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[Bug 410250] Re: Crashes at exit due to issues in external libs

To: yade-dev@xxxxxxxxxxxxxxxxxxx
From: Anton Gladky <410250@xxxxxxxxxxxxxxxxxx>
Date: Fri, 03 Feb 2012 20:24:13 -0000
Reply-to: Bug 410250 <410250@xxxxxxxxxxxxxxxxxx>
Sender: bounces@xxxxxxxxxxxxx
Still appears on Ubuntu 12.04, probably because of ipython 0.12

** Changed in: yade
       Status: Triaged => Confirmed

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https://bugs.launchpad.net/bugs/410250

Title:
  Crashes at exit due to issues in external libs

Status in Yet Another Dynamic Engine:
  Confirmed

Bug description:
  SVN 1929

  ./../bin/yade-new_build rb.py
  Python TCP server listening on localhost:9002, auth cookie is `duaeys'
  Running script rb.py
  /usr/lib/python2.6/dist-packages/pytz/__init__.py:32: UserWarning: Module pylab was already imported from /usr/lib/python2.6/dist-packages/pylab.py, but /usr/lib/python2.6/dist-packages is being added to sys.path
    from pkg_resources import resource_stream
  /usr/lib/python2.6/dist-packages/pytz/__init__.py:32: UserWarning: Module matplotlib was already imported from /usr/lib/python2.6/dist-packages/matplotlib/__init__.py, but /usr/lib/python2.6/dist-packages is being added to sys.path
    from pkg_resources import resource_stream
  Found suitable packing in database (radius=0.0035±0,N=8908,dim=0.1×0.1×0.2,scale=1), created Tue Aug  4 13:23:05 2009
  Timestep 1.2521980674e-06
  init
  init done, will now run.
  /var/lib/python-support/python2.6/IPython/Magic.py:38: DeprecationWarning: the sets module is deprecated
    from sets import Set

  	__   __    ____          ____                      _      
  	\ \ / /_ _|  _ \  ___   / ___|___  _ __  ___  ___ | | ___ 
  	 \ V / _` | | | |/ _ \ | |   / _ \| '_ \/ __|/ _ \| |/ _ \ 
  	  | | (_| | |_| |  __/ | |__| (_) | | | \__ \ (_) | |  __/
  	  |_|\__,_|____/ \___|  \____\___/|_| |_|___/\___/|_|\___|
  	

  In [1]: 20090807T134120p11376 tension 3.10545120759e-05 314893.835573
  20090807T134120p11376 tension 4.95870434758e-05 1220246.47637
  20090807T134120p11376 tension 6.83700144894e-05 1832257.13433
  20090807T134120p11376 tension 8.57755676287e-05 1832257.13433
  20090807T134120p11376 tension 0.000105059417869 2441104.81173
  20090807T134120p11376 tension 0.000124092828496 3248083.27549
  20090807T134120p11376 tension 0.000142750579703 3636421.62995
  20090807T134120p11376 tension 0.000162410089364 3915362.4634
  20090807T134120p11376 tension 0.000177186026561 3915362.4634
  20090807T134120p11376 tension 0.000190960205305 4103619.45267
  20090807T134120p11376 tension 0.000212122352647 4185169.59173
  20090807T134120p11376 tension 0.000232783620761 3969610.64164
  20090807T134120p11376 tension 0.00025407098791 3439140.88348
  20090807T134120p11376 tension 0.000274607036218 3439140.88348
  20090807T134120p11376 tension 0.000294016106266 2971291.5821
  20090807T134120p11376 tension 0.00031355039612 2499888.17851
  20090807T134120p11376 tension 0.000332583806747 2293951.84493
  20090807T134120p11376 tension 0.00035136677776 2010495.72312
  Damaged, switching to compression... 
  init
  Reversing plot data
  init done, will now run.
  20090807T134120p11376 compression -0.000318058309126 -4936274.05841
  20090807T134120p11376 compression -0.00052967978252 -12976089.8308
  20090807T134120p11376 compression -0.000726274879106 -20140908.0995
  20090807T134120p11376 compression -0.000922869975691 -25809947.776
  20090807T134120p11376 compression -0.00112447386455 -25809947.776
  20090807T134120p11376 compression -0.00132106896113 -31087458.3646
  20090807T134120p11376 compression -0.00151515966158 -35096527.8767
  20090807T134120p11376 compression -0.0017029893717 -38098460.6142
  20090807T134120p11376 compression -0.00183321797071 -39105953.8306
  20090807T134120p11376 compression -0.00194842019291 -39105953.8306
  20090807T134120p11376 compression -0.00207363999965 -39177604.9368
  20090807T134120p11376 compression -0.00224644333296 -37684959.9577
  20090807T134120p11376 compression -0.00240171589332 -34156169.5136
  20090807T134120p11376 compression -0.00258328461309 -29564727.8904
  20090807T134120p11376 compression -0.0027636011348 -29564727.8904
  20090807T134120p11376 compression -0.00295268304298 -24495712.7421
  20090807T134120p11376 compression -0.0031405127531 -20386295.3954
  20090807T134120p11376 compression -0.00332208147287 -16592131.2889
  Damaged, stopping.
  Strengths fc=-3.91776e+07, ft=4.18517e+06, |fc/ft|=9.36106
  gnuplot 20090807T134120p11376.gnuplot
  Bye.
  pure virtual method called
  terminate called without an active exception
  SIGSEGV/SIGABRT handler called; gdb batch file is `/home/gladk/.yade-new_build/gdb_crash_batch-pid11376'
  GNU gdb 6.8-debian
  Copyright (C) 2008 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".
  [Thread debugging using libthread_db enabled]
  [New Thread 0x7fe7ccf567f0 (LWP 11376)]
  [New Thread 0x7fe789137950 (LWP 11389)]
  [New Thread 0x7fe78867c950 (LWP 11382)]
  [New Thread 0x7fe78aafc950 (LWP 11379)]
  [New Thread 0x7fe78d3bb950 (LWP 11378)]
  [New Thread 0x7fe7951d3950 (LWP 11377)]
  warning: Lowest section in /usr/lib/libicudata.so.38 is .hash at 0000000000000158
  0x00007fe7c8004742 in select () from /lib/libc.so.6
  No symbol "info" in current context.

  Thread 6 (Thread 0x7fe7951d3950 (LWP 11377)):
  #0  0x00007fe7c8004742 in select () from /lib/libc.so.6
  #1  0x00007fe78740fa76 in ?? () from /usr/lib/python2.6/lib-dynload/readline.so
  #2  0x00007fe7cca1bcaf in PyOS_Readline () from /usr/lib/libpython2.6.so.1.0
  #3  0x00007fe7ccabd4f3 in ?? () from /usr/lib/libpython2.6.so.1.0
  #4  0x00007fe7ccac6dbe in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #5  0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #6  0x00007fe7ccac7202 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #7  0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #8  0x00007fe7ccac7202 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #9  0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #10 0x00007fe7ccac7202 in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #11 0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #12 0x00007fe7cca4ea3d in ?? () from /usr/lib/libpython2.6.so.1.0
  #13 0x00007fe7cca1fc48 in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
  #14 0x00007fe7cca303c0 in ?? () from /usr/lib/libpython2.6.so.1.0
  #15 0x00007fe7cca1fc48 in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
  #16 0x00007fe7cca3109b in ?? () from /usr/lib/libpython2.6.so.1.0
  #17 0x00007fe7cca1fc48 in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
  #18 0x00007fe7ccac550f in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #19 0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #20 0x00007fe7ccac8ac2 in PyEval_EvalCode () from /usr/lib/libpython2.6.so.1.0
  #21 0x00007fe7ccae977a in PyRun_FileExFlags () from /usr/lib/libpython2.6.so.1.0
  #22 0x00007fe7ccae9a6d in PyRun_SimpleFileExFlags () from /usr/lib/libpython2.6.so.1.0
  #23 0x00007fe79654fc0b in PythonUI::execScript (script={static npos = 18446744073709551615, _M_dataplus = {<std::allocator<char>> = {<__gnu_cxx::new_allocator<char>> = {<No data fields>}, <No data fields>}, _M_p = 0x7fe7951d2dd0 "�w&\002"}}) at gui/py/PythonUI.cpp:46
  #24 0x00007fe796551493 in PythonUI::pythonSession () at gui/py/PythonUI.cpp:99
  #25 0x00007fe7cc3a14de in boost::function0<void, std::allocator<boost::function_base> >::operator() () from /usr/lib/libboost_thread-gcc42-mt-1_34_1.so.1.34.1
  #26 0x00007fe7cc3a1162 in ?? () from /usr/lib/libboost_thread-gcc42-mt-1_34_1.so.1.34.1
  #27 0x00007fe7cc7bd3ba in start_thread () from /lib/libpthread.so.0
  #28 0x00007fe7c800bfcd in clone () from /lib/libc.so.6
  #29 0x0000000000000000 in ?? ()

  Thread 5 (Thread 0x7fe78d3bb950 (LWP 11378)):
  #0  0x00007fe7cc7c3281 in sem_wait () from /lib/libpthread.so.0
  #1  0x00007fe7ccaf34b8 in PyThread_acquire_lock () from /usr/lib/libpython2.6.so.1.0
  #2  0x00007fe7ccac2204 in PyEval_RestoreThread () from /usr/lib/libpython2.6.so.1.0
  #3  0x00007fe7ccb19622 in ?? () from /usr/lib/libpython2.6.so.1.0
  #4  0x00007fe7ccac6dbe in PyEval_EvalFrameEx () from /usr/lib/libpython2.6.so.1.0
  #5  0x00007fe7ccac89a9 in PyEval_EvalCodeEx () from /usr/lib/libpython2.6.so.1.0
  #6  0x00007fe7cca4ea3d in ?? () from /usr/lib/libpython2.6.so.1.0
  #7  0x00007fe7cca1fc48 in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
  #8  0x00007fe7cca303c0 in ?? () from /usr/lib/libpython2.6.so.1.0
  #9  0x00007fe7cca1fc48 in PyObject_Call () from /usr/lib/libpython2.6.so.1.0
  #10 0x00007fe7ccac17c6 in PyEval_CallObjectWithKeywords () from /usr/lib/libpython2.6.so.1.0
  #11 0x00007fe7ccaf8dfd in ?? () from /usr/lib/libpython2.6.so.1.0
  #12 0x00007fe7cc7bd3ba in start_thread () from /lib/libpthread.so.0
  #13 0x00007fe7c800bfcd in clone () from /lib/libc.so.6
  #14 0x0000000000000000 in ?? ()

  Thread 4 (Thread 0x7fe78aafc950 (LWP 11379)):
  #0  0x00007fe7c8004742 in select () from /lib/libc.so.6
  #1  0x00007fe78addf504 in ?? () from /usr/lib/libtcl8.5.so.0
  #2  0x00007fe7cc7bd3ba in start_thread () from /lib/libpthread.so.0
  #3  0x00007fe7c800bfcd in clone () from /lib/libc.so.6
  #4  0x0000000000000000 in ?? ()

  Thread 3 (Thread 0x7fe78867c950 (LWP 11382)):
  #0  0x00007fe7c957bbaa in ?? () from /usr/lib/libgomp.so.1
  #1  0x00007fe7c957acdb in ?? () from /usr/lib/libgomp.so.1
  #2  0x00007fe7cc7bd3ba in start_thread () from /lib/libpthread.so.0
  #3  0x00007fe7c800bfcd in clone () from /lib/libc.so.6
  #4  0x0000000000000000 in ?? ()

  Thread 2 (Thread 0x7fe789137950 (LWP 11389)):
  #0  0x00007fe7c7fcd92f in waitpid () from /lib/libc.so.6
  #1  0x00007fe7c7f652d1 in ?? () from /lib/libc.so.6
  #2  0x00007fe7c7f6564c in system () from /lib/libc.so.6
  #3  0x00000000004731c1 in sigHandler (sig=6) at /home/gladk/dem/yade/new_build/trunk/core/yade.cpp:83
  #4  <signal handler called>
  #5  0x00007fe7c7f58fb5 in raise () from /lib/libc.so.6
  #6  0x00007fe7c7f5abc3 in abort () from /lib/libc.so.6
  #7  0x00007fe7c87fe0b4 in __gnu_cxx::__verbose_terminate_handler () from /usr/lib/libstdc++.so.6
  #8  0x00007fe7c87fc4b6 in ?? () from /usr/lib/libstdc++.so.6
  #9  0x00007fe7c87fc4e3 in std::terminate () from /usr/lib/libstdc++.so.6
  #10 0x00007fe7c87fcd8f in __cxa_pure_virtual () from /usr/lib/libstdc++.so.6
  #11 0x00007fe7899ec35e in ~ObjectPtrT (this=0x727f50) at /usr/include/log4cxx/helpers/objectptr.h:100
  #12 0x00007fe7c7f5c6ed in exit () from /lib/libc.so.6
  #13 0x00007fe7ccae7fbf in Py_Exit () from /usr/lib/libpython2.6.so.1.0
  #14 0x00007fe7ccae80f2 in ?? () from /usr/lib/libpython2.6.so.1.0
  #15 0x00007fe7ccae832d in PyErr_PrintEx () from /usr/lib/libpython2.6.so.1.0
  #16 0x00007fe7ccae8625 in PyRun_SimpleStringFlags () from /usr/lib/libpython2.6.so.1.0
  #17 0x00007fe7b529e957 in PeriodicPythonRunner::action (this=0x4493ad0, b=<value optimized out>) at /home/gladk/dem/yade/new_build/build-new_build/include/yade-new_build/yade/pkg-common/PeriodicPythonRunner.hpp:21
  #18 0x00000000004656aa in MetaBody::moveToNextTimeStep (this=0x36b9230) at /home/gladk/dem/yade/new_build/trunk/core/MetaBody.cpp:93
  #19 0x000000000046d3aa in SimulationFlow::singleAction (this=0x1f72230) at /home/gladk/dem/yade/new_build/trunk/core/SimulationFlow.cpp:18
  #20 0x000000000046469c in ThreadRunner::call (this=<value optimized out>) at /home/gladk/dem/yade/new_build/trunk/core/ThreadWorker.cpp:71
  #21 0x0000000000464748 in ThreadRunner::run (this=0x51d84d0) at /home/gladk/dem/yade/new_build/trunk/core/ThreadRunner.cpp:23
  #22 0x00007fe7cc3a14de in boost::function0<void, std::allocator<boost::function_base> >::operator() () from /usr/lib/libboost_thread-gcc42-mt-1_34_1.so.1.34.1
  #23 0x00007fe7cc3a1162 in ?? () from /usr/lib/libboost_thread-gcc42-mt-1_34_1.so.1.34.1
  #24 0x00007fe7cc7bd3ba in start_thread () from /lib/libpthread.so.0
  #25 0x00007fe7c800bfcd in clone () from /lib/libc.so.6
  #26 0x0000000000000000 in ?? ()

  Thread 1 (Thread 0x7fe7ccf567f0 (LWP 11376)):
  #0  0x00007fe7c8004742 in select () from /lib/libc.so.6
  #1  0x00007fe7ca686add in QEventLoop::processEvents () from /usr/lib/libqt-mt.so.3
  #2  0x00007fe7ca6ecec1 in QEventLoop::enterLoop () from /usr/lib/libqt-mt.so.3
  #3  0x00007fe7ca6ecd82 in QEventLoop::exec () from /usr/lib/libqt-mt.so.3
  #4  0x00007fe79685c1ac in QtGUI::run (this=0x1f757d0, argc=2, argv=0x7fffd509d4e8) at gui/qt3/QtGUI.cpp:79
  #5  0x00000000004762a3 in main (argc=2, argv=0x7fffd509d4e8) at /home/gladk/dem/yade/new_build/trunk/core/yade.cpp:304
  #0  0x00007fe7c8004742 in select () from /lib/libc.so.6
  Aborted

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