Garth, Thank you for the reply. I wish I could upgrade, but for the time being, work policy is to use 10.8.5.
One potential fix is to use Dorsal to build enough dependencies of FEniCS-dev with g++ 4.8, which will use the right standard library, and should be able to link to existing software on my machine built with clang++ and libstdc++. What I've done so far is: - built a separate Python 2.7 virtualenv via gcc 4.8, so pip & setup.py should preferentially use GCC 4.8 for building Python packages. Compile logs for packages installed via pip indicate that this premise has borne out so far - set environment variables in a local.platform file for Dorsal so that: CC and CXX equal gcc-4.8 and g++4.8, respectively. I've also set OMPI_CC=gcc-4.8, OMPI_CXX=g++-4.8, and OMPI_FC=gfortran, as in the mountainlion.platform file set up in Dorsal. - I make Dorsal build many dependencies, notably: Open MPI, and anything that looks like it will use an MPI wrapper compiler (boost, parmetis, mpi4py, petsc, petsc4py, slepc, scotch). - Then it should build FEniCS-dev. Where I get stuck is that it seems that Dorsal uses GCC 4.8 inconsistently -- possibly not at all -- in the build process, because I'm still getting clang errors re: shared_ptr. The theory behind having Dorsal build Open MPI, etc., is that it will use libraries it builds preferentially, and will sandbox the installs, so building Open MPI via Dorsal should build an Open MPI wrapper compiler for GCC 4.8 localized to FEniCS. I would rather avoid building libraries by hand, or using Homebrew to build libraries using GCC 4.8, if possible. Any help on getting Dorsal to recognize the right compiler or correct my misunderstandings so far would be much appreciated. Cheers, Geoff On Fri, Mar 28, 2014 at 5:29 AM, Garth N. Wells <[email protected]> wrote: > > On 26 Mar 2014, at 08:55, Geoff Oxberry <[email protected]> wrote: > > > I have a similar error to a user who wrote in 2014-03-03 (see > https://www.mail-archive.com/[email protected]/msg00366.html > ): > > > > Traceback (most recent call last): > > File "demo_poisson.py", line 41, in <module> > > V = FunctionSpace(mesh, "Lagrange", 1) > > File > "~/FEniCS/lib/python2.7/dist-packages/dolfin/functions/functionspace.py", > > line 403, in __init__ > > FunctionSpaceBase.__init__(self, mesh, element, constrained_domain) > > File " > > ~/FEniCS/lib/python2.7/dist-packages/dolfin/functions/functionspace.py", > > > > line 84, in __init__ > > ufc_element, ufc_dofmap = jit(self._ufl_element) > > File " > > ~/FEniCS/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line > > > > 60, in mpi_jit > > return local_jit(*args, **kwargs) > > File " > > ~/FEniCS/lib/python2.7/dist-packages/dolfin/compilemodules/jit.py", line > > > > 122, in jit > > return jit_compile(form, parameters=p, common_cell=common_cell) > > TypeError: jit() got an unexpected keyword argument 'common_cell' > > > > > > In the same thread, Anders Logg suggested updating DOLFIN, UFL, and FFC. > I installed everything through Dorsal; to my knowledge, each package is at > the most recent stable version. If you let me know which files to send, I > can send build logs. > > > > I've also tried using Dorsal to build the development versions of these > packages. On OS X with Homebrew and LLVM 3.3, there seems to be an issue > with the development version of FFC; clang++ throws a number of errors > related to std::shared_ptr (in SWIG-generated interfaces) that have to do > with the version of libstdc++ clang++ is using. If I compile and link with > libc++ instead, those problems go away, but linking errors occur (with > Boost; rebuilding Boost with libc++ does not seem to work either). > > > > Are there other ways to resolve this problem while still building with > Homebrew? > > > > I don't think any developers use (or have access to) OS X 10.8, so it all > be hard for us to fix. I build the FEniCS dev versions on OSX 10.9 with > Xcode 5.1 without problems. I install via Homebrew all the dependencies > that are available in Homebrew, except PETSc which I choose to build myself. > > Garth > > > > Cheers, > > > > Geoff > > _______________________________________________ > > fenics-support mailing list > > [email protected] > > http://fenicsproject.org/mailman/listinfo/fenics-support > > -- Geoffrey Oxberry, Ph.D., E.I.T. [email protected]
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