Re: [FEniCS-support] FEniCS dolfin-ac6f9d186802 Build Problems

Thu, 06 Feb 2014 22:47:47 -0800 

On 02/06/14 14:44, Johannes Ring wrote:

On Thu, Feb 6, 2014 at 2:41 PM, Fredrik Lingvall
<[email protected]> wrote:

On 02/06/14 08:23, Johannes Ring wrote:

On Wed, Feb 5, 2014 at 12:12 PM, Fredrik Lingvall
<[email protected]> wrote:

Hi FEniCS devs,

I'm trying to install FEniCS (on a Gentoo) Linux x86_64 box. I have these
packages build and installed


-- Generating form files in demo, test, bench and dolfin directories. May
take some time...
--

----------------------------------------------------------------------------------------
CMake Error at CMakeLists.txt:779 (message):
    Generation of form files failed:

    Traceback (most recent call last):

      File "/usr/local/bin/ffc", line 40, in <module>
        from ufl.log import UFLException

    ImportError: No module named ufl.log

    Traceback (most recent call last):

      File

"/root/software/fenics/fenics-project-dolfin-ac6f9d186802/cmake/scripts/generate-form-files",
line 73, in <module>
        raise RuntimeError, "Unable to compile form: %s/%s" % (root, f)

    RuntimeError: Unable to compile form: dolfin/ale/Poisson2D.ufl

Please make sure that UFL is installed and that it is available in
PYTHONPATH.

Johannes

-snip-



Hi Johannes,

I installed everything in /usr/local and the UFL package was installed
using:

kalle fenics-project-ufl-807c9581e17e # python2 setup.py install
--prefix=/usr/local

1.3.0+

running install
running build
running build_py
running build_scripts
running install_lib
running install_scripts
changing mode of /usr/local/bin/ufl2py to 755
changing mode of /usr/local/bin/ufl-version to 755
changing mode of /usr/local/bin/form2ufl to 755
changing mode of /usr/local/bin/ufl-analyse to 755
changing mode of /usr/local/bin/ufl-convert to 755
running install_data
running install_egg_info
Removing /usr/local/lib64/python2.7/site-packages/UFL-1.3.0_-py2.7.egg-info
Writing /usr/local/lib64/python2.7/site-packages/UFL-1.3.0_-py2.7.egg-info

and doing, for example, a

kalle build # export PYTHONPATH="${PYTHONPATH}:/usr/local/bin:"

does not help.

Try this instead:

   export PYTHONPATH=/usr/local/lib/python2.7/site-packages:$PYTHONPATH

Johannes

Thanks Johannes, that did it. However, I get this build problem now

kalle build # cmake ..
-- The C compiler identification is GNU 4.8.2
-- The CXX compiler identification is GNU 4.8.2
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++

-snip-

-- The following optional packages were found:
-- -------------------------------------------
-- (OK) OPENMP
-- (OK) MPI
-- (OK) PETSC
-- (OK) CHOLMOD
-- (OK) SCOTCH
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
-- (OK) SPHINX
-- (OK) HDF5
-- (OK) VTK
-- (OK) QT
--
-- The following optional packages were not found:
-- -----------------------------------------------
-- (**) PETSC4PY
-- (**) SLEPC
-- (**) TAO
-- (**) TRILINOS
-- (**) UMFPACK
-- (**) PASTIX
-- (**) PARMETIS
--
--
-- Generating SWIG interface.
-- --------------------------
-- Found Qt4: /usr/bin/qmake (found version "4.8.5")
-- Enabling generation of documentation.
-- Initializing sphinx projects
-- Enabling generation of html-documentation
-- Configuring done
-- Generating done
-- Build files have been written to: /root/software/fenics/fenics-project-dolfin-ac6f9d186802/build 



kalle build # make
Scanning dependencies of target dolfin
[ 0%] Building CXX object dolfin/CMakeFiles/dolfin.dir/plot/VTKPlottableGenericFunction.cpp.o 
In file included from /usr/include/boost/mpi/collectives/reduce.hpp:28:0,
                 from /usr/include/boost/mpi/collectives/all_reduce.hpp:17,
                 from /usr/include/boost/mpi/collectives.hpp:537,
                 from /usr/include/boost/mpi.hpp:23,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/operations.hpp:282:39: error: macro "MPI_Op_create" passed 5 arguments, but takes just 3 
                               &mpi_op));
                                       ^
In file included from /usr/include/boost/mpi/communicator.hpp:20:0,
                 from /usr/include/boost/mpi/collectives.hpp:21,
                 from /usr/include/boost/mpi.hpp:23,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/datatype.hpp: In function 'int boost::mpi::get_mpi_datatype(const T&) [with T = std::pair<long double, int>]': /usr/include/boost/mpi/datatype.hpp:249:1: error: 'MPI_LONG_DOUBLE_INT' was not declared in this scope 
 BOOST_MPI_DATATYPE(std::pair<BOOST_MPI_LIST2(long double, int)>,
 ^
In file included from /usr/include/boost/mpi/collectives/reduce.hpp:28:0,
                 from /usr/include/boost/mpi/collectives/all_reduce.hpp:17,
                 from /usr/include/boost/mpi/collectives.hpp:537,
                 from /usr/include/boost/mpi.hpp:23,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<std::multiplies<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:214:31: error: 'MPI_PROD' was not declared in this scope 
   static MPI_Op op() { return MPI_PROD; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<std::logical_and<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:223:31: error: 'MPI_LAND' was not declared in this scope 
   static MPI_Op op() { return MPI_LAND; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<std::logical_or<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:232:31: error: 'MPI_LOR' was not declared in this scope 
   static MPI_Op op() { return MPI_LOR; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<boost::mpi::logical_xor<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:241:31: error: 'MPI_LXOR' was not declared in this scope 
   static MPI_Op op() { return MPI_LXOR; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<boost::mpi::bitwise_and<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:250:31: error: 'MPI_BAND' was not declared in this scope 
   static MPI_Op op() { return MPI_BAND; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<boost::mpi::bitwise_or<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:259:31: error: 'MPI_BOR' was not declared in this scope 
   static MPI_Op op() { return MPI_BOR; }
                               ^
/usr/include/boost/mpi/operations.hpp: In static member function 'static MPI_Op boost::mpi::is_mpi_op<boost::mpi::bitwise_xor<T>, T>::op()': /usr/include/boost/mpi/operations.hpp:268:31: error: 'MPI_BXOR' was not declared in this scope 
   static MPI_Op op() { return MPI_BXOR; }
                               ^
In file included from /usr/include/boost/mpi/allocator.hpp:16:0,
                 from /usr/include/boost/mpi.hpp:22,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/operations.hpp: In constructor 'boost::mpi::detail::user_op<Op, T>::user_op(Op&)': /usr/include/boost/mpi/operations.hpp:279:7: error: 'MPI_Op_create' was not declared in this scope 
       BOOST_MPI_CHECK_RESULT(MPI_Op_create,
       ^
In file included from /usr/include/boost/mpi.hpp:28:0,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/group.hpp: In member function 'boost::mpi::group::operator MPI_Group() const': /usr/include/boost/mpi/group.hpp:133:14: error: 'MPI_GROUP_EMPTY' was not declared in this scope 
       return MPI_GROUP_EMPTY;
              ^
In file included from /usr/include/boost/mpi.hpp:30:0,
from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/common/MPI.h:35, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Mesh.h:40, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/mesh/Cell.h:33, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/function/FunctionSpace.h:38, from /root/software/fenics/fenics-project-dolfin-ac6f9d186802/dolfin/plot/VTKPlottableGenericFunction.cpp:32: /usr/include/boost/mpi/nonblocking.hpp: In function 'std::pair<boost::mpi::status, ForwardIterator> boost::mpi::wait_any(ForwardIterator, ForwardIterator)': /usr/include/boost/mpi/nonblocking.hpp:94:59: error: 'MPI_ERR_REQUEST' was not declared in this scope boost::throw_exception(exception("MPI_Waitany", MPI_ERR_REQUEST)); 
                                                           ^
make[2]: *** [dolfin/CMakeFiles/dolfin.dir/plot/VTKPlottableGenericFunction.cpp.o] Error 1 
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [all] Error 2

/Fredrik



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