On 30 Mar 2014, at 22:16, Geoff Oxberry <[email protected]> wrote: > I finally figured out how to get FEniCS 1.3.0 to build on OS X 10.8.5. I > don't know that FEniCS-dev can be compiled on 10.8.5 because of the clang++ > libstdc++ issues with C++11 and the restriction that Apple's LLVM must be > used to compile VTK. If a consistent stack can be compiled with libc++, it > will probably work, and I assume that's how the build on OS X 10.9.2 would > work. > > I have a proposal to write this week, but next weekend, I should be able to > contribute a number of patches to Dorsal upstream, along with a platform > file, if you guys are interested. >
Yes, any contribution would be very welcome. It’s unlikely that we have any debs using Dorsal and OSX 10.8 in order to help with testing. Garth > Cheers, > > Geoff > > > On Sun, Mar 30, 2014 at 4:15 AM, Geoff Oxberry <[email protected]> wrote: > More progress. I'm pretty sure that the memory error I'm seeing is due to VTK > being compiled with clang++, and almost everything else being compiled with > g++ 4.8. > > In short, it's impossible to compile VTK with GCC on a Mac due to some > non-standard extensions in Apple header. > > I could try compiling most of the dependencies I can think of with libc++. If > that doesn't work, then I doubt it's possible to build the development > versions of FEniCS packages on OS X 10.8.5. > > Cheers, > > Geoff > > > On Sun, Mar 30, 2014 at 1:09 AM, Geoff Oxberry <[email protected]> wrote: > Oh, by the way, I forgot to mention: this build is with development versions > of packages, rather than the stable package versions. > > Cheers, > > Geoff > > > On Sun, Mar 30, 2014 at 1:07 AM, Geoff Oxberry <[email protected]> wrote: > Garth, > > Here's more progress: now FEniCS builds. I have to build quite a bit with GCC > 4.8; I've attached the local.platform file I've been using, which is by no > means minimal. There are a few Dorsal packages for which I've written custom > package files, and I've updated 8 or 9 more. Once I figure all of this out, > I'll submit pull requests to upstream. > > I figured out that GCC 4.8 is used consistently, provided I make sure to > clean up previous builds by deleting the FEniCS build directory. The only > other exception is PETSc, which still uses Clang++ for some reason, and I'll > have to figure that out later. > > Now, when I run demo_poisson.py, I get the following run-time error: > > ratatoskr:~ goxberry$ env CXX=g++-4.8 python > FEniCS/src/dolfin/demo/documented/poisson/python/demo_poisson.py > Calling FFC just-in-time (JIT) compiler, this may take some time. > Calling DOLFIN just-in-time (JIT) compiler, this may take some time. > Calling DOLFIN just-in-time (JIT) compiler, this may take some time. > Calling FFC just-in-time (JIT) compiler, this may take some time. > Calling FFC just-in-time (JIT) compiler, this may take some time. > Solving linear variational problem. > python(18194,0x7fff7c323180) malloc: *** error for object 0x7fff7bc60570: > pointer being freed was not allocated > *** set a breakpoint in malloc_error_break to debug > [ratatoskr:18194] *** Process received signal *** > [ratatoskr:18194] Signal: Abort trap: 6 (6) > [ratatoskr:18194] Signal code: (0) > [ratatoskr:18194] *** End of error message *** > Abort trap: 6 > > The Dorsal platform file is attached; of particular note is that I build a > Python 2.7.2 interpreter through Dorsal (the python-osx package is a minor > hack that sets PYTHON_LIBRARY to have a .dylib extension instead of an .so > extension). Any ideas of what I may want to look at for debugging? > > Cheers, > > Geoff > > > On Fri, Mar 28, 2014 at 10:45 AM, Geoff Oxberry <[email protected]> wrote: > 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] > > > > -- > Geoffrey Oxberry, Ph.D., E.I.T. > [email protected] > > > > -- > Geoffrey Oxberry, Ph.D., E.I.T. > [email protected] > > > > -- > Geoffrey Oxberry, Ph.D., E.I.T. > [email protected] > > > > -- > Geoffrey Oxberry, Ph.D., E.I.T. > [email protected] _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
