gideonsimpson@titan:~$ ls -lA /Users/gideonsimpson/software/dolfin/lib/python2.7/site-packages/dolfin/cpp/ total 16 -rw-r--r-- 1 gideonsimpson staff 2740 Jan 12 2015 __init__.py -rw-r--r-- 1 gideonsimpson staff 1263 Aug 28 13:26 __init__.pyc gideonsimpson@titan:~$ python -c"import sys; print sys.path" ['', '/Users/gideonsimpson/software/dolfin/lib/python2.7/site-packages', '/opt/auto/07p/python', '/opt/local/lib/petsc/bin/pythonscripts', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python27.zip', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-darwin', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/plat-mac/lib-scriptpackages', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-old', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/readline', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload', '/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages']
-gideon > On Aug 28, 2015, at 1:40 PM, Jan Blechta <[email protected]> wrote: > > 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" > > ? > > 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
