[petsc-users] Error configuring with Parmetis and HDF5 on iMac

[Justin Chang]

Attached are the configure.log and make.log files

Thanks,
Justin


On Mon, Aug 11, 2014 at 5:36 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Send configure.log and make.log
>
>    Delete the entire PETSc directory and trying again without the
> --download-f2cblaslapack  but with —with-fc=gfortran (not f2c) I suspect
> you made multiple attempts to install and some undesirable files got in
> place that are causing the difficultly.
>
>   If the clean install does not work then Send configure.log and make.log
>
>   Barry
>
> On Aug 11, 2014, at 5:31 PM, Justin Chang <jychang48 at gmail.com> wrote:
>
> > Hi all,
> >
> > I am trying to install petsc-3.5.1 onto my school's iMac (version
> 10.9.2) and I have run configure with the following options:
> >
> > ./configure --with-cc=gcc --with-cxx=g++ --with-f2c=gfortran
> --download-f2cblaslapack--download-mpich --with-debugging=1
> --download-ctetgen --download-triangle --with-valgrind=1 -with-cmake=cmake
> --download-metis --download-parmetis --download-netcdf --download-hdf5
> --download-exodusii
> >
> > Then when I run 'make all test' I get the following errors:
> >
> > Undefined symbols for architecture x86_64:
> >   "_MatPartitioningCreate_Parmetis", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PETSC_VIEWER_HDF5_", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerCreate_HDF5", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5GetFileId", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5GetGroup", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5GetTimestep", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5HasAttribute", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5PopGroup", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5PushGroup", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5ReadAttribute", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5SetTimestep", referenced from:
> >       import-atom in libpetsc.dylib
> >   "_PetscViewerHDF5WriteAttribute", referenced from:
> >       import-atom in libpetsc.dylib
> > ld: symbol(s) not found for architecture x86_64
> > clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> > make[3]: [ex19] Error 1 (ignored)
> > /bin/rm -f ex19.o
> >
> > Any help appreciated, thanks
> >
> > Justin
>
>
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