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

Sun, 27 Oct 2013 10:24:56 -0700 

On 2013-10-26 19:18, Gideon Simpson wrote:

I've resisted going up to 10.9 partly to avoid breaking software like
macports. Given your comments, will the macports-fenics be abandoned?
I don't anticipate it being officially abandoned, but making it a success will require a few people throwing their efforts behind it. I'm finding Homebrew much easier/better to work with (because it sticks to a single C/C++ compiler), and can't justify spending more time on Macports.
Ideally, we would have good support for Homebrew and Macports. It all depends on demand and willingness to contribute. 

Garth


 -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 [1]

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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Links:
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[1] https://github.com/Homebrew/homebrew-science

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