[dune-pdelab] Trouble with dune-pdelab and dune-typetree in CentOS 6.8

Shubhangi Gupta sgupta at geomar.de
Fri Jun 17 08:38:22 CEST 2016 

Hi Ansgar,
hi fellow PDELabers,

Thanks again.

With GCC 4.7.2, the dune installation worked out fine on CentOS 6.8.

Yesterday I tried to install dune on our server which has RHEL 6.8.
It has CMake version 2.8.12.2, and GCC version 4.8.
Here again, the dune core modules install without any problem, but new 
project fails with problem in dune-typetree (although, this project is 
working in CentOS 6.8 as well as in Ubuntu 16).
I have attached the dune terminal output for the build for this 
particular project.

Thanks, and best regards,
Shubhangi


On 17.06.2016 00:43, Ansgar Burchardt wrote:
> Hi,
>
> On Wed, 2016-06-15 at 11:05 +0200, Shubhangi Gupta wrote:
>> Thanks a lot for your reply..
>> Yes, you are right, I had GCC 4.4 installed on the CentOS 6.8 .
>> I updated to GCC version 4.7.2, and the projects now compile fine.
>>
>> Although, I now have problem with SuperLU. I am using SuperLU 4.3.
>> Do you think I should install a newer version (5.0)?
> I have no idea about SuperLU.
>
> Please also send replies to the mailing list. That way other people
> could see your questions too.
>
> Ansgar
>
>
>> On 14.06.2016 17:29, Ansgar Burchardt wrote:
>>> Hi,
>>>
>>> On Tue, 2016-06-14 at 17:20 +0200, Shubhangi Gupta wrote:
>>>> I am trying to install DUNE-2.4.1 on CentOS 6.8.
>>>> All Dune core modules (common, grid, geometry, istl,
>>>> localfunctions,
>>>> pdelab, typetree ) compile without error, but pdelab-howto does
>>>> not
>>>> compile.
>>>> The error seems to be coming from typetree. I checked the
>>>> CMakeError.log, but it is essentially empty.
>>>> This same problem also occurs for any other project that I try to
>>>> build.
>>>> On Ubuntu LTS-16 however, everything is working fine!
>>> That looks like the compiler you use on CentOS only supports an
>>> older
>>> C++ standard than dune-typetree requires.
>>>
>>> The README.md for typetree's releases/2.4 branch states that GCC
>>> 4.7 or
>>> later should work. Which version does CentOS 6.8 include?
>>>
>>> Ansgar
>>>
>>>
>>> _______________________________________________
>>> dune-pdelab mailing list
>>> dune-pdelab at dune-project.org
>>> http://lists.dune-project.org/mailman/listinfo/dune-pdelab

-------------- next part --------------
[root at nodule dune]# ./dune-common/bin/dunecontrol --use-cmake --opts=release.opts --builddir=release-build --only=proj_ElastoPlasticity all
--- going to build proj_ElastoPlasticity ---
--- calling all for proj_ElastoPlasticity ---
--- calling vcsetup for proj_ElastoPlasticity ---
--- calling autogen for proj_ElastoPlasticity ---
Skipping dune-autogen because of CMake
--- calling configure for proj_ElastoPlasticity ---
WARNING: could not find module dune-alugrid,
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
dune-alugrid is suggested by dune-pdelab
Skipping dune-alugrid!
/usr/local/dune/dune-geometry/lib/dunegeometryam2cmake.lib for converting options does not exist
/usr/local/dune/dune-localfunctions/lib/dunelocalfunctionsam2cmake.lib for converting options does not exist
/usr/local/dune/dune-typetree/lib/dunetypetreeam2cmake.lib for converting options does not exist
/usr/local/dune/dune-pdelab/lib/dunepdelabam2cmake.lib for converting options does not exist
/usr/local/dune/proj_ElastoPlasticity/lib/projElastoPlasticityam2cmake.lib for converting options does not exist
cmake -DCMAKE_MODULE_PATH="" -DCMAKE_DISABLE_FIND_PACKAGE_MPI=FALSE "-Ddune-common_DIR=/usr/local/dune/dune-common/release-build" "-Ddune-istl_DIR=/usr/local/dune/dune-istl/release-build" "-Ddune-geometry_DIR=/usr/local/dune/dune-geometry/release-build" "-Ddune-grid_DIR=/usr/local/dune/dune-grid/release-build" "-Ddune-localfunctions_DIR=/usr/local/dune/dune-localfunctions/release-build" "-Ddune-typetree_DIR=/usr/local/dune/dune-typetree/release-build" "-Ddune-pdelab_DIR=/usr/local/dune/dune-pdelab/release-build" -DALBERTA_ROOT=/usr/local/dune/external/alberta -DALUGRID_ROOT=/usr/local/dune/external/alugrid -DMETIS_ROOT=/usr/local/dune/external/metis -DPARMETIS_ROOT=/usr/local/dune/external/parmetis -DUG_ROOT=/usr/local/dune/external/ug -DCMAKE_C_COMPILER='/opt/rh/devtoolset-2/root/usr/bin/gcc' -DCMAKE_CXX_COMPILER='/opt/rh/devtoolset-2/root/usr/bin/c++' -DCMAKE_CXX_FLAGS_RELEASE='-O3 -DNDEBUG -g0 -Wno-deprecated-declarations -funroll-loops' -DCMAKE_BUILD_TYPE=Release "/usr/local/dune/proj_ElastoPlasticity"
-- Dependencies for proj_ElastoPlasticity: dune-common;dune-istl;dune-geometry;dune-grid;dune-localfunctions;dune-typetree;dune-pdelab
-- Dependencies for dune-istl: dune-common (>= 2.4.1)
-- Dependencies for dune-geometry: dune-common (>= 2.4.1)
-- Dependencies for dune-grid: dune-common (>= 2.4.1);dune-geometry (>= 2.4.1)
-- Dependencies for dune-localfunctions: dune-geometry (>= 2.4.1)
-- Dependencies for dune-typetree: dune-common (>= 2.4.1)
-- Dependencies for dune-pdelab: dune-common (>= 2.4.1);dune-geometry (>= 2.4.1);dune-grid (>= 2.4.1);dune-localfunctions (>= 2.4.1);dune-istl (>= 2.4.1);dune-typetree (>= 2.4.1)
-- Suggestions for dune-pdelab: dune-alugrid
-- Dependencies for dune-geometry: dune-common (>= 2.4.1)
-- Dependencies for dune-grid: dune-common (>= 2.4.1);dune-geometry (>= 2.4.1)
-- Dependencies for dune-localfunctions: dune-geometry (>= 2.4.1)
-- Dependencies for dune-istl: dune-common (>= 2.4.1)
-- Dependencies for dune-typetree: dune-common (>= 2.4.1)
CMake Warning at /usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:126 (find_package):
Could not find a package configuration file provided by "dune-alugrid" with
any of the following names:

dune-alugridConfig.cmake
dune-alugrid-config.cmake

Add the installation prefix of "dune-alugrid" to CMAKE_PREFIX_PATH or set
"dune-alugrid_DIR" to a directory containing one of the above files. If
"dune-alugrid" provides a separate development package or SDK, be sure it
has been installed.
Call Stack (most recent call first):
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:366 (find_dune_package)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:413 (dune_process_dependency_leafs)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:420 (dune_create_dependency_leafs)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:433 (dune_create_dependency_leafs)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:579 (dune_create_dependency_tree)
CMakeLists.txt:19 (dune_project)


-- No full CMake package configuration support available. Falling back to pkg-config.
-- checking for module 'dune-alugrid '
-- package 'dune-alugrid ' not found
-- Dependencies for dune-geometry: dune-common (>= 2.4.1)
CMake Warning at /usr/local/dune/dune-common/cmake/modules/DuneDoc.cmake:27 (message):
Need latex to create documentation!
Call Stack (most recent call first):
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
CMakeLists.txt:19 (dune_project)


CMake Warning at /usr/local/dune/dune-common/cmake/modules/DuneDoc.cmake:31 (message):
Need bibtex to create documentation!
Call Stack (most recent call first):
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
CMakeLists.txt:19 (dune_project)


CMake Warning at /usr/local/dune/dune-common/cmake/modules/DuneDoc.cmake:35 (message):
Need makeindex to create documentation!
Call Stack (most recent call first):
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
CMakeLists.txt:19 (dune_project)


CMake Warning at /usr/local/dune/dune-common/cmake/modules/DuneDoc.cmake:39 (message):
Need imagemagick to create latex documentation!
Call Stack (most recent call first):
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:654 (include)
CMakeLists.txt:19 (dune_project)


-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Performing tests specific to dune-common from file /usr/local/dune/dune-common/cmake/modules/DuneCommonMacros.cmake.
-- A library with BLAS API not found. Please specify library location.
-- LAPACK requires BLAS
-- A library with LAPACK API not found. Please specify library location.
-- Could NOT find GMP (missing: GMP_INCLUDE_DIR GMP_LIB GMPXX_LIB GMP_HEADER_WORKS GMPXX_LIB_WORKS)
-- Setting dune-common_INCLUDE_DIRS=/usr/local/dune/dune-common
-- Setting dune-common_LIBRARIES=dunecommon
-- Setting dune-geometry_INCLUDE_DIRS=/usr/local/dune/dune-geometry
-- Setting dune-geometry_LIBRARIES=dunegeometry
-- Performing tests specific to dune-typetree from file /usr/local/dune/dune-typetree/cmake/modules/DuneTypetreeMacros.cmake.
-- Setting dune-typetree_INCLUDE_DIRS=/usr/local/dune/dune-typetree
-- Performing tests specific to dune-istl from file /usr/local/dune/dune-istl/cmake/modules/DuneIstlMacros.cmake.
-- Could NOT find Boost
-- Could NOT find Boost
-- Skipping check for Boost::FUSION as Boost is not available.
CMake Warning at /usr/local/dune/dune-istl/cmake/modules/FindSuperLU.cmake:21 (message):
SuperLU requires BLAS which was not found, skipping the test.
Call Stack (most recent call first):
/usr/local/dune/dune-istl/cmake/modules/DuneIstlMacros.cmake:6 (find_package)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:522 (include)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:665 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)


-- Could NOT find SuiteSparse (missing: BLAS_FOUND SUITESPARSE_INCLUDE_DIR SUITESPARSE_LIBRARY)
-- Could NOT find UMFPack (missing: UMFPACK_INCLUDE_DIRS UMFPACK_LIBRARIES)
-- Setting dune-istl_INCLUDE_DIRS=/usr/local/dune/dune-istl
-- Performing tests specific to dune-localfunctions from file /usr/local/dune/dune-localfunctions/cmake/modules/DuneLocalfunctionsMacros.cmake.
-- Setting dune-localfunctions_INCLUDE_DIRS=/usr/local/dune/dune-localfunctions
-- Performing tests specific to dune-grid from file /usr/local/dune/dune-grid/cmake/modules/DuneGridMacros.cmake.
-- Found alberta libraries for dimensions 1;2;3
-- 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)
-- Setting dune-grid_INCLUDE_DIRS=/usr/local/dune/dune-grid
-- Setting dune-grid_LIBRARIES=dunegrid;dunealbertagrid_1d;dunealbertagrid_2d;dunealbertagrid_3d
-- Performing tests specific to dune-pdelab from file /usr/local/dune/dune-pdelab/cmake/modules/DunePdelabMacros.cmake.
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS)
CMake Warning at /usr/local/dune/dune-pdelab/cmake/modules/UseEigen.cmake:1 (find_package):
By not providing "FindEigen3.cmake" in CMAKE_MODULE_PATH this project has
asked CMake to find a package configuration file provided by "Eigen3", but
CMake did not find one.

Could not find a package configuration file provided by "Eigen3" with any
of the following names:

Eigen3Config.cmake
eigen3-config.cmake

Add the installation prefix of "Eigen3" to CMAKE_PREFIX_PATH or set
"Eigen3_DIR" to a directory containing one of the above files. If "Eigen3"
provides a separate development package or SDK, be sure it has been
installed.
Call Stack (most recent call first):
/usr/local/dune/dune-pdelab/cmake/modules/DunePdelabMacros.cmake:3 (include)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:522 (include)
/usr/local/dune/dune-common/cmake/modules/DuneMacros.cmake:665 (dune_process_dependency_macros)
CMakeLists.txt:19 (dune_project)


-- Setting dune-pdelab_INCLUDE_DIRS=/usr/local/dune/dune-pdelab
-- Setting dune-pdelab_LIBRARIES=dunepdelab
-- Performing tests specific to proj_ElastoPlasticity from file /usr/local/dune/proj_ElastoPlasticity/cmake/modules/Proj_ElastoPlasticityMacros.cmake.
-- Using scripts from /usr/local/dune/dune-common/cmake/scripts for creating doxygen stuff.
-- Adding custom target for config.h generation
-- 
-- The following OPTIONAL packages have been found:

* MPI
* PkgConfig
* CXXTemplateAliases
* CXXDecltype
* GCCTypeof
* Threads
* METIS
* ParMETIS
* ALUGrid
* Alberta
* UG (required version >= 3.11.0)

-- The following REQUIRED packages have been found:

* dune-common
* dune-istl
* dune-geometry
* dune-grid
* dune-localfunctions
* dune-typetree
* dune-pdelab

-- The following features have been disabled:

* Experimental grid extensions , Enables additional grid features.

-- The following OPTIONAL packages have not been found:

* dune-alugrid
* ThreadsCMake31
* LATEX
* Doxygen
* LAPACK
* GMP
* Inkscape
* Boost
* BoostFusion
* SuperLU
* SuiteSparse
* UMFPack
* X11
* OpenGL
* Grape
* Psurface
* AmiraMesh
* PETSc
* Eigen3

-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/dune/proj_ElastoPlasticity/release-build
--- calling make for proj_ElastoPlasticity ---
build directory: release-build
cmake --build . --
[100%] Building CXX object src/CMakeFiles/proj_ElastoPlasticity.dir/proj_ElastoPlasticity.cc.o
In file included from /usr/local/dune/proj_ElastoPlasticity/src/proj_ElastoPlasticity.cc:17:0:
/usr/local/dune/dune-common/dune/common/static_assert.hh:6:2: warning: #warning This header and the macro dune_static_assert are deprecated, use static_assert instead. [-Wcpp]
#warning This header and the macro dune_static_assert are deprecated, use static_assert instead.
^
In file included from /usr/local/dune/dune-typetree/dune/typetree/childextraction.hh:11:0,
from /usr/local/dune/dune-typetree/dune/typetree/powernode.hh:14,
from /usr/local/dune/dune-typetree/dune/typetree/typetree.hh:10,
from /usr/local/dune/dune-pdelab/dune/pdelab/common/function.hh:16,
from /usr/local/dune/proj_ElastoPlasticity/src/proj_ElastoPlasticity.cc:29:
/usr/local/dune/dune-typetree/dune/typetree/treepath.hh:443:46: error: use of parameter âtpâ outside function body
-> decltype(treePathEntry<treePathSize(tp)-1>(tp))
^
In file included from /usr/local/dune/dune-pdelab/dune/pdelab/gridfunctionspace/gridfunctionspace.hh:25:0,
from /usr/local/dune/dune-pdelab/dune/pdelab/constraints/common/constraints.hh:14,
from /usr/local/dune/proj_ElastoPlasticity/src/proj_ElastoPlasticity.cc:32:
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh:534:50: error: parse error in template argument list
static constexpr bool hasAllEntities(Dune::Dim<Grid::dimension + 1>)
^
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh: In member function âvoid Dune::PDELab::PartitionViewEntitySetIndexSet<GV, P>::update_codim(Dune::Codim<cd>)â:
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh:572:19: error: âcontainsâ is not a member of âDune::Partitionsâ
if (Partitions::contains(e.partitionType()))
^
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh: In member function âvoid Dune::PDELab::PartitionViewEntitySetIndexSet<GV, P>::update_codims(std::false_type)â:
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh:587:18: error: âcontainsâ is not a member of âDune::Partitionsâ
if (!Partitions::contains(e.partitionType()))
^
/usr/local/dune/dune-pdelab/dune/pdelab/common/partitionviewentityset.hh:591:47: error: âGridâ is not a class, namespace, or enumeration
for (dim_type codim = 0; codim <= Grid::dimension; ++codim)
^
gmake[2]: *** [src/CMakeFiles/proj_ElastoPlasticity.dir/proj_ElastoPlasticity.cc.o] Error 1
gmake[1]: *** [src/CMakeFiles/proj_ElastoPlasticity.dir/all] Error 2
gmake: *** [all] Error 2
--- Failed to build proj_ElastoPlasticity ---
Terminating dunecontrol due to previous errors!

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