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[Question #155671]: problem with yade-bz2823 on Mandriva (real machine, non-virtual)

 

New question #155671 on Yade:
https://answers.launchpad.net/yade/+question/155671

Hello again,

After crashing my debian lenny machine during upgrade to squeeze (without backup ;), I compiled yade again on Mandriva (on two machines 64bit and 32bit). Compiling was successfull. Note, that this time I used real machines, not virtual machines!
On both machines occured the same problem while executing yade-bz2823:

[me@mandriva bin]$ yade-bz2823 --debug
Welcome to Yade 0.60 (debug build)
TCP python prompt on localhost:9000, auth cookie `sdysae'
XMLRPC info provider on http://localhost:21000
SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-w7YqgU/tmp-0'
GNU gdb (GDB) 7.1-1mdv2010.1 (Mandriva Linux release 2010.1)
Copyright (C) 2010 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-mandriva-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>.
[Thread debugging using libthread_db enabled]
[New Thread 0x7f8f7bfff710 (LWP 4117)]
[New Thread 0x7f8f80821710 (LWP 4116)]
0x00007f8f99fbeadd in waitpid () from /lib64/libc.so.6
No symbol "info" in current context.

Thread 3 (Thread 0x7f8f80821710 (LWP 4116)):
#0  0x00007f8f99ff1cf3 in select () from /lib64/libc.so.6
#1  0x00007f8f81cf23a4 in ?? () from /usr/lib64/python2.6/lib-dynload/select.so
#2  0x00007f8f9a360707 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#3  0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#4  0x00007f8f9a36082b in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#5  0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#6  0x00007f8f9a2f54af in ?? () from /usr/lib64/libpython2.6.so.1.0
#7  0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#8  0x00007f8f9a2e0d0f in ?? () from /usr/lib64/libpython2.6.so.1.0
#9  0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#10 0x00007f8f9a35ac13 in PyEval_CallObjectWithKeywords () from /usr/lib64/libpython2.6.so.1.0
#11 0x00007f8f8082a6db in ?? () from /usr/lib64/python2.6/site-packages/sip.so
#12 0x00007f8f80abf577 in ?? () from /usr/lib64/python2.6/site-packages/PyQt4/QtCore.so
#13 0x00007f8f80aefed9 in ?? () from /usr/lib64/python2.6/site-packages/PyQt4/QtCore.so
#14 0x00007f8f94df1b45 in ?? () from /usr/lib64/libQtCore.so.4
#15 0x00007f8f99b04a5d in start_thread () from /lib64/libpthread.so.0
#16 0x00007f8f99ff915d in clone () from /lib64/libc.so.6
#17 0x0000000000000000 in ?? ()

Thread 2 (Thread 0x7f8f7bfff710 (LWP 4117)):
#0  0x00007f8f99ff1cf3 in select () from /lib64/libc.so.6
#1  0x00007f8f81cf23a4 in ?? () from /usr/lib64/python2.6/lib-dynload/select.so
#2  0x00007f8f9a360707 in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#3  0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#4  0x00007f8f9a36082b in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#5  0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#6  0x00007f8f9a2f54af in ?? () from /usr/lib64/libpython2.6.so.1.0
#7  0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#8  0x00007f8f9a2e0d0f in ?? () from /usr/lib64/libpython2.6.so.1.0
#9  0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#10 0x00007f8f9a35ac13 in PyEval_CallObjectWithKeywords () from /usr/lib64/libpython2.6.so.1.0
#11 0x00007f8f8082a6db in ?? () from /usr/lib64/python2.6/site-packages/sip.so
#12 0x00007f8f80abf577 in ?? () from /usr/lib64/python2.6/site-packages/PyQt4/QtCore.so
#13 0x00007f8f80aefed9 in ?? () from /usr/lib64/python2.6/site-packages/PyQt4/QtCore.so
#14 0x00007f8f94df1b45 in ?? () from /usr/lib64/libQtCore.so.4
#15 0x00007f8f99b04a5d in start_thread () from /lib64/libpthread.so.0
#16 0x00007f8f99ff915d in clone () from /lib64/libc.so.6
#17 0x0000000000000000 in ?? ()

Thread 1 (Thread 0x7f8f9a815700 (LWP 4113)):
#0  0x00007f8f99fbeadd in waitpid () from /lib64/libc.so.6
#1  0x00007f8f99f5a861 in do_system () from /lib64/libc.so.6
#2  0x00007f8f99f5abc0 in system () from /lib64/libc.so.6
#3  0x00007f8f97a63f82 in crashHandler (sig=11) at core/main/pyboot.cpp:45
#4  <signal handler called>
#5  0x00007f8f963aedeb in glutInit () from /usr/lib64/libglut.so.3
#6  0x00007f8f88931948 in OpenGLRenderer::init (this=<value optimized out>) at /opt/yade-0.60.2/pkg/common/OpenGLRenderer.cpp:46
#7  0x00007f8f7ae0ad71 in OpenGLManager::OpenGLManager (this=0x1a854b0, parent=<value optimized out>) at gui/qt4/OpenGLManager.cpp:11
#8  0x00007f8f7adffb1c in init_module__GLViewer () at gui/qt4/_GLViewer.cpp:91
#9  0x00007f8f9661031b in boost::python::handle_exception_impl(boost::function0<void>) () from /usr/lib64/libboost_python.so.1.42.0
#10 0x00007f8f96611023 in boost::python::detail::init_module(char const*, void (*)()) () from /usr/lib64/libboost_python.so.1.42.0
#11 0x00007f8f9a375728 in _PyImport_LoadDynamicModule () from /usr/lib64/libpython2.6.so.1.0
#12 0x00007f8f9a373765 in ?? () from /usr/lib64/libpython2.6.so.1.0
#13 0x00007f8f9a3739f4 in ?? () from /usr/lib64/libpython2.6.so.1.0
#14 0x00007f8f9a37409e in ?? () from /usr/lib64/libpython2.6.so.1.0
#15 0x00007f8f9a374dd4 in PyImport_ImportModuleLevel () from /usr/lib64/libpython2.6.so.1.0
#16 0x00007f8f9a35a6bf in ?? () from /usr/lib64/libpython2.6.so.1.0
#17 0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#18 0x00007f8f9a35ac13 in PyEval_CallObjectWithKeywords () from /usr/lib64/libpython2.6.so.1.0
#19 0x00007f8f9a35d4ce in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#20 0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#21 0x00007f8f9a362692 in PyEval_EvalCode () from /usr/lib64/libpython2.6.so.1.0
#22 0x00007f8f9a371d82 in PyImport_ExecCodeModuleEx () from /usr/lib64/libpython2.6.so.1.0
#23 0x00007f8f9a372276 in ?? () from /usr/lib64/libpython2.6.so.1.0
#24 0x00007f8f9a37304f in ?? () from /usr/lib64/libpython2.6.so.1.0
#25 0x00007f8f9a373765 in ?? () from /usr/lib64/libpython2.6.so.1.0
#26 0x00007f8f9a3739f4 in ?? () from /usr/lib64/libpython2.6.so.1.0
#27 0x00007f8f9a37409e in ?? () from /usr/lib64/libpython2.6.so.1.0
#28 0x00007f8f9a374dd4 in PyImport_ImportModuleLevel () from /usr/lib64/libpython2.6.so.1.0
#29 0x00007f8f9a35a6bf in ?? () from /usr/lib64/libpython2.6.so.1.0
#30 0x00007f8f9a2ce103 in PyObject_Call () from /usr/lib64/libpython2.6.so.1.0
#31 0x00007f8f9a35ac13 in PyEval_CallObjectWithKeywords () from /usr/lib64/libpython2.6.so.1.0
#32 0x00007f8f9a35d4ce in PyEval_EvalFrameEx () from /usr/lib64/libpython2.6.so.1.0
#33 0x00007f8f9a3625c0 in PyEval_EvalCodeEx () from /usr/lib64/libpython2.6.so.1.0
#34 0x00007f8f9a362692 in PyEval_EvalCode () from /usr/lib64/libpython2.6.so.1.0
#35 0x00007f8f9a37cb5c in ?? () from /usr/lib64/libpython2.6.so.1.0
#36 0x00007f8f9a37cc30 in PyRun_FileExFlags () from /usr/lib64/libpython2.6.so.1.0
#37 0x00007f8f9a37e10c in PyRun_SimpleFileExFlags () from /usr/lib64/libpython2.6.so.1.0
#38 0x00007f8f9a38a751 in Py_Main () from /usr/lib64/libpython2.6.so.1.0
#39 0x00007f8f99f3cafd in __libc_start_main () from /lib64/libc.so.6
#40 0x0000000000400689 in _start ()
Segmentation fault

*damn*
I think I have a Deja-vu ^^ (see question 152794 	compiled YADE ?!)

[me@mandriva bin]$ yade-bz2823 --debug --test
Math: Matrix3 operations ... ok
Math: Quaternion operations ... ok
Math: Vector2 operations ... ok
Math: Vector3 operations ... ok
Core: correct types are instantiated ... ok
Core: dispatcher ctors with functors ... ok
Core: InteractionLoop special ctor ... ok
Core: invalid attribute access raises AttributeError ... ok
Core: ParallelEngine special ctor ... ok
Core: class ctor's attributes ... ok
Core: dispatcher and functor type mismatch is detected ... ok
Bodies: erased bodies are None in python ... ok
Bodies: Iterator silently skips erased ones ... ok
Bodies: Iteration ... ok
Bodies: len(O.bodies) ... ok
Bodies: Negative index counts backwards (like python sequences). ... ok
Cell: updates Hsize automatically when refSize is updated ... ok
I/O: All classes can be saved and loaded with boost::serialization ... INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
...
...
WARNING: cannot open files used for capillary law, all forces will be null. Instructions on how to download and install them is found here : https://yade-dem.org/wiki/CapillaryTriaxialTest.
INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
FATAL /opt/yade-0.60.2/pkg/common/Facet.cpp:25 postLoad: Facet has coincident vertices 0 (0 0 0) and 1 (0 0 0)!
FATAL /opt/yade-0.60.2/pkg/common/Facet.cpp:25 postLoad: Facet has coincident vertices 1 (0 0 0) and 2 (0 0 0)!
FATAL /opt/yade-0.60.2/pkg/common/Facet.cpp:25 postLoad: Facet has coincident vertices 2 (0 0 0) and 0 (0 0 0)!

...
...
INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
ok
Material+State: CpmMat returns CpmState when asked for newAssocState ... ok
Material+State: throws when body has material and state that don't work together. ... ok
Material+State: throws when body has material but NULL state. ... ok
Material: find by index or label; KeyError raised for invalid label. ... ok
Material: iteration over O.materials ... ok
Material: len(O.materials) ... ok
Material: negative index counts backwards. ... ok
Material: shared_ptr's makes change in material immediate everywhere ... ok
Material: shared_ptr's are preserved when saving/loading ... INFO  /opt/yade-0.60.2/core/Omega.cpp:244 saveSimulation: Saving file :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:246 saveSimulation: Overwriting in-memory saved simulation :memory:
INFO  /opt/yade-0.60.2/core/Omega.cpp:222 loadSimulation: Loading file :memory:
ok
PBC: (homoDeform==1) homothetic cell deformation adjusts particle position ... ok
PBC: (homoDeform==3) homothetic cell deformation adjusts particle velocity ... ok
PBC: (homoDeform==3) utils.kineticEnergy considers only fluctuation velocity, not the velocity gradient ... ok
PBC: (homoDeform==1) utils.kineticEnergy considers only fluctuation velocity, not the velocity gradient ... ok
PBC: (homoDeform==3) ScGeom computes incident velocity correctly ... ok
PBC: (homoDeform==1) ScGeom computes incident velocity correctly ... ok
Clump: ids and flags consistency ... ok
Clump: mass, centroid, intertia ... ok
Clump: velocities of member assigned by NewtonIntegrator ... ok
Doctest: yade.eudoxos.IntrSmooth3d ... ok
Doctest: yade.pack.SpherePack_toSimulation ... ok
Doctest: yade.plot.plot ... FAIL
Doctest: yade.utils.SpherePWaveTimeStep ... ok
Doctest: yade.utils.saveVars ... /opt/yade-0.60.2/lib/yade-bz2823/dbg/py/yade/utils.py:57: UserWarning: Overwriting yade.params.mark which already exists.
  if mark in yade.params.__dict__: warnings.warn('Overwriting yade.params.%s which already exists.'%mark)
ok
Doctest: yade.utils.sphere ... ok
Doctest: yade.utils.typedEngine ... ok

======================================================================
FAIL: Doctest: yade.plot.plot
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib64/python2.6/doctest.py", line 2152, in runTest
    raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for yade.plot.plot
  File "/opt/yade-0.60.2/lib/yade-bz2823/dbg/py/yade/plot.py", line 236, in plot

----------------------------------------------------------------------
File "/opt/yade-0.60.2/lib/yade-bz2823/dbg/py/yade/plot.py", line 243, in yade.plot.plot
Failed example:
    plot.plot(noShow=True).savefig('someFile.pdf')
Exception raised:
    Traceback (most recent call last):
      File "/usr/lib64/python2.6/doctest.py", line 1248, in __run
        compileflags, 1) in test.globs
      File "<doctest yade.plot.plot[2]>", line 1, in <module>
        plot.plot(noShow=True).savefig('someFile.pdf')
      File "/usr/lib64/python2.6/site-packages/matplotlib/figure.py", line 1084, in savefig
        self.canvas.print_figure(*args, **kwargs)
      File "/usr/lib64/python2.6/site-packages/matplotlib/backend_bases.py", line 1923, in print_figure
        **kwargs)
      File "/usr/lib64/python2.6/site-packages/matplotlib/backend_bases.py", line 1733, in print_pdf
        return pdf.print_pdf(*args, **kwargs)
      File "/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_pdf.py", line 2150, in print_pdf
        file = PdfFile(filename)
      File "/usr/lib64/python2.6/site-packages/matplotlib/backends/backend_pdf.py", line 370, in __init__
        fh = file(filename, 'wb')
    IOError: [Errno 13] Permission denied: 'someFile.pdf'
----------------------------------------------------------------------
File "/opt/yade-0.60.2/lib/yade-bz2823/dbg/py/yade/plot.py", line 245, in yade.plot.plot
Failed example:
    os.path.exists('someFile.pdf')
Expected:
    True
Got:
    False


----------------------------------------------------------------------
Ran 43 tests in 0.177s

FAILED (failures=1)
******************** SOME TESTS FAILED ********************

[me@mandriva bin]$ yade-bz2823 --debug --check
Usage: yade-bz2823 [options] [ simulation.xml[.bz2] | script.py [script options]]

yade-bz2823: error: no such option: --check


Does anyone know how to solve the problem?

Regards,

Christian

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