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

[Barry Smith]

  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