[Kratos] Trilinos Mistakes

maireni en cimne.upc.edu maireni en cimne.upc.edu
Mie Jun 19 10:20:22 CEST 2013 

  

The last version was comipiled and install suscessfuly. 

Now i am
compiling kratos kratos and its all OK. 

However when i begin to run
the bechmarking examples 

defined in trilinos applications appears the
following; 

dofs for the dynamic structural solution added
correctly
Linear elastic model
selected
line49
0.0
line49
0.001
line49
0.002
line49
0.003
line49
0.004
0
: BaseType::mEquationSystemSize = 2002
0 : mLocalSystemSize = 2002
0 :
free_offset = 2002
entering
ResizeAndInitializeVectors
TSparseSpace::Size1(*pA) :
2002
TSparseSpace::Size(*pb) : 2002
finished
ResizeAndInitializeVectors
[nelson:03271] *** Process received signal
***
[nelson:03271] Signal: Segmentation fault (11)
[nelson:03271] Signal
code: Address not mapped (1)
[nelson:03271] Failing at address:
0x80551ed40
[nelson:03271] [ 0] /lib/libpthread.so.0(+0xf8f0)
[0x7ff8edd8d8f0]
[nelson:03271] [ 1]
/home/nelson/kratos/libs/KratosStructuralApplication.so(_ZN6Kratos6Face2D12CalculateAllERN5boost7numeric5ublas6matrixIdNS3_15basic_row_majorImlEENS3_15unbounded_arrayIdSaIdEEEEERNS3_6vectorIdS9_EERNS_11ProcessInfoEbb+0x1ef)
[0x7ff8e36f16ff]
[nelson:03271] [ 2]
/home/nelson/kratos/libs/KratosStructuralApplication.so(_ZN6Kratos6Face2D20CalculateLocalSystemERN5boost7numeric5ublas6matrixIdNS3_15basic_row_majorImlEENS3_15unbounded_arrayIdSaIdEEEEERNS3_6vectorIdS9_EERNS_11ProcessInfoE+0xf)
[0x7ff8e36f14ff]
[nelson:03271] [ 3]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN6Kratos50TrilinosResidualBasedIncrementalUpdateStaticSchemeINS_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS_10UblasSpaceIdN5boost7numeric5ublas6matrixIdNS8_15basic_row_majorImlEENS8_15unbounded_arrayIdSaIdEEEEENS8_6vectorIdSE_EEEEE38Condition_CalculateSystemContributionsENS6_10shared_ptrINS_9ConditionEEERSF_RSH_RSt6vectorImSaImEERNS_11ProcessInfoE+0x55)
[0x7ff8e2098da5]
[nelson:03271] [ 4]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN6Kratos29TrilinosBlockBuilderAndSolverINS_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS_10UblasSpaceIdN5boost7numeric5ublas6matrixIdNS8_15basic_row_majorImlEENS8_15unbounded_arrayIdSaIdEEEEENS8_6vectorIdSE_EEEENS_12LinearSolverIS4_SI_NS_9ReordererIS4_SI_EEEEE5BuildENS6_10shared_ptrINS_6SchemeIS4_SI_EEEERNS_9ModelPartERS2_RS3_+0x371)
[0x7ff8e21dede1]
[nelson:03271] [ 5]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN6Kratos29TrilinosBlockBuilderAndSolverINS_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS_10UblasSpaceIdN5boost7numeric5ublas6matrixIdNS8_15basic_row_majorImlEENS8_15unbounded_arrayIdSaIdEEEEENS8_6vectorIdSE_EEEENS_12LinearSolverIS4_SI_NS_9ReordererIS4_SI_EEEEE13BuildAndSolveENS6_10shared_ptrINS_6SchemeIS4_SI_EEEERNS_9ModelPartERS2_RS3_SV_+0x84)
[0x7ff8e21e2274]
[nelson:03271] [ 6]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN5boost6python6detail6invokeIiMN6Kratos29TrilinosBlockBuilderAndSolverINS3_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS3_10UblasSpaceIdNS_7numeric5ublas6matrixIdNSB_15basic_row_majorImlEENSB_15unbounded_arrayIdSaIdEEEEENSB_6vectorIdSH_EEEENS3_12LinearSolverIS8_SL_NS3_9ReordererIS8_SL_EEEEEEFvNS_10shared_ptrINS3_6SchemeIS8_SL_EEEERNS3_9ModelPartERS6_RS7_SY_ENS0_15arg_from_pythonIRSQ_EENS11_ISU_EENS11_ISW_EENS11_ISX_EENS11_ISY_EES17_EEP7_objectNS1_11invoke_tag_ILb1ELb1EEERKT_RT0_RT1_RT2_RT3_RT4_RT5_RT6_+0x9d)
[0x7ff8e22218fd]
[nelson:03271] [ 7]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN5boost6python6detail12caller_arityILj6EE4implIMN6Kratos29TrilinosBlockBuilderAndSolverINS5_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS5_10UblasSpaceIdNS_7numeric5ublas6matrixIdNSD_15basic_row_majorImlEENSD_15unbounded_arrayIdSaIdEEEEENSD_6vectorIdSJ_EEEENS5_12LinearSolverISA_SN_NS5_9ReordererISA_SN_EEEEEEFvNS_10shared_ptrINS5_6SchemeISA_SN_EEEERNS5_9ModelPartERS8_RS9_S10_ENS0_21default_call_policiesENS_3mpl7vector7IvRSS_SW_SY_SZ_S10_S10_EEEclEP7_objectS1A_+0x354)
[0x7ff8e2221684]
[nelson:03271] [ 8]
/home/nelson/kratos/libs/KratosTrilinosApplication.so(_ZN5boost6python7objects23caller_py_function_implINS0_6detail6callerIMN6Kratos29TrilinosBlockBuilderAndSolverINS5_13TrilinosSpaceI18Epetra_FECrsMatrix15Epetra_FEVectorEENS5_10UblasSpaceIdNS_7numeric5ublas6matrixIdNSD_15basic_row_majorImlEENSD_15unbounded_arrayIdSaIdEEEEENSD_6vectorIdSJ_EEEENS5_12LinearSolverISA_SN_NS5_9ReordererISA_SN_EEEEEEFvNS_10shared_ptrINS5_6SchemeISA_SN_EEEERNS5_9ModelPartERS8_RS9_S10_ENS0_21default_call_policiesENS_3mpl7vector7IvRSS_SW_SY_SZ_S10_S10_EEEEEclEP7_objectS1B_+0xa)
[0x7ff8e222132a]
[nelson:03271] [ 9]
/usr/local/lib/libboost_python.so.1.53.0(_ZNK5boost6python7objects8function4callEP7_objectS4_+0x101)
[0x7ff8eb3b9a11]
[nelson:03271] [10]
/usr/local/lib/libboost_python.so.1.53.0(+0x31ea8)
[0x7ff8eb3b9ea8]
[nelson:03271] [11]
/usr/local/lib/libboost_python.so.1.53.0(_ZN5boost6python21handle_exception_implENS_9function0IvEE+0x5b)
[0x7ff8eb3c1b5b]
[nelson:03271] [12]
/usr/local/lib/libboost_python.so.1.53.0(+0x2e6d8)
[0x7ff8eb3b66d8]
[nelson:03271] [13] python(PyObject_Call+0x47)
[0x41f227]
[nelson:03271] [14] python(PyEval_EvalFrameEx+0x4888)
[0x4a7518]
[nelson:03271] [15] python(PyEval_EvalFrameEx+0x5a60)
[0x4a86f0]
[nelson:03271] *** End of error message
***
--------------------------------------------------------------------------
mpirun
noticed that process rank 0 with PID 3271 on node nelson exited on
signal 11 (Segmentation fault).

On Wed, 19 Jun 2013 08:46:26 +0200,
Riccardo Rossi wrote: 

> Dear Nelson,
> 
> please make sure you updated
to the latest version of the cmake_modules directory
> 
> also please
check carefully for the trilinos install path you give to the kratos
>

> Riccardo
> 
> On Tue, Jun 18, 2013 at 6:44 PM, wrote:
> 
>> Hi Bui

>> 
>> I use the last version of trilinus. The compilation and the
instalation was perfect. 
>> 
>> However, when compile Kratos apears
thi: 
>> 
>> **** configuring KratosTrilinosApplication ****
>> -- Could
NOT find EPETRA (missing: EPETRA_LIBRARY) 
>> -- Could NOT find TEUCHOS
(missing: TEUCHOS_LIBRARY) 
>> -- Could NOT find TRIUTILS (missing:
TRIUTILS_LIBRARY) 
>> CMake Error at
cmake_modules/FindTRILINOS.cmake:221 (MESSAGE):
>> Could not find
Trilinos or one of its packages. Please set the cmake var
>>
TRILINOS_ROOT or the environment vars MY_TRILINOS_INC_DIRS and
>>
MY_TRILINOS_LIB_DIRS
>> Call Stack (most recent call first):
>>
applications/trilinos_application/CMakeLists.txt:15 (find_package) 
>>

>> I set in the .basrc the corresponding path: 
>> 
>> export
LD_LIBRARY_PATH=/usr/local/trilinos-11.2.3/lib:$LD_LIBRARY_PATH 
>> 
>>
but no compile yet. Any idea? 
>> 
>> Regards 
>> 
>> Nelson 
>> 
>> On
Tue, 18 Jun 2013 17:46:25 +0200, Hoang Giang Bui wrote: 
>> 
>>> Hi
>>>

>>> Just a comment, you don't need PyTrilinos to work with kratos. You
can turn this off by
>>> 
>>> -D Trilinos_ENABLE_PyTrilinos=OFF 
>>>

>>> to your configure script.
>>> 
>>> Ciao
>>> Bui
>>> 
>>> On Tue,
Jun 18, 2013 at 4:22 PM, Nelson Lafontaine wrote: 
>>> 
>>>> Hi frinds
Trying to compile and install trilinos i have this mistake.
>>>> 
>>>> [
91%] Building CXX object
packages/PyTrilinos/src/CMakeFiles/EpetraExt.dir/EpetraExtPYTHON_wrap.cpp.o
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:
In function 'PyObject* _wrap_CrsGraph_MapColoring___call__(PyObject*,
PyObject*)':
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9019:
error: 'arg2' declared as reference but not initialized
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9026:
error: 'result' declared as reference but not initialized
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9042:
error: cannot declare pointer to 'class Epetra_CrsGraph&'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9042:
error: cannot declare pointer to 'class Epetra_CrsGraph&'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/packages/epetra/src/Epetra_MapColoring.h:300:
error: 'Epetra_MapColoring& Epetra_MapColoring::operator=(const
Epetra_MapColoring&)' is private
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9050:
error: within this context
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9082:
error: cannot declare reference to 'class Epetra_MapColoring&'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9082:
error: new cannot be applied to a reference type
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:
In function 'PyObject*
_wrap_CrsGraph_MapColoringIndex___call__(PyObject*, PyObject*)':
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9213:
error: 'OriginalTypeRef' was not declared in this scope
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9213:
error: expected ';' before 'arg2'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9220:
error: 'NewTypeRef' was not declared in this scope
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9220:
error: expected ';' before 'result'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: 'temp' was not declared in this scope
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: expected type-specifier before 'OriginalTypeRef'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: expected '>' before 'OriginalTypeRef'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: expected '(' before 'OriginalTypeRef'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: expected primary-expression before '>' token
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9236:
error: expected ')' before ';' token
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9237:
error: 'arg2' was not declared in this scope
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9238:
error: type '' argument given to 'delete', expected pointer 
>>>> 
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9244:
error: 'result' was not declared in this scope
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9244:
error: 'arg2' was not declared in this scope
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9276:
error: expected type-specifier before 'NewTypeRef'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9276:
error: expected ')' before 'NewTypeRef'
>>>>
/home/nelson/compiled_libraries/trilinos-10.2.0-Source/trilinos-build/packages/PyTrilinos/src/EpetraExtPYTHON_wrap.cpp:9276:
error: expected ')' before ';' token
>>>> make[2]: ***
[packages/PyTrilinos/src/CMakeFiles/EpetraExt.dir/EpetraExtPYTHON_wrap.cpp.o]
Error 1
>>>> make[1]: ***
[packages/PyTrilinos/src/CMakeFiles/EpetraExt.dir/all] Error 2
>>>>
make: *** [all] Error 2
>>>> nelson en nelson:~/compiled_librari
>>>> 
>>>>
Any idea? I am watching the file, but i did not founf any anormal
>>>>
thing.
>>>> 
>>>> regards
>>>> 
>>>> Nelson
>>>> 
>>>> -- 
>>>> Ing.
Nelson M. Lafontaine
>>>> 
>>>>
_______________________________________________
>>>> Kratos mailing
list
>>>> Kratos en listas.cimne.upc.edu [1]
>>>>
http://listas.cimne.upc.edu/cgi-bin/mailman/listinfo/kratos [2]
>>> 
>>>
-- 
>>> With Best Regards !
>>> Giang Bui 
>>> To learn and to excel
>>

>> _______________________________________________
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list
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>>
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> 
> --

> 
> Dr. Riccardo Rossi, Civil Engineer
> 
> Member of Kratos Team 
>

> International Center for Numerical Methods in Engineering - CIMNE
>
Campus Norte, Edificio C1 
> 
> c/ Gran Capitán s/n 
> 
> 08034
Barcelona, España 
> 
> Tel: (+34) 93 401 56 96 
> 
> Fax: (+34)
93.401.6517 web: www.cimne.com [7]

 

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