[Trilinos-Users] [EXTERNAL] Re: building Trilinos with hdf5 for Albany

[Bosler, Peter Andrew]

Thanks for the suggestions.  It turned out that something in HDF5 version
1.8.13 doesn¹t work with Trilinos.

I switched to version 1.8.12 and Trilinos built properly.

Pete



On 9/5/14, 3:11 AM, "Nico Schlömer" <nico.schloemer at gmail.com> wrote:

>Also, make sure to install HDF5 with *parallel* support.
>If you can't do that, you need
>
>-DSEACASExodus_ENABLE_MPI:BOOL=OFF
>
>--Nico
>
>On Fri, Sep 5, 2014 at 8:51 AM, Radu Popescu <i.radu.popescu at gmail.com>
>wrote:
>> Hello Peter,
>>
>> Maybe the version of HDF5 that you are using is not recent enough. I
>> remember that MPI-IO collective operations were introduced to HDF5
>>during
>> the 1.8.X cycle.
>> Installing a more recent version could fix this.
>>
>> Best regards,
>> Radu
>>
>>
>> On Wed, Sep 3, 2014 at 8:01 PM, Bosler, Peter Andrew
>><pabosle at sandia.gov>
>> wrote:
>>>
>>> Good morning,
>>>
>>> I need to use both Albany¹s master branch and its Tpetra branch, so I¹m
>>> trying to build Trilinos to support Albany on a Mac using gcc49 and
>>>OpenMPI,
>>> with the required TPLs (Boost, BoostLib, GML, HDF5, SuperLU, and
>>>NetCDF).
>>> My configure script runs fine and Cmake is able to find all the
>>>libraries,
>>> but build process keeps getting stuck on an EPetraExt target, with the
>>> output below.
>>>
>>> I¹ve double checked that the HDF5 headers are in the Hdf5_INCLUDE_DIRS
>>> path set in the configure file; any suggestions on what else I should
>>>try?
>>>
>>> Thank you for your time.
>>>
>>> Pete Bosler
>>>
>>>
>>> 
>>>/Users/pabosle/Trilinos/packages/epetraext/src/inout/EpetraExt_HDF5.cpp:
>>> In member function 'void EpetraExt::HDF5::Write(const string&, const
>>> string&, int, int, int, const void*)':
>>>
>>> 
>>>/Users/pabosle/Trilinos/packages/epetraext/src/inout/EpetraExt_HDF5.cpp:
>>>1691:51:
>>> error: 'H5Pset_dxpl_mpio' was not declared in this scope
>>>    H5Pset_dxpl_mpio(plist_id_, H5FD_MPIO_COLLECTIVE);
>>>                                                    ^
>>> Scanning dependencies of target thyra_nonlinear_test_models
>>> [ 70%] Building CXX object
>>> 
>>>packages/epetraext/src/CMakeFiles/epetraext.dir/block/EpetraExt_BlockMul
>>>tiVector.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/core/test/nonlinear/models/CMakeFiles/thyra_nonlinear_tes
>>>t_models.dir/Thyra_DiagonalQuadraticResponseOnlyModelEvaluator.cpp.o
>>> make[2]: ***
>>> 
>>>[packages/epetraext/src/CMakeFiles/epetraext.dir/inout/EpetraExt_HDF5.cp
>>>p.o]
>>> Error 1
>>> make[2]: *** Waiting for unfinished jobs....
>>> Scanning dependencies of target thyraepetra
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_Diag
>>>onalEpetraLinearOpWithSolveFactory.cpp.o
>>> [ 70%] Built target stkclassic_util_diag
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/core/test/nonlinear/models/CMakeFiles/thyra_nonlinear_tes
>>>t_models.dir/Thyra_DiagonalScalarProd.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_Epet
>>>raLinearOp.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/core/test/nonlinear/models/CMakeFiles/thyra_nonlinear_tes
>>>t_models.dir/Thyra_DummyTestModelEvaluator.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/core/test/nonlinear/models/CMakeFiles/thyra_nonlinear_tes
>>>t_models.dir/Thyra_Simple2DModelEvaluator.cpp.o
>>>
>>> 
>>>/Users/pabosle/Trilinos/packages/epetraext/src/model_evaluator/EpetraExt
>>>_ModelEvaluatorScalingTools.cpp:71:6:
>>> warning: 'void {anonymous}::assertModelVarScalings(const
>>> EpetraExt::ModelEvaluator::InArgs&)' defined but not used
>>> [-Wunused-function]
>>>  void assertModelVarScalings(
>>>       ^
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_Epet
>>>raOperatorViewExtractorStd.cpp.o
>>> make[1]: *** [packages/epetraext/src/CMakeFiles/epetraext.dir/all]
>>>Error 2
>>> make[1]: *** Waiting for unfinished jobs....
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_Epet
>>>raOperatorWrapper.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_Epet
>>>raThyraWrappers.cpp.o
>>> [ 70%] Building CXX object
>>> 
>>>packages/thyra/adapters/epetra/src/CMakeFiles/thyraepetra.dir/Thyra_get_
>>>Epetra_Operator.cpp.o
>>> Linking CXX static library libthyra_nonlinear_test_models.a
>>> warning: /opt/local/bin/ranlib: warning for library:
>>> libthyra_nonlinear_test_models.a the table of contents is empty (no
>>>object
>>> file members in the library define global symbols)
>>> [ 70%] Built target thyra_nonlinear_test_models
>>> Linking CXX static library libthyraepetra.a
>>> [ 70%] Built target thyraepetra
>>> make: *** [all] Error 2
>>>
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>>
>>
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