The problem could be that CMAKE_CXX_FLAGS and CMAKE_EXE_LINKER_FLAGS are
overwritten when you specify them at the command line like I told you in an
earlier post. Instead of doing that, you can add them directly to the main
CMakeLists.txt file like this:
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -L/opt/local/lib -ldmumps")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS -L/opt/local/lib
-ldmumps")
Johannes
On Tue, Sep 1, 2015 at 10:35 AM Gideon Simpson <[email protected]>
wrote:
> I deleted the entire directory, opened the .tar.gz again, and repeated,
> and I got the same error.
>
> -gideon
>
> On Aug 28, 2015, at 6:44 PM, Jan Blechta <[email protected]>
> wrote:
>
> On Fri, 28 Aug 2015 16:30:14 -0400
> Gideon Simpson <[email protected]> wrote:
>
> Now that you mentioned them, I was able to get rid of them by
> switching back to Swig 3.0.5. But I now experience the following
> issues:
>
>
> Try again after removing all build artifacts by
>
> $dolfin-1.5.0> git clean -fdx
>
> or by
>
> $dolfin-1.5.0> cd ../
> $somewhere> rm -rf dolfin-1.5.0
>
> if you are not using git repo. There may be something bad cached.
>
> Jan
>
>
> During cmake, I see:
>
> -- Generating SWIG interface.
> -- --------------------------
> -- Found Qt4: /opt/local/bin/qmake (found version "4.8.7")
> -- QT not found, or QT/VTK not enabled in DOLFIN. Not building
> demo_plot-qt -- Disabling generation of documentation because Sphinx
> is missing. -- Configuring done
> -- Generating done
> -- Build files have been written
> to: /Users/gideonsimpson/software/dolfin-1.5.0/build
>
> I am not sure if that is significant.
>
> But during make, I see the following:
>
> [ 92%] Built target copy_swig_files
> [ 92%] Swig source
> :3: Error: Unable to find 'python.swg'
>
> /Users/gideonsimpson/software/dolfin-1.5.0/build/dolfin/swig/shared_ptr_classes.i:40:
> Error: Unable to find
> 'std_shared_ptr.i'
> /Users/gideonsimpson/software/dolfin-1.5.0/build/dolfin/swig/globalincludes.i:48:
> Error: Unable to find 'std_string.i' make[2]: ***
> [dolfin/swig/modules/mesh/modulePYTHON_wrap.cxx] Error 1 make[1]: ***
> [dolfin/swig/modules/mesh/CMakeFiles/_mesh.dir/all] Error 2 make: ***
> [all] Error 2
>
>
> -gideon
>
> On Aug 28, 2015, at 4:15 PM, Jan Blechta
> <[email protected]> wrote:
>
> Did the CMake message about incompatible SWIG disappear?
>
> Jan
>
>
> On Fri, 28 Aug 2015 15:52:10 -0400
> Gideon Simpson <[email protected]> wrote:
>
> I rebuilt it, again. It builds fine. But there is the same
> problem with python.
>
> -gideon
>
> On Aug 28, 2015, at 3:17 PM, Jan Blechta
> <[email protected]> wrote:
>
> I’m having the same problem as before. here’s the output.
>
>
> I see you're struggling here with invoking cmake. The procedure is
> simple:
>
> $ mkdir build
> $ cd build
> $ cmake <src_dir> [parameters]
>
> thus in your case
>
> $dolfin-1.5.0>
> $dolfin-1.5.0> cd some_build_dir
> $some_build_dir> #rm -rf * # eventually, to start from scratch
> $some_build_dir> cmake .. [other params]
>
>
> gideonsimpson@titan:dolfin-1.5.0$ cmake build/
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin cmake
> -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps" CMake Error: The
> source directory
> "/Users/gideonsimpson/software/dolfin-1.5.0/cmake" does not
> appear to contain CMakeLists.txt. Specify --help for usage, or
> press the help button on the CMake GUI.
> gideonsimpson@titan:dolfin-1.5.0$
> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps"
> gideonsimpson@titan:dolfin-1.5.0$ cmake build/
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> cmake -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps"
> gideonsimpson@titan:dolfin-1.5.0$ cmake build/
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> gideonsimpson@titan:dolfin-1.5.0$ mkdir build2
> gideonsimpson@titan:dolfin-1.5.0$ cmake build2/
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps" CMake Error: The
> source directory
> "/Users/gideonsimpson/software/dolfin-1.5.0/build2" does not
> appear to contain CMakeLists.txt. Specify --help for usage, or
> press the help button on the CMake GUI.
> gideonsimpson@titan:dolfin-1.5.0$
> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps"
> gideonsimpson@titan:dolfin-1.5.0$ cd build2/
> gideonsimpson@titan:build2$ cmake
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps"
> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps"
> gideonsimpson@titan:build2$ cmake gideonsimpson@titan:build2$
> cd .. gideonsimpson@titan:dolfin-1.5.0$ cmake build2
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps"
> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps" CMake
> Error: The source directory
> "/Users/gideonsimpson/software/dolfin-1.5.0/build2" does not
> appear to contain CMakeLists.txt. Specify --help for usage, or
> press the help button on the CMake GUI.
> gideonsimpson@titan:dolfin-1.5.0$ cd build2/
> gideonsimpson@titan:build2$ cd ..
> gideonsimpson@titan:dolfin-1.5.0$ cmake build/
> -DCMAKE_INSTALL_PREFIX=/Users/gideonsimpson/software/dolfin
> -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps"
> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps" fatal: Not
> a git repository (or any of the parent directories): .git --
> Checking whether Fortran compiler has -isysroot -- Checking
> whether Fortran compiler has -isysroot - yes -- Checking whether
> Fortran compiler supports OSX deployment target flag -- Checking
> whether Fortran compiler supports OSX deployment target flag -
> yes -- Try OpenMP C flag = [ ] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-fopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [/openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-Qopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-xopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [+Oopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-qsmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-mp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [ ] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [/openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-Qopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-xopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [+Oopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-qsmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP CXX flag = [-mp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Could NOT find OpenMP (missing: OpenMP_C_FLAGS
> OpenMP_CXX_FLAGS) -- Try OpenMP C flag = [ ] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-fopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [/openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-Qopenmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-openmp] -- Performing Test
> OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED -
> Failed -- Try OpenMP C flag = [-xopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP C flag = [+Oopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP C flag = [-qsmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP C flag = [-mp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [ ]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-fopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [/openmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-Qopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-openmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-xopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [+Oopenmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-qsmp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Try OpenMP CXX flag = [-mp]
> -- Performing Test OpenMP_FLAG_DETECTED
> -- Performing Test OpenMP_FLAG_DETECTED - Failed
> -- Could NOT find OpenMP (missing: OpenMP_C_FLAGS
> OpenMP_CXX_FLAGS) -- Boost version: 1.59.0
> -- Found the following Boost libraries:
> -- filesystem
> -- program_options
> -- system
> -- thread
> -- iostreams
> -- UFC version: 1.5.0
> -- Checking for package 'PETSc'
> -- PETSC_DIR is /opt/local/lib/petsc
> -- PETSC_ARCH is empty
> -- Found petscconf.h
> -- Unable to find library gfortran
> -- Performing test PETSC_TEST_RUNS - Success
> -- PETSc configured without Cusp support
> -- Checking for package 'PETSc4Py'
> -- PETSc4py could not be found. Be sure to set PYTHONPATH
> appropriately. (missing: PETSC4PY_INCLUDE_DIRS PETSC4PY_VERSION)
> -- Checking for package 'SLEPc' -- SLEPC_DIR
> is /opt/local/lib/slepc -- Performing test SLEPC_TEST_RUNS -
> Success -- Checking for package 'SLEPc4Py'
> -- SLEPc4py could not be found. Be sure to set PYTHONPATH
> appropriately. (missing: SLEPC4PY_INCLUDE_DIRS SLEPC4PY_VERSION
> SLEPC4PY_VERSION_OK) (Required is at least version "3.5.1") --
> Checking for package 'SCOTCH-PT' -- Found SCOTCH (version 6) --
> Performing test SCOTCH_TEST_RUNS -- Performing test
> SCOTCH_TEST_RUNS
> - Success -- Checking for package 'AMD'
> -- Checking for package 'UMFPACK'
> -- Checking for package 'AMD'
> -- Checking for package 'CHOLMOD'
> -- Checking for package 'AMD'
> -- A library with BLAS API found.
> -- Checking for package 'CHOLMOD'
> -- Checking for package 'AMD'
> -- A library with BLAS API found.
> -- HDF5 has been found, but is missing parallel support. It will
> not be enabled. -- A library with BLAS API found.
> -- PaStiX could not be found. Be sure to set PASTIX_DIR.
> (missing: PASTIX_INCLUDE_DIRS PASTIX_TEST_RUNS PASTIX_VERSION
> PASTIX_VERSION_OK) -- Checking for Trilinos -- Unable to find
> Trilinos (>= 11.0.0) -- Trilinos could not be found
> -- checking for module 'cppunit'
> -- package 'cppunit' not found
> -- CPPUNIT could not be found. Be sure to set CPPUNIT_DIR.
> (missing: CPPUNIT_LIBRARIES CPPUNIT_INCLUDE_DIRS) -- Checking for
> package 'Sphinx' -- Could NOT find Sphinx (missing:
> SPHINX_EXECUTABLE SPHINX_VERSION_OK) (Required is at least
> version "1.1.0") -- Found Qt4: /opt/local/bin/qmake (found
> version "4.8.7") -- Found VTK: /opt/local/lib/vtk-5.10 (found
> version "5.10") -- -- The following optional packages were found:
> -- -------------------------------------------
> -- (OK) MPI
> -- (OK) PETSC
> -- (OK) SLEPC
> -- (OK) UMFPACK
> -- (OK) CHOLMOD
> -- (OK) SCOTCH
> -- (OK) PARMETIS
> -- (OK) ZLIB
> -- (OK) PYTHON
> -- (OK) VTK
> -- (OK) QT
> --
> -- The following optional packages were not found:
> -- -----------------------------------------------
> -- (**) OPENMP
> -- (**) PETSC4PY
> -- (**) SLEPC4PY
> -- (**) TRILINOS
> -- (**) PASTIX
> -- (**) SPHINX
> -- (**) HDF5
> --
> -- QVTK not found, disabling QT for plotting
> CMake Warning at dolfin/CMakeLists.txt:317 (message):
> UFC compiled with different version of SWIG. Please install SWIG
> version 3.0.5 or recompile UFC with present SWIG.
>
>
> Here's the actual problem. That's why Python extension has not
> been built. You need to consolidate your SWIG versions on the
> system and use the same for compiling FFC and DOLFIN.
>
> Try locating SWIG 3.0.5 used for FFC and specify it as
> SWIG_EXECUTABLE to cmake.
>
> Jan
>
>
>
> -- Found Qt4: /opt/local/bin/qmake (found version "4.8.7")
> -- QT not found, or QT/VTK not enabled in DOLFIN. Not building
> demo_plot-qt -- Disabling generation of documentation because
> Sphinx is missing. -- Configuring done
> -- Generating done
> -- Build files have been written
> to: /Users/gideonsimpson/software/dolfin-1.5.0/build
>
>
>
>
> _______________________________________________
> fenics-support mailing list
> [email protected]
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>
>
> _______________________________________________
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>
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