Dorsal installation fails on Snow Leopard

[Sergey Alyaev]

I tried installing Fenics on Mac OS Snow leopard using Dorsal following all the installation steps.
During the installation I get a warning wich causes a error of installation, here is the log:

Fatal Python error: Interpreter not initialized (version mismatch?)
CMake Warning at dolfin/CMakeLists.txt:233 (message):
  Unable to import UFC. Install latest UFC or check that PYTHONPATH is set
  appropriately. Python will be disabled.

-- Configuring done
-- Generating done
-- Build files have been written to: /Users/aliner/Work/FEniCS/src/dolfin-0.9.9/dorsal_build_dir
Scanning dependencies of target dolfin
[ 1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/graph/GraphBuilder.cpp.o
[ 1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/graph/SCOTCH.cpp.o
[ 1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/DefaultFactory.cpp.o
[ 1%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/EpetraVector.cpp.o
[ 2%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScFactory.cpp.o
[ 2%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovMatrix.cpp.o
[ 2%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScKrylovSolver.cpp.o
[ 4%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScLUSolver.cpp.o
[ 4%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScMatrix.cpp.o
[ 5%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScPreconditioner.cpp.o
[ 5%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScUserPreconditioner.cpp.o
[ 5%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/PETScVector.cpp.o
[ 5%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/SLEPcEigenSolver.cpp.o
[ 6%] Building CXX object dolfin/CMakeFiles/dolfin.dir/la/uBLASVector.cpp.o
[ 8%] Building CXX object dolfin/CMakeFiles/dolfin.dir/main/SubSystemsManager.cpp.o
Linking CXX shared library libdolfin.dylib
Undefined symbols:
  "boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
  "typeinfo for boost::program_options::value_semantic_codecvt_helper<char>", referenced from:
      typeinfo for boost::program_options::typed_value<int, char>in Parameters.cpp.o
      typeinfo for boost::program_options::typed_value<bool, char>in Parameters.cpp.o
      typeinfo for boost::program_options::typed_value<double, char>in Parameters.cpp.o
      typeinfo for boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>in Parameters.cpp.o
  "vtable for boost::program_options::value_semantic_codecvt_helper<char>", referenced from:
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>* boost::program_options::value<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::basic_string<char, std::char_traits<char>, std::allocator<char> >*)in Parameters.cpp.o
      boost::program_options::typed_value<double, char>* boost::program_options::value<double>(double*)in Parameters.cpp.o
      boost::program_options::typed_value<bool, char>* boost::program_options::value<bool>(bool*)in Parameters.cpp.o
      boost::program_options::typed_value<int, char>* boost::program_options::value<int>(int*)in Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<double, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<double, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<int, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<int, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<int, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<int, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<double, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<double, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::~typed_value()in Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::~typed_value()in Parameters.cpp.o
  "boost::program_options::abstract_variables_map::operator[](std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const", referenced from:
      dolfin::Parameters::read_vm(boost::program_options::variables_map&, dolfin::Parameters&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in Parameters.cpp.o
      dolfin::Parameters::read_vm(boost::program_options::variables_map&, dolfin::Parameters&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in Parameters.cpp.o
      dolfin::Parameters::read_vm(boost::program_options::variables_map&, dolfin::Parameters&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in Parameters.cpp.o
      dolfin::Parameters::read_vm(boost::program_options::variables_map&, dolfin::Parameters&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >)in Parameters.cpp.o
  "vtable for boost::program_options::validation_error", referenced from:
      boost::program_options::validation_error::validation_error(boost::program_options::validation_error const&)in Parameters.cpp.o
      boost::program_options::validation_error::~validation_error()in Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::rethrow() constin Parameters.cpp.o
      boost::exception_detail::error_info_injector<boost::program_options::validation_error>::~error_info_injector()in Parameters.cpp.o
      boost::program_options::invalid_option_value::~invalid_option_value()in Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::rethrow() constin Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::rethrow() constin Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::clone() constin Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::clone() constin Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::clone() constin Parameters.cpp.o
      boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::clone() constin Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      std::basic_string<char, std::char_traits<char>, std::allocator<char> > const& boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool)in Parameters.cpp.o
      void boost::program_options::validate<double, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)in Parameters.cpp.o
      void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)in Parameters.cpp.o
      boost::program_options::invalid_option_value::~invalid_option_value()in Parameters.cpp.o
      boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>::~error_info_injector()in Parameters.cpp.o
  "boost::program_options::options_description_easy_init::operator()(char const*, boost::program_options::value_semantic const*, char const*)", referenced from:
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
  "boost::program_options::invalid_option_value::invalid_option_value(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
      void boost::program_options::validate<double, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)in Parameters.cpp.o
      void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)in Parameters.cpp.o
  "boost::program_options::operator<<(std::basic_ostream<char, std::char_traits<char> >&, boost::program_options::options_description const&)", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::arg", referenced from:
      boost::program_options::typed_value<int, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<int, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<bool, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<double, char>::name() constin Parameters.cpp.o
      boost::program_options::typed_value<double, char>::name() constin Parameters.cpp.o
  "boost::program_options::notify(boost::program_options::variables_map&)", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::detail::cmdline::cmdline(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)", referenced from:
      boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int, char**)in Parameters.cpp.o
  "boost::program_options::validation_error::what() const", referenced from:
      vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>in Parameters.cpp.o
      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >in Parameters.cpp.o
      vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>in Parameters.cpp.o
      vtable for boost::program_options::invalid_option_valuein Parameters.cpp.o
      vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >in Parameters.cpp.o
  "boost::program_options::options_description::m_default_line_length", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool) const", referenced from:
      vtable for boost::program_options::typed_value<int, char>in Parameters.cpp.o
      vtable for boost::program_options::typed_value<bool, char>in Parameters.cpp.o
      vtable for boost::program_options::typed_value<double, char>in Parameters.cpp.o
      vtable for boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>in Parameters.cpp.o
  "boost::program_options::validate(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)", referenced from:
      boost::program_options::typed_value<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) constin Parameters.cpp.o
  "typeinfo for boost::program_options::validation_error", referenced from:
      typeinfo for boost::exception_detail::error_info_injector<boost::program_options::validation_error>in Parameters.cpp.o
      typeinfo for boost::program_options::invalid_option_valuein Parameters.cpp.o
  "boost::program_options::options_description::add_options()", referenced from:
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::add_parameter_set_to_po(boost::program_options::options_description&, dolfin::Parameters const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> >) constin Parameters.cpp.o
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "vtable for boost::program_options::variables_map", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::detail::cmdline::set_options_description(boost::program_options::options_description const&)", referenced from:
      boost::program_options::basic_command_line_parser<char>::options(boost::program_options::options_description const&)in Parameters.cpp.o
  "boost::program_options::to_internal(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)", referenced from:
      std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > boost::program_options::to_internal<std::basic_string<char, std::char_traits<char>, std::allocator<char> > >(std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&)in Parameters.cpp.o
  "boost::program_options::validate(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, bool*, int)", referenced from:
      boost::program_options::typed_value<bool, char>::xparse(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&) constin Parameters.cpp.o
  "boost::program_options::validators::check_first_occurrence(boost::any const&)", referenced from:
      void boost::program_options::validate<double, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, double*, long)in Parameters.cpp.o
      void boost::program_options::validate<int, char>(boost::any&, std::vector<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::basic_string<char, std::char_traits<char>, std::allocator<char> > > > const&, int*, long)in Parameters.cpp.o
  "boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)", referenced from:
      boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)in Parameters.cpp.o
  "boost::program_options::detail::cmdline::run()", referenced from:
      boost::program_options::basic_command_line_parser<char>::run() in Parameters.cpp.o
  "boost::program_options::variables_map::variables_map()", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::options_description_easy_init::operator()(char const*, char const*)", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::options_description::options_description(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned int)", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::store(boost::program_options::basic_parsed_options<char> const&, boost::program_options::variables_map&, bool)", referenced from:
      dolfin::Parameters::parse_dolfin(int, char**)in Parameters.cpp.o
  "boost::program_options::detail::cmdline::style(int)", referenced from:
      boost::program_options::basic_command_line_parser<char>::style(int)in Parameters.cpp.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [dolfin/libdolfin.0.9.9.dylib] Error 1
make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2
make: *** [all] Error 2
Failure with exit status: 2
Exit message: There was a problem building dolfin-0.9.9.

Here is what Dorsal required from me at startup and all of it was successfully processed:
 Via Macports, you need to install the following packages:

 sudo port install wget autogen readline pkgconfig libxml2 libtool \
 cgal gmp zlib python26 swig-python py26-numpy bzr bzrtools git-core \
 ginac boost +python26 vtk-devel +python26 suitesparse \
 py26-scientific cppunit

 Before proceeding, you need to make sure that Python 2.6 installed
 by MacPorts is the default one on your machine:

 sudo port install python_select
 sudo python_select python26

[Harish Narayanan (hnarayanan)]

Does any Boost expert see the problem with MacPorts' Boost?

[Sergey Alyaev (cobxo3bot)]

After cleaning macPorts and installing everything from scratch over again I have got a slightly different error message which hoever still has something to do with either PYTHONPATH or UFC:

Building dolfin-0.9.9
-- Checking for package 'Armadillo'
CMake Error: Generator: execution of make failed. Make command was: /opt/local/bin/gmake "cmTryCompileExec/fast"
-- Checking for package 'SCOTCH-PT'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'UMFPACK'
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'LAPACK'
-- Found CHOLMOD: /opt/local/include/ufsparse
-- Found CHOLMOD: /opt/local/lib/libcholmod.a;/opt/local/lib/libamd.a;/opt/local/lib/libcamd.a;/opt/local/lib/libcolamd.a;/opt/local/lib/libccolamd.a;/usr/lib/libatlas.dylib;/Users/aliner/Work/FEniCS/lib/libparmetis.a;/opt/local/lib/libmetis.dylib;/usr/lib/liblapack.dylib
-- Checking for package 'Trilinos'
-- Checking for package 'MTL4'
-- Checking for package 'BLAS'
-- Checking for package 'PETSc'
-- PETSC_DIR is /Users/aliner/Work/FEniCS/src/petsc-3.1-p4
-- PETSC_ARCH is darwin10.0.0-cxx-opt
-- Found petscconf.h
CMake Error at cmake/modules/FindPETSc.cmake:120 (string):
  string sub-command REPLACE requires at least four arguments.
Call Stack (most recent call first):
  CMakeLists.txt:221 (find_package)

-- PETSc test runs
-- PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH. (missing: PETSC_INCLUDE_DIRS PETSC_LIBRARIES)
-- Checking for package 'CGAL'
-- Checking for package 'CPPUNIT'
--
-- The following optional packages were found:
-- -------------------------------------------
-- (OK) MPI
-- (OK) MTL4
-- (OK) UMFPACK
-- (OK) CHOLMOD
-- (OK) SCOTCH
-- (OK) PARMETIS
-- (OK) CGAL
-- (OK) ZLIB
-- (OK) PYTHON
--
-- The following optional packages were not enabled:
-- -------------------------------------------------
-- (--) GMP
--
-- The following optional packages could not be found:
-- ---------------------------------------------------
-- (**) PETSC
-- (**) SLEPC
-- (**) TRILINOS
--
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: No module named ufc
CMake Warning at dolfin/CMakeLists.txt:233 (message):
  Unable to import UFC. Install latest UFC or check that PYTHONPATH is set
  appropriately. Python will be disabled.

-- Configuring incomplete, errors occurred!
Failure with exit status: 1
Exit message: There was a problem building dolfin-0.9.9.

[Sergey Alyaev (cobxo3bot)]

Sorry,

The error message that I posted previously was a bit wrong as it turns out that it used parts of pacage-installed FEniCS.
After disabling it the compilation was still unsuccessful but with a slightly different errors:

Building dolfin-0.9.9
-- The C compiler identification is GNU
-- The CXX compiler identification is GNU
-- Checking whether C compiler has -isysroot
-- Checking whether C compiler has -isysroot - yes
-- Checking whether C compiler supports OSX deployment target flag
-- Checking whether C compiler supports OSX deployment target flag - yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Checking whether CXX compiler has -isysroot
-- Checking whether CXX compiler has -isysroot - yes
-- Checking whether CXX compiler supports OSX deployment target flag
-- Checking whether CXX compiler supports OSX deployment target flag - yes
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Performing Test HAVE_PIPE
-- Performing Test HAVE_PIPE - Success
-- Performing Test HAVE_PEDANTIC
-- Performing Test HAVE_PEDANTIC - Success
-- Performing Test HAVE_STD
-- Performing Test HAVE_STD - Success
-- Performing Test HAVE_DEBUG
-- Performing Test HAVE_DEBUG - Success
-- Performing Test HAVE_O2_OPTIMISATION
-- Performing Test HAVE_O2_OPTIMISATION - Success
-- Boost version: 1.45.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- Checking for package 'Armadillo'
-- Performing Test ARMADILLO_TEST_RUNS
-- Performing Test ARMADILLO_TEST_RUNS - Success
-- Found Armadillo: TRUE
-- Found LibXml2: /opt/local/lib/libxml2.dylib
-- Found PythonInterp: /opt/local/bin/python2.7
-- Found PythonLibs: /opt/local/lib/libpython2.7.dylib
-- NumPy headers found
-- Found SWIG: /opt/local/bin/swig (found version "2.0.1")
-- Found MPI: /usr/lib/libmpi_cxx.dylib
-- Performing Test PARMETIS_TEST_RUNS
-- Performing Test PARMETIS_TEST_RUNS - Success
-- Found ParMETIS: 1
-- Checking for package 'SCOTCH-PT'
-- Found SCOTCH: /Users/aliner/Work/FEniCS/include
-- Checking for package 'AMD'
-- Found AMD: /opt/local/include/ufsparse
-- Checking for package 'BLAS'
-- Found BLAS: /System/Library/Frameworks/vecLib.framework/Headers
-- Checking for package 'UMFPACK'
-- Performing Test UMFPACK_TEST_RUNS
-- Performing Test UMFPACK_TEST_RUNS - Success
-- Found UMFPACK: /opt/local/include/ufsparse
-- Checking for package 'CHOLMOD'
-- Checking for package 'AMD'
-- Checking for package 'BLAS'
-- Checking for package 'LAPACK'
-- Found LAPACK: /usr/lib/liblapack.dylib
-- Performing Test CHOLMOD_TEST_RUNS
-- Performing Test CHOLMOD_TEST_RUNS - Success
-- Found CHOLMOD: /opt/local/include/ufsparse
-- Found CHOLMOD: /opt/local/lib/libcholmod.a;/opt/local/lib/libamd.a;/opt/local/lib/libcamd.a;/opt/local/lib/libcolamd.a;/opt/local/lib/libccolamd.a;/usr/lib/libatlas.dylib;/Users/aliner/Work/FEniCS/lib/libparmetis.a;/opt/local/lib/libmetis.dylib;/usr/lib/liblapack.dylib
-- Checking f...

[Harish Narayanan (hnarayanan)]

This is a known error (I think). It has something to do with UFC being installed in python2.7 site-packages while the rest of the FEniCS stuff goes into the python2.6 site-packages folder.

Could you help him, Andre?

[Fredrik Valdmanis (fredva)]

I get a similar error when using dorsal, choosing to build unstable packages. Dorsal completes, but importing dolfin afterwards fails with the following error:

fredva:FEniCS$ python -c "import dolfin"
Fatal Python error: Interpreter not initialized (version mismatch?)
[ves2-1x-dhcp385:35191] *** Process received signal ***
[ves2-1x-dhcp385:35191] Signal: Abort trap (6)
[ves2-1x-dhcp385:35191] Signal code: (0)
[ves2-1x-dhcp385:35191] [ 0] 2 libSystem.B.dylib 0x00007fff8061067a _sigtramp + 26
[ves2-1x-dhcp385:35191] [ 1] 3 ??? 0x0000000101146990 0x0 + 4313082256
[ves2-1x-dhcp385:35191] [ 2] 4 Python 0x0000000101f98ce1 Py_FatalError + 49
[ves2-1x-dhcp385:35191] [ 3] 5 Python 0x0000000101f941dc Py_InitModule4_64 + 396
[ves2-1x-dhcp385:35191] [ 4] 6 _cpp.so 0x00000001013d6a0c init_cpp + 268
[ves2-1x-dhcp385:35191] [ 5] 7 Python 0x00000001000d3911 _PyImport_LoadDynamicModule + 177
[ves2-1x-dhcp385:35191] [ 6] 8 Python 0x00000001000d3228 imp_load_module + 184
[ves2-1x-dhcp385:35191] [ 7] 9 Python 0x00000001000b8d48 PyEval_EvalFrameEx + 28696
[ves2-1x-dhcp385:35191] [ 8] 10 Python 0x00000001000b7eea PyEval_EvalFrameEx + 25018
[ves2-1x-dhcp385:35191] [ 9] 11 Python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
[ves2-1x-dhcp385:35191] [10] 12 Python 0x00000001000b9c16 PyEval_EvalCode + 54
[ves2-1x-dhcp385:35191] [11] 13 Python 0x00000001000ceac0 PyImport_ExecCodeModuleEx + 208
[ves2-1x-dhcp385:35191] [12] 14 Python 0x00000001000cfd22 load_source_module + 722
[ves2-1x-dhcp385:35191] [13] 15 Python 0x00000001000d1bcf import_submodule + 383
[ves2-1x-dhcp385:35191] [14] 16 Python 0x00000001000d20ea load_next + 234
[ves2-1x-dhcp385:35191] [15] 17 Python 0x00000001000d243e PyImport_ImportModuleLevel + 430
[ves2-1x-dhcp385:35191] [16] 18 Python 0x00000001000af973 builtin___import__ + 131
[ves2-1x-dhcp385:35191] [17] 19 Python 0x000000010000b902 PyObject_Call + 98
[ves2-1x-dhcp385:35191] [18] 20 Python 0x00000001000b0bb7 PyEval_CallObjectWithKeywords + 87
[ves2-1x-dhcp385:35191] [19] 21 Python 0x00000001000b4e7e PyEval_EvalFrameEx + 12622
[ves2-1x-dhcp385:35191] [20] 22 Python 0x00000001000b9af5 PyEval_EvalCodeEx + 2197
[ves2-1x-dhcp385:35191] [21] 23 Python 0x00000001000b9c16 PyEval_EvalCode + 54
[ves2-1x-dhcp385:35191] [22] 24 Python 0x00000001000ceac0 PyImport_ExecCodeModuleEx + 208
[ves2-1x-dhcp385:35191] [23] 25 Python 0x00000001000cfd22 load_source_module + 722
[ves2-1x-dhcp385:35191] [24] 26 Python 0x00000001000d1bcf i...

[Johannes Ring (johannr)]

In the latest Dorsal (lp:dorsal) Python 2.7 from MacPorts is used as the default Python. To use a different Python version one must define the CMake variables PYTHON_EXECUTABLE and PYTHON_LIBRARIES when building UFC and DOLFIN. This can be done by adding the following to the CONFOPTS variable in the respective .package file in Dorsal:

  -DPYTHON_EXECUTABLE:FILEPATH=/opt/local/bin/python2.6 -DPYTHON_LIBRARY:FILEPATH=/opt/local/lib/libpython2.6.dylib

Note that one must also adjust these variables for Trilinos if Dorsal is set to build this package.

[Sergey Alyaev (cobxo3bot)]

Sorry for a stupid question, but can you, please, provide a step-by-step explanation.
I am not quite sure what exactly I am supposed to add to .package files.
Is it just these to lines or something with CONFOPTS?

[Johannes Ring (johannr)]

First, please make sure you have the latest Dorsal. You can check out the development version from Launchpad by running

  bzr branch lp:dorsal

If your are fine with running Python 2.7 then simply run dorsal.sh as normally and follow the instructions. This is the recommended approach.

If you for some reason needs to use a different version of Python then you will need to tweak some files before running Dorsal. These files are ufc.package, dolfin.package, and trilinos.package and they are all located under the FEniCS/packages subdirectory. What you need to do is to add

  -DPYTHON_EXECUTABLE:FILEPATH=/opt/local/bin/python2.6

and

  -DPYTHON_LIBRARY:FILEPATH=/opt/local/lib/libpython2.6.dylib

to the CONFOPTS variable in these files (assuming you want to use Python 2.6 from MacPorts). Note that the ufc.package file does not contain the CONFOPTS variable so you need to create it by yourself. Look in dolfin.package and trilinos.package if you are unsure on how to do it. Finally run dorsal.sh but make sure you select your desired Python version by running 'python_select' first.

[Sergey Alyaev (cobxo3bot)]

I was trying to install from release version rather then development version before. And that version was suggesting using python26.
I tried installing from development version this time and the installation fails with the following message:

-- Boost version: 1.45.0
-- Found the following Boost libraries:
-- filesystem
-- program_options
-- system
-- Checking for package 'Armadillo'
-- Performing Test ARMADILLO_TEST_RUNS
-- Performing Test ARMADILLO_TEST_RUNS - Failed
-- Checking for package 'LAPACK'
-- Found LAPACK: /usr/lib/liblapack.dylib
-- Performing Test ARMADILLO_LAPACK_TEST_RUNS
-- Performing Test ARMADILLO_LAPACK_TEST_RUNS - Failed
CMake Error at /opt/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:91 (MESSAGE):
  Armadillo could not be found. Be sure to set ARMADILLO_DIR. (missing:
  ARMADILLO_TEST_RUNS)
Call Stack (most recent call first):
  /opt/local/share/cmake-2.8/Modules/FindPackageHandleStandardArgs.cmake:252 (_FPHSA_FAILURE_MESSAGE)
  cmake/modules/FindArmadillo.cmake:139 (find_package_handle_standard_args)
  CMakeLists.txt:156 (find_package)

-- Configuring incomplete, errors occurred!
Failure with exit status: 1
Exit message: There was a problem configuring dolfin-0.9.9.

I have also tried changing CONFOPTS as Johannes suggested but this does not work either. But I fell that I need to change dependent packages to python26 as well and not follow Dorsal's step-by-step manual.

[Johannes Ring (johannr)]

Try to let Dorsal build the unstable FEniCS packages by setting STABLE_BUILD=false in dorsal.cfg.

[Sergey Alyaev (cobxo3bot)]

Thank you, Johannes!
I managed to install it with your help: however there are a few questions that remain unanswered:

-What does it mean for me that the built is not stable?
-Having installed it now with dorsal I have the same problem that I had using the pacage installation, namely it says:

*** Warning: PETSc has not been compiled with the HYPRE library for algebraic multigrid. Default PETSc solver will be used. For performance, installation of HYPRE is recommended.

which was a reason for me to use Dorsal installation. Can I do something about it?

[Garth Wells (garth-wells)]

On 15/02/11 13:39, Sergey Alyaev wrote:
> Thank you, Johannes!
> I managed to install it with your help: however there are a few questions that remain unanswered:
>
> -What does it mean for me that the built is not stable?

"STABLE = false" means that the development version of the FEniCS
packages are used. These have quite a few build fixes.

> -Having installed it now with dorsal I have the same problem that I had using the pacage installation, namely it says:
>
> *** Warning: PETSc has not been compiled with the HYPRE library for
> algebraic multigrid. Default PETSc solver will be used. For performance,
> installation of HYPRE is recommended.
>
> which was a reason for me to use Dorsal installation. Can I do something
> about it?
>

The problem here is the Fortran compilers that ship with OSX, and Hypre
requires a Fortran compiler. If you want AMG, try using the Epetra backend,

  parameters["linear_algebra_backend"] = "Epetra";

Harish: what the latest on using maybe using Fortran from MacPorts?

Garth

[Sergey Alyaev (cobxo3bot)]

Where should I specify that parameter?
Does it require any extras installed on the system?

[Garth Wells (garth-wells)]

On 15/02/11 14:36, Sergey Alyaev wrote:
> Where should I specify that parameter?

Just at the top of your programs.

> Does it require any extras installed on the system?
>

Sorry - looks like Trilinos/Epetra is disabled for Snow Leopard via Dorsal.

Harish: any reason for this?

Garth

[Harish Narayanan (hnarayanan)]

Trilinos is disabled because I haven't gotten gfortran from MacPorts to work. The only person I know who's actually done this is Andre Massing, but he's rebuilt everything (GCC, OpenMPI etc.) in some weird mix of MacPorts and by hand.

He can help Sergey if this is really important, but I don't want to make it the default for Snow Leopard and have to support it.

[Garth Wells (garth-wells)]

On 15/02/11 15:46, Harish Narayanan wrote:
> Trilinos is disabled because I haven't gotten gfortran from MacPorts to
> work.

Does Trilinos require Fortran?

> The only person I know who's actually done this is Andre Massing,
> but he's rebuilt everything (GCC, OpenMPI etc.) in some weird mix of
> MacPorts and by hand.
>
> He can help Sergey if this is really important, but I don't want to make
> it the default for Snow Leopard and have to support it.
>

[Harish Narayanan (hnarayanan)]

I thought the default build wanted it. Perhaps this can be disabled using some flag as in petsc.

[Johannes Ring (johannr)]

Fortran is disabled in trilinos.package.

[Harish Narayanan (hnarayanan)]

So, do you know if it works without gfortran?

[Johannes Ring (johannr)]

I tried to build Trilinos with Dorsal on Mac but it fails when building PyTrilinos (see error in attachment).

[Andre Massing (massing)]

Den 16.02.11 11.14, skrev Johannes Ring:
> I tried to build Trilinos with Dorsal on Mac but it fails when building
> PyTrilinos (see error in attachment).
>
> ** Attachment added: "pytrilinos-error.log"
> https://bugs.launchpad.net/dorsal/+bug/704076/+attachment/1853394/+files/pytrilinos-error.log
>

I tried also to compile trilinos on my mac machine and ran into the
exactly same problem.

--
André Massing email: <email address hidden>
Ph.D. student mobile: [phone]
Simula Research Laboratory
NO-1367 Fornebu, Norway

[Sergey Alyaev (cobxo3bot)]

I have installed FEniCS on ubuntu in VirtualBox on Mac

Then, if I delete disc and graphical output from Navier-Stokes Demo it has 2 times faster performance with multigrid on virtual machine. I assume that the difference would be even more noticeable on larger tests.

PS: it is quite disappointing to use without multigrid.

Garth,

>> Where should I specify that parameter?
> Just at the top of your programs.
It does not work saying:

  File "demo2.py", line 15, in <module>
    parameters["linear_algebra_backend"] = "Epetra";
  File "/Users/aliner/Work/FEniCS/lib/python2.7/site-packages/dolfin/cpp.py", line 2107, in __setitem__
    par._assign(value)
RuntimeError: *** Error: Illegal value for parameter. Allowed values are: [MTL4, PETSc, STL, uBLAS]

[Anders Logg (logg)]

The reason is obvious: You have not compiled DOLFIN with Trilinos support so the Trilinos backed is not available (only MTL4, uBLAS, PETSc, STL).

[Sergey Alyaev (cobxo3bot)]

It is obvious, but from the conversation it seems that there is no straightforward way to compile it with Trilinos on Mac.

[Sergey Alyaev (cobxo3bot)]

What does the fix change?

[Harish Narayanan (hnarayanan)]

I defaulted to Python 2.7 on Snow Leopard, which fixes the original bug that Dorsal fails to build FEniCS.

(This does not fix your problem regarding hypre for petsc nor does it add trilinos support on Snow Leopard. Please register a separate bug for either of those if their functionality is critical for you. The discussion under this current bug report is being side-tracked into too many different things.)