---------- Forwarded message ---------- From: Garth N. Wells <[email protected]> Date: 2 September 2013 20:10 Subject: Re: [FEniCS-support] MPI-related fatal error when importing Dolfin To: Timothée Lecomte <[email protected]> Cc: [email protected]
On 2 September 2013 14:47, Timothée Lecomte <[email protected]> wrote: > Dear all, > > I am using Fenics on MacOS X (Snow Leopard). I used to have it working fine > until recently when I updated some packages from Homebrew (a package manager > for MacOS, similar to MacPorts). I had something similar a few days ago with MacPorts - OpenMPI was updates and everything broke. OSX is a disaster is this respect. > I then rebuilt Fenics using Dorsal, and I > get the following error : > > $ python > Python 2.7.5 (default, Aug 28 2013, 10:09:22) > [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> from dolfin import * > Attempting to use an MPI routine before initializing MPICH > <python exits> > > I have the following packages built with Homebrew: MPICH 3.0.4 Boost 1.54 > (with MPI support) CGAL 4.2 Python 2.7.5 Swig 2.0.10 Parmetis 4.0.2 Vtk > 5.10.1 > > In Dorsal, I use the following: > > PACKAGES=( > petschypre > slepc > scotch > fiat > ufc > ufl > ffc > viper > instant > dolfin > ) > > When I remove PETSc from Dorsal (petschypre is just PETSc with the Hypre > preconditioners enabled) (and slepc since it depends on PETSc), the above > error does not appear and Dolfin works fine. Of course, I then miss the > PETSc assemblers and solvers, and I am only left with uBLAS. > > When building dolfin, the following message sums up the packages that are > found on my machine: > > -- The following optional packages were found: > -- ------------------------------------------- > -- (OK) OPENMP > -- (OK) MPI > -- (OK) PETSC > -- (OK) SLEPC > -- (OK) UMFPACK > -- (OK) CHOLMOD > -- (OK) SCOTCH > -- (OK) PARMETIS > -- (OK) CGAL > -- (OK) ZLIB > -- (OK) PYTHON > -- (OK) SPHINX > -- (OK) VTK > -- (OK) QT > -- > -- The following optional packages were not be found: > -- -------------------------------------------------- > -- (**) TRILINOS > -- (**) PASTIX > -- (**) HDF5 > > I suspect there is something wrong with MPICH3 but I tried to revert to > MPICH2 1.5 without success. > I use MPICH3 under Linux - it works fine. > Can you please help solve this issue ? > You might want to check your GCC versions - from your Python output, it looks like some packages have been built with the Apple (and very old) version of GCC. Garth > Thank you very much, > > Best regards, > > Timothée > > P.S. : I am not using the binaries for MacOS offered on the website for > three reasons: 1) I have found that the plotting is buggy compared to what I > get when I build the stack myself, 2) I have Numpy, Scipy and friends built > for the python interpreter from Homebrew, 3) I need the AMG preconditioners > provided by Hypre (for fluid mechanics problems). > > > > _______________________________________________ > fenics-support mailing list > [email protected] > http://fenicsproject.org/mailman/listinfo/fenics-support > -- Garth N. Wells Department of Engineering, University of Cambridge http://www.eng.cam.ac.uk/~gnw20 _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
