject_Call (func=0xe7e280, arg=0x7fff572268c0,
kw=0x0) at ../Objects/abstract.c:2492
#11 0x00000000004a199c in do_call (f=0x1f76cc0, throwflag=<value optimized
out>) at ../Python/ceval.c:3924
#12 call_function (f=0x1f76cc0, throwflag=<value optimized out>) at
../Python/ceval.c:3729
#13 PyEval_EvalFrameEx (f=0x1f76cc0, throwflag=<value optimized out>) at
../Python/ceval.c:2389
#14 0x00000000004a40e0 in PyEval_EvalCodeEx (co=0x1dd4288, globals=<value
optimized out>, locals=<value optimized out>, args=0x0, argcount=<value
optimized out>, kws=<value optimized out>, kwcount=0, defs=0x0, defcount=0,
closure=0x0) at ../Python/ceval.c:2968
#15 0x00000000004a41b2 in PyEval_EvalCode (co=0x7fff572268d0,
globals=0x7fff572268c0, locals=0x0) at ../Python/ceval.c:522
#16 0x00000000004c33a0 in run_mod (fp=0xd51fb0, filename=<value optimized
out>, start=<value optimized out>, globals=<value optimized out>,
locals=0xcfd270, closeit=1, flags=0x0) at ../Python/pythonrun.c:1335
#17 PyRun_FileExFlags (fp=0xd51fb0, filename=<value optimized out>,
start=<value optimized out>, globals=<value optimized out>, locals=0xcfd270,
closeit=1, flags=0x0) at ../Python/pythonrun.c:1321
#18 0x000000000049b757 in builtin_execfile (self=<value optimized out>,
args=<value optimized out>) at ../Python/bltinmodule.c:790
#19 0x00000000004a290d in call_function (f=0xd51cf0, throwflag=<value
optimized out>) at ../Python/ceval.c:3706
#20 PyEval_EvalFrameEx (f=0xd51cf0, throwflag=<value optimized out>) at
../Python/ceval.c:2389
#21 0x00000000004a40e0 in PyEval_EvalCodeEx (co=0x7fbaca751918,
globals=<value optimized out>, locals=<value optimized out>, args=0x0,
argcount=<value optimized out>, kws=<value optimized out>, kwcount=0,
defs=0x0, defcount=0, closure=0x0) at ../Python/ceval.c:2968
#22 0x00000000004a41b2 in PyEval_EvalCode (co=0x7fff572268d0,
globals=0x7fff572268c0, locals=0x0) at ../Python/ceval.c:522
#23 0x00000000004c33a0 in run_mod (fp=0xd4cd10, filename=<value optimized
out>, start=<value optimized out>, globals=<value optimized out>,
locals=0xcfd270, closeit=1, flags=0x7fff57227250) at
../Python/pythonrun.c:1335
#24 PyRun_FileExFlags (fp=0xd4cd10, filename=<value optimized out>,
start=<value optimized out>, globals=<value optimized out>, locals=0xcfd270,
closeit=1, flags=0x7fff57227250) at ../Python/pythonrun.c:1321
#25 0x00000000004c3564 in PyRun_SimpleFileExFlags (fp=<value optimized out>,
filename=0x7fff57228578 "./../bin/yade-currentMono", closeit=1,
flags=0x7fff57227250) at ../Python/pythonrun.c:931
#26 0x0000000000418ab7 in Py_Main (argc=-898355072, argv=<value optimized
out>) at ../Modules/main.c:599
#27 0x00007fbac982aabd in __libc_start_main (main=<value optimized out>,
argc=<value optimized out>, ubp_av=<value optimized out>, init=<value
optimized out>, fini=<value optimized out>, rtld_fini=<value optimized out>,
stack_end=0x7fff57227368) at libc-start.c:220
#28 0x0000000000417ca9 in _start () at ../sysdeps/x86_64/elf/start.S:113
Segmentation fault
______________________________


Anton Gladkyy


2010/1/11 Bruno Chareyre <bruno.chareyre@xxxxxxxxxxx>

> They should not crash. What happens exactly?
>
> B.
>
> Anton Gladky a écrit :
>
>> Hi, all,
>>
>> I read a lot of emails during holidays about periodic cells and decided to
>> check what is it.
>> The problem is that almost all periodic* scripts crash. Is it a normal
>> behavior or not?
>>
>> Thank you.
>> ______________________________
>> Anton Gladkyy
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Mailing list: https://launchpad.net/~yade-dev<https://launchpad.net/%7Eyade-dev>
>> Post to     : yade-dev@xxxxxxxxxxxxxxxxxxx
>> Unsubscribe : https://launchpad.net/~yade-dev<https://launchpad.net/%7Eyade-dev>
>> More help   : https://help.launchpad.net/ListHelp
>>
>>
>
>
> --
> _______________
> Bruno Chareyre
> Associate Professor
> Grenoble INP
> Lab. 3SR
> BP 53 - 38041, Grenoble cedex 9 - France
> Tél : 33 4 56 52 86 21
> Fax : 33 4 76 82 70 43
> ________________
>
>
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> More help   : https://help.launchpad.net/ListHelp
>
Follow ups

Re: Periodic* test crashes
From: Bruno Chareyre, 2010-01-11
References

Periodic* test crashes
From: Anton Gladky, 2010-01-11
Re: Periodic* test crashes
From: Bruno Chareyre, 2010-01-11