What's the output of $ ls -lA /Users/gideonsimpson/software/dolfin/lib/python2.7/site-packages/dolfin/cpp/ $ python -c"import sys; print sys.path"
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Jan On Fri, 28 Aug 2015 13:28:48 -0400 Gideon Simpson <[email protected]> wrote: > Ok, I have installed dolfin to a local directory using > -DCMAKE_INSTALL_PREFIX, but I am still having trouble: > > > gideonsimpson@titan:~$ > source /Users/gideonsimpson/software/dolfin/share/dolfin/dolfin.conf > gideonsimpson@titan:~$ python Python 2.7.10 (default, Aug 18 2015, > 11:31:52) [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on > darwin Type "help", "copyright", "credits" or "license" for more > information. > >>> import dolfin > Traceback (most recent call last): > File "<stdin>", line 1, in <module> > File > "/Users/gideonsimpson/software/dolfin/lib/python2.7/site-packages/dolfin/__init__.py", > line 16, in <module> from . import cpp File > "/Users/gideonsimpson/software/dolfin/lib/python2.7/site-packages/dolfin/cpp/__init__.py", > line 42, in <module> exec("from . import %s" % module_name) File > "<string>", line 1, in <module> ImportError: cannot import name common > > > > > -gideon > > > On Aug 28, 2015, at 12:26 PM, Jan Blechta > > <[email protected]> wrote: > > > > On Fri, 28 Aug 2015 12:10:28 -0400 > > Gideon Simpson <[email protected] > > <mailto:[email protected]>> wrote: > > > >> That seems to have worked, though I did get: > >> > >> clang: warning: -ldmumps: 'linker' input unused > >> clang: warning: argument unused during compilation: > >> '-L/opt/local/lib' > >> > >> throughout. > >> > >> Is there something else I need to do to get the python module of > >> dolfin working? I added > >> > >> $HOME/software/dolfin-1.5.0/site-packages > > > > It seems that this is your src dir, not the build or install dir. > > DOLFIN build system should generate > > > > <build_dir>/dolfin.conf after successful build > > > > and > > > > <install_dir>/share/dolfin.conf after successful install > > > > Just source one of those. > > > > Jan > > > >> > >> to my PYTHONPATH, but when I try to import dolfin, I get the > >> following: > >> > >> > >> Python 2.7.10 (default, Aug 18 2015, 11:31:52) > >> [GCC 4.2.1 Compatible Apple LLVM 6.1.0 (clang-602.0.53)] on darwin > >> Type "help", "copyright", "credits" or "license" for more > >> information. > >>>>> import dolfin > >> Traceback (most recent call last): > >> File "<stdin>", line 1, in <module> > >> File > >> "/Users/gideonsimpson/software/dolfin-1.5.0/site-packages/dolfin/__init__.py", > >> line 16, in <module> from . import cpp File > >> "/Users/gideonsimpson/software/dolfin-1.5.0/site-packages/dolfin/cpp/__init__.py", > >> line 42, in <module> exec("from . import %s" % module_name) File > >> "<string>", line 1, in <module> ImportError: cannot import name > >> common > >> > >> > >> -gideon > >> > >>> On Aug 28, 2015, at 9:12 AM, Johannes Ring <[email protected]> > >>> wrote: > >>> > >>> You can pass them to cmake like this: > >>> > >>> cmake -DCMAKE_CXX_FLAGS="-L/opt/local/lib -ldmumps" > >>> -DCMAKE_EXE_LINKER_FLAGS="-L/opt/local/lib -ldmumps" .. > >>> > >>> Johannes > >>> > >>> On Fri, Aug 28, 2015 at 3:04 PM <[email protected] > >>> <mailto:[email protected] > >>> <mailto:[email protected]>>> wrote: Are these command line > >>> flags or is there a file I edit? > >>> > >>> Sent from my iPhone > >>> > >>> On Aug 28, 2015, at 8:54 AM, Johannes Ring <[email protected] > >>> <mailto:[email protected]> <mailto:[email protected] > >>> <mailto:[email protected]>>> wrote: > >>> > >>>> Try adding "-L/opt/local/lib -ldmumps" to CMAKE_CXX_FLAGS and > >>>> CMAKE_EXE_LINKER_FLAGS. > >>>> > >>>> Johannes > >>>> > >>>> On Fri, Aug 28, 2015 at 2:43 PM Gideon Simpson > >>>> <[email protected] <mailto:[email protected]> > >>>> <mailto:[email protected] > >>>> <mailto:[email protected]>>> wrote: Is there a way to > >>>> manually give it a path for mumps? > >>>> > >>>> -gideon > >>>> > >>>>> On Aug 28, 2015, at 8:38 AM, Jan Blechta > >>>>> <[email protected] <mailto:[email protected]> > >>>>> <mailto:[email protected] > >>>>> <mailto:[email protected]>>> wrote: > >>>>> > >>>>> On Fri, 28 Aug 2015 08:25:38 -0400 > >>>>> Gideon Simpson <[email protected] > >>>>> <mailto:[email protected]> > >>>>> <mailto:[email protected] > >>>>> <mailto:[email protected]>>> wrote: > >>>>> > >>>>>> I have no problem if my fenics installation doesn’t have mumps > >>>>>> support, I just need some basic functionality. Is there a way > >>>>>> to get it to ignore it? > >>>>> > >>>>> You can only disable whole PETSc by > >>>>> > >>>>> cd <dolfin_build_dir> > >>>>> cmake <dolfin_src_dir> -DDOLFIN_ENABLE_PETSC:BOOL=OFF > >>>>> make > >>>>> make install > >>>>> > >>>>> Sequential Eigen backend (DOLFIN 1.6.0) or uBLAS backend (DOLFIN > >>>>> 1.5.0) will be available instead of parallel PETSc backend. > >>>>> > >>>>> Or you can try patching dolfin/la/MUMPSLUSolver.* somehow to > >>>>> inhibit MUMPSLUSolver class. > >>>>> > >>>>> Jan > >>>>> > >>>>>> > >>>>>> -gideon > >>>>>> > >>>>>>> On Aug 28, 2015, at 8:24 AM, Jan Blechta > >>>>>>> <[email protected] > >>>>>>> <mailto:[email protected]> > >>>>>>> <mailto:[email protected] > >>>>>>> <mailto:[email protected]>>> wrote: > >>>>>>> > >>>>>>> On Fri, 28 Aug 2015 08:17:15 -0400 > >>>>>>> Gideon Simpson <[email protected] > >>>>>>> <mailto:[email protected]> > >>>>>>> <mailto:[email protected] > >>>>>>> <mailto:[email protected]>>> wrote: > >>>>>>> > >>>>>>>> By virtue of the way macports installed petsc, my mumps > >>>>>>>> library is in /opt/local/lib, and not in the petsc sub > >>>>>>>> directory. > >>>>>>> > >>>>>>> I'm afraid I can't help you here as I don't know Apple. Maybe > >>>>>>> Garth or Johannes. > >>>>>>> > >>>>>>> Jan > >>>>>>> > >>>>>>>> > >>>>>>>> -gideon > >>>>>>>> > >>>>>>>>> On Aug 28, 2015, at 4:46 AM, Jan Blechta > >>>>>>>>> <[email protected] > >>>>>>>>> <mailto:[email protected]> > >>>>>>>>> <mailto:[email protected] > >>>>>>>>> <mailto:[email protected]>>> wrote: > >>>>>>>>> > >>>>>>>>> I'm afraid that this will not work, Garth. MUMPSLUSolver is > >>>>>>>>> toggled by > >>>>>>>>> > >>>>>>>>> #ifdef PETSC_HAVE_MUMPS > >>>>>>>>> > >>>>>>>>> There is a linking problem to $PETSC_DIR/lib/libdmumps.a. > >>>>>>>>> Ensure that the object is visible to linker. > >>>>>>>>> > >>>>>>>>> Jan > >>>>>>>>> > >>>>>>>>> > >>>>>>>>> On Fri, 28 Aug 2015 09:36:43 +0100 > >>>>>>>>> "Garth N. Wells" <[email protected] <mailto:[email protected]> > >>>>>>>>> <mailto:[email protected] <mailto:[email protected]>>> wrote: > >>>>>>>>> > >>>>>>>>>> As a work-around, try using -DDOLFIN_ENABLE_MUMPS=False > >>>>>>>>>> when building DOLFIN. > >>>>>>>>>> > >>>>>>>>>> I'm not aware of any FEniCS developers using MacPorts for > >>>>>>>>>> dependencies (I use Homebrew), so support will be patchy. > >>>>>>>>>> > >>>>>>>>>> Garth > >>>>>>>>>> > >>>>>>>>>> On 28 August 2015 at 00:41, Gideon Simpson > >>>>>>>>>> <[email protected] > >>>>>>>>>> <mailto:[email protected]> > >>>>>>>>>> <mailto:[email protected] > >>>>>>>>>> <mailto:[email protected]>>> wrote: > >>>>>>>>>> > >>>>>>>>>>> Hi, I’m trying to get dolfin installed by source since the > >>>>>>>>>>> current macports version is broken. I have (from > >>>>>>>>>>> macports) installed 1.5 versions for ffc,ufl,fiat, and > >>>>>>>>>>> instant, along with petsc and slepc. Following the > >>>>>>>>>>> instructions, it seems to go fine, except at the very > >>>>>>>>>>> end, where I get the following error: > >>>>>>>>>>> > >>>>>>>>>>> [100%] Building CXX object > >>>>>>>>>>> dolfin/CMakeFiles/dolfin.dir/refinement/RegularCutRefinement.cpp.o > >>>>>>>>>>> [100%] Building CXX object > >>>>>>>>>>> dolfin/CMakeFiles/dolfin.dir/refinement/UniformMeshRefinement.cpp.o > >>>>>>>>>>> [100%] *Linking CXX shared library libdolfin.dylib* > >>>>>>>>>>> Undefined symbols for architecture x86_64: > >>>>>>>>>>> "_dmumps_c", referenced from: > >>>>>>>>>>> dolfin::MUMPSLUSolver::solve(dolfin::GenericVector&, > >>>>>>>>>>> dolfin::GenericVector const&) in MUMPSLUSolver.cpp.o > >>>>>>>>>>> ld: symbol(s) not found for architecture x86_64 > >>>>>>>>>>> clang: error: linker command failed with exit code 1 (use > >>>>>>>>>>> -v to see invocation) > >>>>>>>>>>> make[2]: *** [dolfin/libdolfin.1.5.0.dylib] Error 1 > >>>>>>>>>>> make[1]: *** [dolfin/CMakeFiles/dolfin.dir/all] Error 2 > >>>>>>>>>>> make: *** [all] Error 2 > >>>>>>>>>>> > >>>>>>>>>>> -gideon > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>>>> _______________________________________________ > >>>>>>>>>>> fenics-support mailing list > >>>>>>>>>>> [email protected] > >>>>>>>>>>> <mailto:[email protected]> > >>>>>>>>>>> <mailto:[email protected] > >>>>>>>>>>> <mailto:[email protected]>> > >>>>>>>>>>> http://fenicsproject.org/mailman/listinfo/fenics-support > >>>>>>>>>>> <http://fenicsproject.org/mailman/listinfo/fenics-support> > >>>>>>>>>>> <http://fenicsproject.org/mailman/listinfo/fenics-support > >>>>>>>>>>> <http://fenicsproject.org/mailman/listinfo/fenics-support>> > >>>>>>>>>>> > >>>>>>>>>>> > >>>>>>>>> > >>>>>>>> > >>>>>>> > >>>>>> > >>>>> > >>>> > >>>> _______________________________________________ > >>>> fenics-support mailing list > >>>> [email protected] > >>>> <mailto:[email protected]> > >>>> <mailto:[email protected] > >>>> <mailto:[email protected]>> > >>>> http://fenicsproject.org/mailman/listinfo/fenics-support > >>>> <http://fenicsproject.org/mailman/listinfo/fenics-support> > >>>> <http://fenicsproject.org/mailman/listinfo/fenics-support > >>>> <http://fenicsproject.org/mailman/listinfo/fenics-support>> > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
