Re: [FEniCS-support] macports-fenics and OS X

Sat, 26 Oct 2013 10:42:00 -0700 

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

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