Dear all, I managed to compile all packages as specified in the dorsal lion.package file and dorsal reports all is well. Unfortunately, the import of dolfin in python fails:
Python 2.7.5 (default, Aug 24 2013, 04:50:09) [GCC 4.2.1 Compatible Apple Clang 3.0 (tags/Apple/clang-211.12)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> from dolfin import * Fatal Python error: Interpreter not initialized (version mismatch?) Abort trap: 6 I am using which python /opt/local/bin/python which I think is supposed to be the correct (Mac Ports) Version of python. Any help is greatly appreciated. Regards, Stephan On 12 Sep 2013, at 16:03, Garth N. Wells wrote: > On 12 September 2013 15:22, Schmidt, Stephan <[email protected]> wrote: >> Thank you for your support! Just a quick clarification: Are you referring to >> the development version of FEniCS that can be enabled in dorsal.cfg > > Yes, but I don't use Dorsal. I install manually (cloning each of the > FEniCS projects). > > (I have been using that and it gives the same error messages) or is > there also a development version of dorsal? >> > > You can also get a development version of Dorsal at > https://bitbucket.org/fenics-project/dorsal. > > Garth > >> A MacPorts port would be much appreciated! >> >> Regards, >> Stephan Schmidt >> >> Am 12.09.2013 um 14:20 schrieb "Garth N. Wells" <[email protected]>: >> >>> I'd recommend using the development version - it has quite a few build >>> fixes for OSX. >>> >>> I build DOLFIN under OSX 10.8, but I don't use Dorsal. You can get >>> almost everything you need from Macports. To make it work, I: >>> >>> 1. Install all the available dependencies via Macports >>> 2. Set default gcc/g++ to GCC 4.7 or 4.8 (there is a Macports command >>> that is easy to find on the net, but I don't recall it) >>> 3. Set default Python toy python2.7 via Macports >>> 4. Set compiler variables: >>> >>> export OMPI_CC=gcc >>> export OMPI_CXX=g++ >>> export CXX=g++ >>> export CC=gcc >>> >>> From memory, the only Macports package that may give you trouble is >>> Armadillo, which you may need to installed by hand. >>> >>> There is a Macports 'port' in the works. >>> >>> Garth >>> >>> On 12 September 2013 12:05, Schmidt, Stephan <[email protected]> >>> wrote: >>>> Dear all, >>>> >>>> I was re-directed here after posting an installation specific question >>>> here: >>>> http://fenicsproject.org/qa/1186/how-to-build-and-install-fenics-using-dorsal-on-osx-10-7 >>>> >>>> In the meantime, I figured out that these error messages: >>>> >>>> Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/adapt.cpp.o >>>> In file included from /opt/local/include/boost/mpi/config.hpp:20, >>>> from /opt/local/include/boost/mpi/allocator.hpp:15, >>>> from /opt/local/include/boost/mpi.hpp:22, >>>> from >>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/common/MPI.h:35, >>>> from >>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/fem/UFCCell.h:31, >>>> from >>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/fem/FiniteElement.h:27, >>>> from >>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/adaptivity/adapt.cpp:24: >>>> /opt/local/include/openmpi/mpi.h:367: error: wrong number of arguments >>>> specified for ‘deprecated’ attribute >>>> >>>> stem from the fact that dorsal is always using the gcc compiler in >>>> >>>> /usr/bin/gcc --version >>>> i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build >>>> 5658) (LLVM build 2336.1.00) >>>> Copyright (C) 2007 Free Software Foundation, Inc. >>>> This is free software; see the source for copying conditions. There is NO >>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>>> >>>> which is llvm-gcc-4.2 and that cannot handle those ‘deprecated’ >>>> attributes. In the meantime, I managed to compile dolfin by enforcing the >>>> use of >>>> >>>> /opt/local/bin/gcc --version >>>> gcc (MacPorts gcc48 4.8.1_3) 4.8.1 >>>> Copyright (C) 2013 Free Software Foundation, Inc. >>>> This is free software; see the source for copying conditions. There is NO >>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. >>>> >>>> which does handle those ‘deprecated’ attribute and dolfin seems to work >>>> fine! >>>> >>>> However, I noticed dorsal uses many tricks to always use /usr/bin/gcc. I >>>> thought changing >>>> #export CC=/usr/bin/gcc >>>> #export CXX=/usr/bin/g++ >>>> export CC=/opt/local/bin/gcc >>>> export CXX=/opt/local/bin/g++ >>>> >>>> and >>>> #Change mpicc (which is always mpicc built upon llvm-gcc-4.2 to mpicc >>>> built upon gcc-4.8 >>>> #for CMD in /opt/local/bin/openmpi* >>>> #do >>>> # ln -sf ${CMD} ${INSTALL_PATH}/bin/`basename ${CMD} | cut -b 5-` >>>> #done >>>> for CMD in /Users/sschmidt/Documents/FEniCS/MyOpenMPI/bin/openmpi* >>>> do >>>> ln -sf ${CMD} ${INSTALL_PATH}/bin/`basename ${CMD} | cut -b 5-` >>>> done >>>> >>>> in /platforms/supported/lion.platform would change this behaviour, but >>>> this seems not to work. I still have to add >>>> -DCMAKE_CXX_COMPILER:STRING=g++ \ >>>> -DCMAKE_C_COMPILER:STRING=gcc \ >>>> -DCMAKE_Fortran_COMPILER:STRING=gfortran " >>>> >>>> to all .package-files in order to make dorsal use the default compiler >>>> gcc-4.8, which can handle ‘deprecated’ attributes. >>>> >>>> Thus, I would much appreciate it, if you could give a hint on what is the >>>> recommended compiler for dolfin and how to easily set the compiler for all >>>> .package-files. >>>> Many thanks for any helping with this! >>>> >>>> _______________________________________________ >>>> 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
