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

[Justin Chang]

I did what Barry suggested: deleting the directory and all. And it works
fine now. Thanks all


On Mon, Aug 11, 2014 at 5:56 PM, Satish Balay <balay at mcs.anl.gov> wrote:

> Hm - a bunch of sourcefiles are not getting compiled. I'm not sure why.
>
> can you try the following - and see if the problem goes away?
>
> make allclean all
>
> If not - try:
>
> make allclean all-cmake
>
> Satish
>
> On Mon, 11 Aug 2014, Justin Chang wrote:
>
> > 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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