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? > >> 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? > > 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 >
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