Dear FEniCS community,
since a few days I am trying to install FEniCS 1.5.0 from source on a HPC
cluster (CentOS 6.5, Intel Xeon CPU's).
The dependencies were all installed from source:
- GCC 4.8.2
- CMake 2.8.12
- Python 2.7.6
- Swig 3.0.5
- QT 4.8.4
- VTK 6.1.0
- szip 2.1
- hdf5 1.8.12
- BOOST 1.55.0
- Eigen 3.2.1
- ScientificPython 2.9.4
- numpy 1.9.2
- fiat 1.5.0
- instant 1.5.0
- ufl 1.5.0
- ffc 1.5.0
- ufc 2.3.0
- ply 3.4
- petsc 3.5.3 + petsc4py 3.5.1
- slepc 3.5.3 + slepc4py 3.5.1
On the FEniCS web page, it was indicated which dependencies FEniCS has, but not
which versions of the dependencies work with FEniCS 1.5.0.
When trying to finally install Dolfin, I disabled the parallel features and
made sure that CMake finds all the dependencies. When starting the compilation
everything looked good until I reached 96 %, then I got this strange error:
[ 96%] Building CXX object
dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o
cd
/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build/dolfin/swig/modules/mesh
&& /cluster/apps/gcc/4.8.2/bin/c++ -DBOOST_UBLAS_NDEBUG
-DDOLFIN_GIT_COMMIT_HASH=\"\" -DDOLFIN_LA_INDEX_SIZE=4 -DDOLFIN_SIZE_T=8
-DDOLFIN_VERSION=\"1.5.0\" -DENABLE_PETSC_SNES -DENABLE_PETSC_TAO -DHAS_OPENMP
-DHAS_PETSC -DHAS_PETSC4PY -DHAS_QT4 -DHAS_QVTK -DHAS_SLEPC -DHAS_SLEPC4PY
-DHAS_VTK -DHAS_ZLIB -DNPY_NO_DEPRECATED_API=NPY_1_9_API_VERSION
-DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MICRO=2 -DNUMPY_VERSION_MINOR=9
-DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -D_mesh_EXPORTS
-DvtkRenderingCore_AUTOINIT="4(vtkInteractionStyle,vtkRenderingFreeType,vtkRenderingFreeTypeOpenGL,vtkRenderingOpenGL)"
-DvtkRenderingVolume_AUTOINIT="1(vtkRenderingVolumeOpenGL)" -std=c++11
-Wno-deprecated -fopenmp -O2 -g -DNDEBUG -fPIC
-I/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build -isystem
/cluster/apps/qt/4.8.4/x86_64/lib64/qt/include -isystem
/cluster/apps/qt/4.8.4/x86_64/lib64/qt/include/QtGui -isystem
/cluster/apps/qt/4.8.4/x86_64/lib64/qt/include/QtCore -isystem
/cluster/apps/vtk/6.1.0/x86_64/include/vtk-6.1 -isystem /usr/include/freetype2
-isystem /cluster/apps/python/2.7.6/x86_64/include/python2.7 -isystem
/cluster/apps/netcdf/4.3.2/x86_64/gcc_4.8.2/serial/include -isystem
/cluster/apps/hdf5/1.8.13/x86_64/gcc_4.8.2/serial/include -isystem
/usr/include/libxml2 -I/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0
-I/cluster/home/muelfabi/python/include
-I/cluster/home/muelfabi/fenics/SLEPC/include -isystem
/cluster/home/muelfabi/fenics/EIGEN3/include/eigen3 -isystem
/cluster/apps/boost/1.55.0/x86_64/serial/gcc_4.8.2/include -isystem
/cluster/home/muelfabi/fenics/PETSC/include -isystem
/cluster/home/muelfabi/fenics/PETSC/include/mpiuni
-I/cluster/home/muelfabi/python/lib64/python2.7/site-packages/numpy/core/include
-I/cluster/home/muelfabi/python/lib64/python2.7/site-packages/petsc4py/include
-I/cluster/home/muelfabi/python/lib64/python2.7/site-packages/slepc4py/include
-o CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o -c
/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx
/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:
In function ât SWIG_AsVal_MPI_Comm(PyObject*,
MPI_Comm*)â/cluster/home/muelfabfenics/SOURCES/dolfin-1.5.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:4780:43:
error: âSWIGTYPE_p_MPI_Commâas not declared in this scope
int res = SWIG_ConvertPtr(input,&argp,SWIGTYPE_p_MPI_Comm, 0);
^
/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build/dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx:2959:37:
note: in definition of macro âIG_ConvertPtrâ SWIG_convert_ptr(o,
pptr, type, flags)
^
make[2]: ***
[dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/modulePYTHON_wrap.cxx.o] Error 1
make[2]: Leaving directory
`/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build'
make[1]: *** [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2
make[1]: Leaving directory
`/cluster/home/muelfabi/fenics/SOURCES/dolfin-1.5.0/build'
make: *** [all] Error 2
There was a similar post in the FEniCS mailing list
(http://fenicsproject.org/pipermail/fenics-support/2014-December/001026.html),
but there the problem happened for Dolfin 1.4.0, and I could not really
understand if the problem was solved or if the author of the thread gave up.
Any help is appreciated.
Best regards
Samuel Fux
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