[dune-pdelab] ALUGrid and PQDGLocalFiniteElementMap

Thu Jun 9 19:10:23 CEST 2016

Hey Dune,

Thank you for all the replies. The problem with
PQDGLocalFiniteElementMap was fixed by using a 2D grid :-) Thank you.
Only the ALUGrid problem remains...

I have cleaned the cache and attached the output of the command:
sudo dune-common/bin/dunecontrol  --only=dune-spl configure
"--with-ug=/home/dune/Libs/ug --with-alugrid=/home/dune/Libs/ALUGrid
--with-superlu=/home/dune/Libs/SuperLU_4.3
--with-superlu-lib=libsuperlu_4.3.a".

Furthermore, some information about the installed compilers:
G++ and GCC
Version: 4:4.8.2-1ubuntu6

Regards,
Christian Kaltenecker

Am 08.06.2016 um 11:15 schrieb Andreas Nüßing:
>
> Hi Christian,
>
> I did not compile the module, but from the lines below I extract that
> you are using a Dune::OneDGrid (i.e. dimension 1) with a 2d first
> order QkDG local basis (check the order of the template parameters),
> which is why the parameters of "evaluateFunction" are not convertible.
>
> Best,
>     Andreas
>
> /home/dune/Dune/dune-pdelab/dune/pdelab/newton/newton.hh:239:11:  
> required from 'void Dune::PDELab::NewtonSolver<GOS, S, TrlV,
> TstV>::apply() [with GOS =
> Dune::PDELab::GridOperator<Dune::PDELab::GridFunctionSpace<Dune::GridView<Dune::DefaultLeafGridViewTraits<const
> Dune::OneDGrid, (Dune::PartitionIteratorType)4u> >,
> Dune::PDELab::QkDGLocalFiniteElementMap<double, double, 1, 2>,
> Dune::PDELab::ConformingDirichletConstraints,
> Dune::PDELab::istl::VectorBackend<> >,
> Dune::PDELab::GridFunctionSpace<Dune::GridView<Dune::DefaultLeafGridViewTraits<const
> Dune::OneDGrid, (Dune::PartitionIteratorType)4u> >,
> Dune::PDELab::QkDGLocalFiniteElementMap<double, double, 1, 2>,
> Dune::PDELab::ConformingDirichletConstraints,
> Dune::PDELab::istl::VectorBackend<> >,
> Dune::PDELab::ConvectionDiffusionDG<Dune::SPL::ProblemA<Dune::GridView<Dune::DefaultLeafGridViewTraits<const
> Dune::OneDGrid, (Dune::PartitionIteratorType)4u> >, double>,
> Dune::PDELab::QkDGLocalFiniteElementMap<double, double, 1, 2> >,
> Dune::PDELab::ISTLMatrixBackend, double, double, double,
> Dune::PDELab::ConstraintsTransformation<Dune::PDELab::DOFIndex<long
> unsigned int, 1ul, 2ul>, Dune::PDELab::MultiIndex<long unsigned int,
> 1ul>, double>,
> Dune::PDELab::ConstraintsTransformation<Dune::PDELab::DOFIndex<long
> unsigned int, 1ul, 2ul>, Dune::PDELab::MultiIndex<long unsigned int,
> 1ul>, double> >; S = Dune::PDELab::ISTLBackend_SEQ_BCGS_Jac; TrlV =
> Dune::PDELab::istl::BlockVector<Dune::PDELab::GridFunctionSpace<Dune::GridView<Dune::DefaultLeafGridViewTraits<const
> Dune::OneDGrid, (Dune::PartitionIteratorType)4u> >,
> Dune::PDELab::QkDGLocalFiniteElementMap<double, double, 1, 2>,
> Dune::PDELab::ConformingDirichletConstraints,
> Dune::PDELab::istl::VectorBackend<> >,
> Dune::BlockVector<Dune::FieldVector<double, 1>,
> std::allocator<Dune::FieldVector<double, 1> > > >; TstV =
> Dune::PDELab::istl::BlockVector<Dune::PDELab::GridFunctionSpace<Dune::GridView<Dune::DefaultLeafGridViewTraits<const
> Dune::OneDGrid, (Dune::PartitionIteratorType)4u> >,
> Dune::PDELab::QkDGLocalFiniteElementMap<double, double, 1, 2>,
> Dune::PDELab::ConformingDirichletConstraints,
> Dune::PDELab::istl::VectorBackend<> >,
> Dune::BlockVector<Dune::FieldVector<double, 1>,
> std::allocator<Dune::FieldVector<double, 1> > > >]'
> /home/dune/Dune/dune-spl/src/diffusion.cc:193:15:   required from here
> /home/dune/Dune/dune-pdelab/dune/pdelab/localoperator/convectiondiffusiondg.hh:939:102:
> error: no matching function for call to
> 'Dune::PDELab::LocalBasisCache<Dune::QkStuff::QkLocalBasis<double,
> double, 1, 2> >::evaluateFunction(const Vector&, const
> LocalBasisType&) const'
>              auto& phi =
> cache[order].evaluateFunction(ip.position(),lfsv.finiteElement().localBasis());
>                                                                                                      
> ^
> /home/dune/Dune/dune-pdelab/dune/pdelab/localoperator/convectiondiffusiondg.hh:939:102:
> note: candidate is:
> In file included from
> /home/dune/Dune/dune-pdelab/dune/pdelab/localoperator/convectiondiffusiondg.hh:17:0,
>                  from /home/dune/Dune/dune-spl/src/diffusion.cc:53:
> /home/dune/Dune/dune-pdelab/dune/pdelab/finiteelement/localbasiscache.hh:47:7:
> note: const std::vector<typename LB::Traits::RangeType>&
> Dune::PDELab::LocalBasisCache<LocalBasisType>::evaluateFunction(const
> DomainType&, const LocalBasisType&) const [with LocalBasisType =
> Dune::QkStuff::QkLocalBasis<double, double, 1, 2>; typename
> LB::Traits::RangeType = Dune::FieldVector<double, 1>;
> Dune::PDELab::LocalBasisCache<LocalBasisType>::DomainType =
> Dune::FieldVector<double, 2>]
>        evaluateFunction (const DomainType& position, const
> LocalBasisType& localbasis) const
>        ^
> /home/dune/Dune/dune-pdelab/dune/pdelab/finiteelement/localbasiscache.hh:47:7:
> note:   no known conversion for argument 1 from 'const Vector {aka
> const Dune::FieldVector<double, 1>}' to 'const DomainType& {aka const
> Dune::FieldVector<double, 2>&}'
>
>
> On 08.06.2016 09:38, Christian Kaltenecker wrote:
>> Hello Dune,
>>
>> I am currently working with Alexander Grebhahn from the university of
>> Passau on creating an automatic analysis program to find several
>> variation points within a Dune application.
>>
>> For the evaluation part, I want to generate several variants of the
>> diffusion-convection simulation by also using dune-testtools.
>> Above others, I am using ALUGrid (both dune-alugrid and the external
>> ALUGrid(v1.52) library), UGGrid(v3.11) and SuperLU(v4.3).
>> I have successfully compiled and linked those libraries.
>> Furthermore, I have checked out the "releases/2.4" branches of every
>> Dune module in order to have all Dune modules in the same version
>> (every module except my module compiles without errors).
>> Moreover, the whole Dune framework is running in a docker container.
>>
>> I am executing dunecontrol with the following commands:
>> sudo dune-common/bin/dunecontrol configure "--with-ug=/home/dune/Libs/ug
>> --with-alugrid=/home/dune/Libs/ALUGrid
>> --with-superlu=/home/dune/Libs/SuperLU_4.3
>> --with-superlu-lib=libsuperlu_4.3.a"
>> sudo dune-common/bin/dunecontrol make all
>>
>> The errors (as well as the output of configure) are included in the
>> attachment.
>>
>> If you want to try it on your own, I have also included my Dune module
>> (dune-spl).
>> Note that I have commented out the variability that is not working in
>> the meta ini file, diffusion.mini. Also note, that you need dune-testtools.
>>
>> What could I do to fix the problems that occurr in the log-files? Do I have to add some additional configuration parameters? I am writing to this mailing list because the errors are thrown in the dune-pdelab module.
>>
>> Thanks in advance!
>>
>> Regards,
>> Christian Kaltenecker
>>
>>
>>
>> _______________________________________________
>> dune-pdelab mailing list
>> dune-pdelab at dune-project.org
>> http://lists.dune-project.org/mailman/listinfo/dune-pdelab
>

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--- going to build dune-common dune-python dune-geometry dune-grid dune-alugrid dune-testtools dune-spgrid dune-istl dune-localfunctions dune-typetree dune-pdelab dune-fem dune-spl  ---
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  CMakeLists.txt:19 (dune_project)

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-- The following OPTIONAL packages have been found:

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-- The following REQUIRED packages have been found:

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/home/dune/Dune/dune-geometry/lib/dunegeometryam2cmake.lib for converting options does not exist
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-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/libmpichcxx.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so  
-- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/libmpichf90.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so  
-- Looking for MPI_Finalized
-- Looking for MPI_Finalized - found
-- Performing Test MPI_VERSION_SUPPORTED
-- Performing Test MPI_VERSION_SUPPORTED - Success
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
CMake Warning at /home/dune/Dune/dune-common/cmake/modules/DuneDoc.cmake:27 (message):
   Need latex to create documentation!
Call Stack (most recent call first):
  /home/dune/Dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
  CMakeLists.txt:21 (dune_project)

-- Found Doxygen: /usr/bin/doxygen (found version "1.8.6") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Performing tests specific to dune-common from file /home/dune/Dune/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - found
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Looking for C++ include gmpxx.h
-- Looking for C++ include gmpxx.h - found
-- Looking for __gmpz_abs in /usr/lib/x86_64-linux-gnu/libgmp.so
-- Looking for __gmpz_abs in /usr/lib/x86_64-linux-gnu/libgmp.so - found
-- Found GMP: /usr/include  
-- Looking for sys/mman.h
-- Looking for sys/mman.h - found
-- Performing Test HAVE_MPROTECT
-- Performing Test HAVE_MPROTECT - Success
-- Setting dune-common_INCLUDE_DIRS=/home/dune/Dune/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Using scripts from /home/dune/Dune/dune-common/cmake/scripts for creating doxygen stuff.
-- using /home/dune/Dune/dune-common/doc/doxygen/Doxystyle to create doxystyle file
CMake Warning at /home/dune/Dune/dune-common/cmake/modules/DuneDoc.cmake:91 (message):
  Not adding rule to create refinement.pdf as LaTeX is not usable!
Call Stack (most recent call first):
  doc/refinement/CMakeLists.txt:9 (dune_add_latex_document)

-- Adding custom target for config.h generation
-- 
-- The following OPTIONAL packages have been found:

 * MPI
 * Doxygen
 * PkgConfig
 * BLAS
 * Threads
 * LAPACK
 * GMP
 * Inkscape

-- The following REQUIRED packages have been found:

 * dune-common

-- The following OPTIONAL packages have not been found:

 * ThreadsCMake31
 * LATEX

-- Configuring done
-- Generating done
-- Build files have been written to: /home/dune/Dune/dune-geometry/build-cmake
--- dune-geometry done ---
--- calling configure for dune-grid ---
/home/dune/Dune/dune-geometry/lib/dunegeometryam2cmake.lib for converting options does not exist
 cmake -DCMAKE_MODULE_PATH=""  -DCMAKE_DISABLE_FIND_PACKAGE_MPI=FALSE "-Ddune-common_DIR=/home/dune/Dune/dune-common/build-cmake" "-Ddune-geometry_DIR=/home/dune/Dune/dune-geometry/build-cmake" -DALUGRID_ROOT=/home/dune/Libs/ALUGrid -DUG_ROOT=/home/dune/Libs/ug  "/home/dune/Dune/dune-grid"
-- Dependencies for dune-grid: dune-common (>= 2.4.1);dune-geometry (>= 2.4.1)
-- Dependencies for dune-geometry: dune-common (>= 2.4.1)
-- Performing Test cxx_std_flag_14
-- Performing Test cxx_std_flag_14 - Failed
-- Performing Test cxx_std_flag_1y
-- Performing Test cxx_std_flag_1y - Success
-- Performing Test compiler_supports_cxx14
-- Performing Test compiler_supports_cxx14 - Failed
-- Performing Test cxx_std_flag_11
-- Performing Test cxx_std_flag_11 - Success
-- Performing Test compiler_supports_cxx11
-- Performing Test compiler_supports_cxx11 - Success
-- Performing Test HAVE_NULLPTR
-- Performing Test HAVE_NULLPTR - Success
-- Performing Test HAVE_NULLPTR_T
-- Performing Test HAVE_NULLPTR_T - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- Performing Test HAVE_CONSTEXPR
-- Performing Test HAVE_CONSTEXPR - Success
-- Performing Test HAVE_KEYWORD_FINAL
-- Performing Test HAVE_KEYWORD_FINAL - Success
-- Performing Test HAVE_RANGE_BASED_FOR
-- Performing Test HAVE_RANGE_BASED_FOR - Success
-- Performing Test HAVE_NOEXCEPT_SPECIFIER
-- Performing Test HAVE_NOEXCEPT_SPECIFIER - Success
-- Performing Test HAVE_STD_DECLVAL
-- Performing Test HAVE_STD_DECLVAL - Success
-- Performing Test HAVE_IS_INDEXABLE_SUPPORT
-- Performing Test HAVE_IS_INDEXABLE_SUPPORT - Success
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE  
-- Performing Test STDTHREAD_WORKS
-- Performing Test STDTHREAD_WORKS - Success
-- Performing Test HAVE_CXA_DEMANGLE
-- Performing Test HAVE_CXA_DEMANGLE - Success
-- Found MPI_C: /usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so  
-- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/libmpichcxx.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so  
-- Found MPI_Fortran: /usr/lib/x86_64-linux-gnu/libmpichf90.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so  
-- Looking for MPI_Finalized
-- Looking for MPI_Finalized - found
-- Performing Test MPI_VERSION_SUPPORTED
-- Performing Test MPI_VERSION_SUPPORTED - Success
-- Verifying Fortran/CXX Compiler Compatibility
-- Verifying Fortran/CXX Compiler Compatibility - Success
CMake Warning at /home/dune/Dune/dune-common/cmake/modules/DuneDoc.cmake:27 (message):
   Need latex to create documentation!
Call Stack (most recent call first):
  /home/dune/Dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
  CMakeLists.txt:22 (dune_project)

-- Found Doxygen: /usr/bin/doxygen (found version "1.8.6") 
-- Found PkgConfig: /usr/bin/pkg-config (found version "0.26") 
-- Performing tests specific to dune-common from file /home/dune/Dune/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- Looking for Fortran dgemm
-- Looking for Fortran dgemm - found
-- A library with BLAS API found.
-- Looking for Fortran cheev
-- Looking for Fortran cheev - found
-- A library with LAPACK API found.
-- Looking for C++ include gmpxx.h
-- Looking for C++ include gmpxx.h - found
-- Looking for __gmpz_abs in /usr/lib/x86_64-linux-gnu/libgmp.so
-- Looking for __gmpz_abs in /usr/lib/x86_64-linux-gnu/libgmp.so - found
-- Found GMP: /usr/include  
-- Looking for sys/mman.h
-- Looking for sys/mman.h - found
-- Performing Test HAVE_MPROTECT
-- Performing Test HAVE_MPROTECT - Success
-- Setting dune-common_INCLUDE_DIRS=/home/dune/Dune/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Setting dune-geometry_INCLUDE_DIRS=/home/dune/Dune/dune-geometry
-- Setting dune-geometry_LIBRARIES=dunegeometry
-- Performing tests specific to dune-grid from file /home/dune/Dune/dune-grid/cmake/modules/DuneGridMacros.cmake.
-- Looking for mkstemp
-- Looking for mkstemp - found
-- Looking for metis.h
-- Looking for metis.h - not found
-- Could NOT find METIS (missing:  METIS_INCLUDE_DIR METIS_LIBRARY HAVE_METIS_PARTGRAPHKWAY) 
-- Looking for parmetis.h
-- Looking for parmetis.h - not found
-- Could NOT find ParMETIS (missing:  PARMETIS_INCLUDE_DIR PARMETIS_LIBRARY HAVE_PARMETIS) 
-- checking for module 'alugrid'
--   found alugrid, version 1.52
-- Looking for malloc in alugrid
-- Looking for malloc in alugrid - found
-- Looking for C++ include stlheaders.h
-- Looking for C++ include stlheaders.h - found
-- Performing Test ALUGRID_PARALLEL_FOUND
-- Performing Test ALUGRID_PARALLEL_FOUND - Failed
-- Found ALUGrid: 1.52  
CMake Warning at cmake/modules/UseUG.cmake:20 (message):
  Could not find file ug-config.cmake relative to given UG_ROOT
Call Stack (most recent call first):
  cmake/modules/DuneGridMacros.cmake:16 (include)
  /home/dune/Dune/dune-common/cmake/modules/DuneMacros.cmake:522 (include)
  /home/dune/Dune/dune-common/cmake/modules/DuneMacros.cmake:665 (dune_process_dependency_macros)
  CMakeLists.txt:22 (dune_project)

-- Found UG: /usr/local/lib/cmake/ug  
-- Could NOT find OpenGL (missing:  OPENGL_gl_LIBRARY OPENGL_INCLUDE_DIR) 
-- Could NOT find Grape (missing:  X11_FOUND OPENGL_FOUND GRAPE_INCLUDE_DIR GRAPE_LIBRARY _GRAPE_LIB_FUNCTIONAL _GRAPE_HEADER_USABLE) 
-- checking for one of the modules 'psurface'
-- checking for module 'psurface'
--   package 'psurface' not found
-- Could NOT find psurface (missing:  PSURFACE_INCLUDE_DIR PSURFACE_LIBRARY) 
-- Could NOT find AmiraMesh (missing:  AMIRAMESH_INCLUDE_DIR AMIRAMESH_LIBRARY) 
-- Using scripts from /home/dune/Dune/dune-common/cmake/scripts for creating doxygen stuff.
-- using /home/dune/Dune/dune-common/doc/doxygen/Doxystyle to create doxystyle file
-- Adding custom target for config.h generation
-- 
-- The following OPTIONAL packages have been found:

 * MPI
 * Doxygen
 * PkgConfig
 * BLAS
 * Threads
 * LAPACK
 * GMP
 * Inkscape
 * ALUGrid
 * UG (required version >= 3.11.0)

-- The following REQUIRED packages have been found:

 * dune-common
 * dune-geometry

-- The following features have been disabled: