[Kratos] Problemas

Farshid Mossaiby mossaiby en yahoo.com
Jue Ago 25 23:49:39 CEST 2011


Dear Nelson,
 
You may try running the debug version of your program this way:
 
gdb --args python test.py
 
While at gdb's prompt, issue the following command:
 
run
 
When gdb says that your program has received a SEGFAULT, issue the below command:
 
where
 
to trace back to the point the problem has occured. This may not be always accurate, but may help. If this did not help, try putting a breakpoint on Kratos functions you suspect using `break' command:
 
break Kratos::somfunction
 
You may use TAB key (but use it with care when there are a lot of candidates!).
 
Hope this helps,
 
Best regards
Farshid Mossaiby
 
From: Nelson Lafontaine <inglafontaine en gmail.com>
To: Kratos maining list <kratos en listas.cimne.upc.edu>; Pooyan Dadvand <Pooyan.Dadvand en gmail.com>; Julio Marcelo Marti <marti.jm en gmail.com>
Sent: Friday, August 26, 2011 1:40 AM
Subject: [Kratos] Problemas


Hola,

Quiero pedirles un favor:
He estado esta tarde mirando este error fastasma y no he dado con la solucion.
No he hecho nada en absoluto,  y no entiendo el porque del segmentation fault 
leyendo los datos de entrada. Es mas cuando compilo con intel, pasa que a la hora de ver los elementos 
que tengo,  poseo uno mas de los que el data file me indica. Ni idea del porque me pasa esto.


Esto es el valgrind:
Si me pueden dar un poco de luz, gracias.


Saludos
 

Thu Aug 25 23:01:54 2011
Applications Available:
Import_ALEApplication: False
Import_IncompressibleFluidApplication: False
Import_StructuralApplication: False
Import_ConvectionDiffusionApplication: False
Import_FSIApplication: False
Import_ExternalSolversApplication: False
Import_ULFApplication: False
Import_MeshingApplication: False
Import_KratosMKLSolversApplication: False
Import_KratosTrilinosApplication: False
Import_KratosMetisApplication: False
Import_PoissonApplication: False
Import_ElectrostaticApplication: False
Import_MagnetostaticApplication: False
Import_DamApplication: False
Import_TestApplication: False
Import_OpenCLApplication: False
Import_PodApplication: False
Import_LevelSetApplication: False
Import_FluidDynamicsApplication: False
Import_KratosMixedElementApplication: False
Applications Available:
Import_ALEApplication: False
Import_IncompressibleFluidApplication: False
Import_StructuralApplication: True
Import_ConvectionDiffusionApplication: False
Import_FSIApplication: False
Import_ExternalSolversApplication: False
Import_ULFApplication: False
Import_MeshingApplication: False
Import_KratosTrilinosApplication: False
Import_KratosMetisApplication: False
Import_PoissonApplication: False
Import_ElectrostaticApplication: False
Import_MagnetostaticApplication: False
Import_DamApplication: False
Import_TestApplication: False
Import_OpenCLApplication: False
Import_PodApplication: False
Import_LevelSetApplication:False
Import_FluidDynamicsApplication: False
Import_KratosMixedElementApplication: False
importing KratosStructuralApplication ...
"kerneal entered in AddApplication" : kerneal entered in AddApplication
Initializing KratosStructuralApplication... 
"Application Registered" : Application Registered
"Variables Registered" : Variables Registered
"Elements Registered" : Elements Registered
"Conditions Registered" : Conditions Registered
KratosStructuralApplication Succesfully imported
Variables for the dynamic structural solution added correctly
check_contact_21_penalty opened for io
check_contact_21_penalty.node opened for io
check_contact_21_penalty.prop opened for io
check_contact_21_penalty.elem opened for io
check_contact_21_penalty.cond opened for io
check_contact_21_penalty.init opened for io
initializing result files
Reading Nodes : 216 nodes read
        Reading Elements : 352 TotalLagrangian2D3N read
lines read : 795
==6112== Invalid read of size 4
==6112==    at 0x972B7E4: __cxa_allocate_exception (in /usr/lib/libstdc++.so.6.0.13)
==6112==    by 0x8D8E4BD: boost::python::throw_error_already_set() (errors.cpp:61)
==6112==    by 0x819FDA3: boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next::operator()(boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&) (iterator.hpp:64)
==6112==    by 0x819FBAF: _object* boost::python::detail::invoke<boost::python::to_python_value<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&>, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::arg_from_python<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul,
 Kratos::Dof<double> > > > > > >&> >(boost::python::detail::invoke_tag_<false, false>, boost::python::to_python_value<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&> const&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next&, boost::python::arg_from_python<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >,
 std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&>&) (invoke.hpp:75)
==6112==    by 0x819F996: boost::python::detail::caller_arity<1u>::impl<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, boost::mpl::vector2<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> >
 >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&> >::operator()(_object*, _object*) (caller.hpp:223)
==6112==    by 0x819F80A: boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, boost::mpl::vector2<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*,
 std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&> > >::operator()(_object*, _object*) (py_function.hpp:38)
==6112==    by 0x8D86C2D: boost::python::objects::function::call(_object*, _object*) const (py_function.hpp:143)
==6112==    by 0x8D86ED7: boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) (function.cpp:581)
==6112==    by 0x8D8E54A: boost::python::handle_exception_impl(boost::function0<void>) (function_template.hpp:1013)
==6112==    by 0x8D837D7: function_call (errors.hpp:29)
==6112==    by 0x41F0C6: PyObject_Call (in /usr/bin/python2.6)
==6112==    by 0x427DFE: ??? (in /usr/bin/python2.6)
==6112==  Address 0x18 is not stack'd, malloc'd or (recently) free'd
==6112== 
==6112== 
==6112== Process terminating with default action of signal 11 (SIGSEGV)
==6112==  Access not within mapped region at address 0x18
==6112==    at 0x972B7E4: __cxa_allocate_exception (in /usr/lib/libstdc++.so.6.0.13)
==6112==    by 0x8D8E4BD: boost::python::throw_error_already_set() (errors.cpp:61)
==6112==    by 0x819FDA3: boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next::operator()(boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&) (iterator.hpp:64)
==6112==    by 0x819FBAF: _object* boost::python::detail::invoke<boost::python::to_python_value<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&>, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::arg_from_python<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul,
 Kratos::Dof<double> > > > > > >&> >(boost::python::detail::invoke_tag_<false, false>, boost::python::to_python_value<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&> const&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next&, boost::python::arg_from_python<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >,
 std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&>&) (invoke.hpp:75)
==6112==    by 0x819F996: boost::python::detail::caller_arity<1u>::impl<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, boost::mpl::vector2<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> >
 >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&> >::operator()(_object*, _object*) (caller.hpp:223)
==6112==    by 0x819F80A: boost::python::objects::caller_py_function_impl<boost::python::detail::caller<boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*, std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >::next, boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, boost::mpl::vector2<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >&, boost::python::objects::iterator_range<boost::python::return_value_policy<boost::python::return_by_value, boost::python::default_call_policies>, __gnu_cxx::__normal_iterator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >*,
 std::vector<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > >, std::allocator<boost::shared_ptr<Kratos::Node<3ul, Kratos::Dof<double> > > > > > >&> > >::operator()(_object*, _object*) (py_function.hpp:38)
==6112==    by 0x8D86C2D: boost::python::objects::function::call(_object*, _object*) const (py_function.hpp:143)
==6112==    by 0x8D86ED7: boost::detail::function::void_function_ref_invoker0<boost::python::objects::(anonymous namespace)::bind_return, void>::invoke(boost::detail::function::function_buffer&) (function.cpp:581)
==6112==    by 0x8D8E54A: boost::python::handle_exception_impl(boost::function0<void>) (function_template.hpp:1013)
==6112==    by 0x8D837D7: function_call (errors.hpp:29)
==6112==    by 0x41F0C6: PyObject_Call (in /usr/bin/python2.6)
==6112==    by 0x427DFE: ??? (in /usr/bin/python2.6)
==6112==  If you believe this happened as a result of a stack
==6112==  overflow in your program's main thread (unlikely but
==6112==  possible), you can try to increase the size of the
==6112==  main thread stack using the --main-stacksize= flag.
==6112==  The main thread stack size used in this run was 8388608.
==6112== 
==6112== HEAP SUMMARY:
==6112==     in use at exit: 5,975,338 bytes in 22,427 blocks
==6112==   total heap usage: 42,911 allocs, 20,484 frees, 10,915,930 bytes allocated
==6112== 
==6112== LEAK SUMMARY:
==6112==    definitely lost: 136 bytes in 1 blocks
==6112==    indirectly lost: 0 bytes in 0 blocks
==6112==      possibly lost: 1,456,007 bytes in 8,384 blocks
==6112==    still reachable: 4,519,195 bytes in 14,042 blocks
==6112==         suppressed: 0 bytes in 0 blocks
==6112== Rerun with --leak-check=full to see details of leaked memory
==6112== 
==6112== For counts of detected and suppressed errors, rerun with: -v
==6112== Use --track-origins=yes to see where uninitialised values come from
==6112== ERROR SUMMARY: 548 errors from 53 contexts (suppressed: 28 from 7)
Violación de segmento
nelson en nelson:~/kratosfiles/check_contact_21_penalty.gid$ 




-- 
Ing. Nelson M. Lafontaine



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