I've resisted going up to 10.9 partly to avoid breaking software like macports. Given your comments, will the macports-fenics be abandoned?
-gideon On Oct 26, 2013, at 1:41 PM, Garth N. Wells <[email protected]> wrote: > On 2013-10-25 21:41, Gideon Simpson wrote: >> Thanks for responding, see my comments/queries below >> -gideon >> On Oct 25, 2013, at 2:43 PM, Garth N. Wells <[email protected]> wrote: >>> On 25 Oct 2013, at 20:39, Gideon Simpson <[email protected]> >>> wrote: >>>> Hi, I posted to bitbucket about this, but was curious if anyone >>>> had a solution. I had previously installed (successfully) the >>>> macports fenics on an OS X 10.8.5 machine, and was trying it on a >>>> new one. I've had less success. I end up with the following >>>> errors: >>>> First, I get the following errors during configuration: >>>> -- Try OpenMP C flag = [-fopenmp] >>>> -- Performing Test OpenMP_FLAG_DETECTED >>>> -- Performing Test OpenMP_FLAG_DETECTED - Failed >>>> and likewise for anything involving OpenMP, which surprised me. I >>>> also see: >>> You must be using Clang - it doesn’t support OpenMP. >> Ok. Though the instructions made it a point to install gcc48. So >> shouldn't we be compiling with that? > > DOLFIN builds with Clang, but I would recommend using GCC if you're using > Macports because Macports generally uses GCC to build the libraries that > DOLFIN depends on. > > Make sure you set CC=gcc and CXX=g++. If you're using OpenMPI from Macports, > you might want to also set OMPI_CC=gcc and OMPI_CXX=g++. > >>>> dyld: Symbol not found: __cg_jpeg_resync_to_restart >>>> ImportError: No module named ply.lex >>> Trying installing ‘ply' (py27-ply?) through MacPorts. >> Thanks. >>>> and >>> The below message means you have CGAL 4.3, which just came out and >>> has an interface change. You need to update to the latest DOLFIN or >>> disable CGAL. >> Thanks. Has anyone playing with the macports-fenics done either of >> these things? > > I've just abandoned Macports, partly because it's completely broken with OSX > 10.9. I'm now using Homebrew, and it's worlds better (simpler, faster and > more robust). Homebrew uses the native OSX compiler which avoids many of the > problems encountered with Macports + FEniCS. Homebrew has a good collection > of scientific packages at > > https://github.com/Homebrew/homebrew-science > > Garth > >>> Garth >>> -- Found unsuitable Qt version "" from NOTFOUND >>> -- QT not found, or QT/VTK not enabled in DOLFIN. Not building >>> demo_plot-qt >>> -- Disabling generation of documentation because Sphinx is missing. >>> During the build phase, I get a sequence of errors like: >>> [ 29%] Building CXX object >> dolfin/CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o >>> cd >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/build/dolfin >>> && /opt/local/lib/openmpi/bin/mpicxx -DBOOST_UBLAS_NDEBUG >>> -DDOLFIN_VERSION="1.2.0+" -DHAS_CGAL -DHAS_CHOLMOD -DHAS_CPPUNIT >>> -DHAS_HDF5 -DHAS_MPI -DHAS_PARMETIS -DHAS_PETSC -DHAS_SCOTCH >>> -DHAS_UMFPACK -DHAS_VTK -DHAS_ZLIB -Ddolfin_EXPORTS -pipe -Os -arch >>> x86_64 -pipe -Os -arch x86_64 -Wno-deprecated -DNDEBUG -arch x86_64 >>> -fPIC -isystem /opt/local/include/vtk-5.10 >> -I/opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0 >>> -I/opt/local/include/libxml2 -isystem /opt/local/include -isystem >>> /opt/local/lib/petsc/include -isystem /opt/local/include/eigen3 >>> -isystem /opt/local/include/openmpi -o >>> CMakeFiles/dolfin.dir/generation/ImplicitDomainMeshGenerator.cpp.o >>> -c >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:77:15: >>> error: no template named 'Mesh_cell_base_3' in namespace 'CGAL'; did >>> you mean 'Mesh_vertex_base_3'? >>> typedef CGAL::Mesh_cell_base_3<Geom_traits, Mesh_domain, >>> ~~~~~~^~~~~~~~~~~~~~~~ >>> Mesh_vertex_base_3 >>> /opt/local/include/CGAL/Mesh_vertex_base_3.h:46:7: note: >>> 'Mesh_vertex_base_3' declared here >>> class Mesh_vertex_base_3 >>> ^ >>> In file included from >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:29: >>> In file included from >>> /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:38: >> /opt/local/include/CGAL/Mesh_3/Mesh_complex_3_in_triangulation_3_base.h:61:30: >>> error: no type named 'Subdomain_index' in >> 'CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, C >>> GAL::Epick, CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_vertex_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_vertex_base_3<void> > > >, >> CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Tria >>> ngulation_ds_cell_base_3<void> > > > > > > > >' >>> typedef typename Tr::Cell::Subdomain_index Subdomain_index; >>> ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ >>> /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:48:10: >>> note: in instantiation of template class >> 'CGAL::Mesh_3::Mesh_complex_3_in_triangulation_3_base<CGAL::Regular_triangulation_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_vertex_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_vertex_base_3<void> > > >, >> CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_ >>> traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_cell_base_3<void> > > > > > >' requested here >>> public Mesh_3::Mesh_complex_3_in_triangulation_3_base<Tr> >>> ^ >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:128:17: >>> note: in instantiation of template class >> 'CGAL::Mesh_complex_3_in_triangulation_3<CGAL::Regular_triangulation_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_vertex_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_vertex_base_3<v >>> oid> > > >, >> CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_cell_base_3<void> > > > > >, int, int>' >>> requested here >>> C3t3 c3t3 = build_cgal_triangulation<C3t3>(surface, criteria); >>> ^ >>> In file included from >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/dolfin/generation/ImplicitDomainMeshGenerator.cpp:29: >>> In file included from >>> /opt/local/include/CGAL/Mesh_complex_3_in_triangulation_3.h:38: >> /opt/local/include/CGAL/Mesh_3/Mesh_complex_3_in_triangulation_3_base.h:62:30: >>> error: no type named 'Surface_patch_index' in >> 'CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_ds_cell_base_3<CGAL::Triangulation_data_structure_3<CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>) >>> , CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_vertex_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL::Triangulation_ds_vertex_base_3<void> > > >, >> CGAL::Mesh_vertex_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Mesh_domain_with_polyline_features_3<CGAL::Implicit_mesh_domain_3<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick, >>> CGAL::Mesh_3::Implicit_to_labeled_function_wrapper<const >>> boost::function<double (CGAL::Point_3<CGAL::Epick>)>, CGAL::Epick> > >>>> , CGAL::Triangulation_cell_base_with_info_3<int, >>> CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >> CGAL::Triangulation_cell_base_3<CGAL::Robust_weighted_circumcenter_filtered_traits_3<CGAL::Epick>, >>> CGAL:: >>> Triangulation_ds_cell_base_3<void> > > > > > > > >' >>> typedef typename Tr::Cell::Surface_patch_index Surface_patch_index; >>> ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ >>> /opt/local/bin/cmake -E cmake_progress_report >> /opt/local/var/macports/build/_Users_gideon_code_ports_fenics-macports_dolfin/dolfin/work/dolfin-1.2.0/build/CMakeFiles >>> -gideon >>> _______________________________________________ >>> fenics-support mailing list >>> [email protected] >>> http://fenicsproject.org/mailman/listinfo/fenics-support >> _______________________________________________ >> fenics-support mailing list >> [email protected] >> http://fenicsproject.org/mailman/listinfo/fenics-support
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