[Nek5000-users] nek+moab problem on mac osx 10.9 using macports

[nek5000-users at lists.mcs.anl.gov]

AFAIK, these routines have not been deprecated in clang. Can you print
out the version of your compilers so that we can see if some
implementation is missing ? clang --version.

You should also use LDFLAGS+="-stdlib=libstdc++" on the linker command
since OSX Mavericks might have a different behavior by default in
choosing the standard C++ runtime libraries. If that doesn't fix the
undefined errors, let us know the detailed messages.

Vijay


On Sat, Nov 30, 2013 at 11:53 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> Hello
>
> I have installed moab on osx 10.9 using openmpi from macports. gfortran is
> also from macports.
>
>
> When I try to compile nek I get this error. openmpicc/c++ uses apple clang
> but gfortran seems to use gcc48 from macports. Is there any way to fix this.
>
>
> openmpif77 -o nek5000  obj/ray.o obj/drive.o obj/drive1.o obj/drive2.o
> obj/plan4.o obj/bdry.o obj/coef.o obj/conduct.o obj/connect1.o
> obj/connect2.o obj/dssum.o obj/edgec.o obj/eigsolv.o obj/gauss.o
> obj/genxyz.o obj/navier1.o obj/makeq.o obj/navier0.o obj/navier2.o
> obj/navier3.o obj/navier4.o obj/prepost.o obj/speclib.o obj/map2.o
> obj/turb.o obj/mvmesh.o obj/ic.o obj/ssolv.o obj/planx.o obj/math.o
> obj/mxm_wrapper.o obj/hmholtz.o obj/gfdm_par.o obj/gfdm_op.o
> obj/gfdm_solve.o obj/subs1.o obj/subs2.o obj/genbox.o obj/gmres.o obj/hsmg.o
> obj/convect.o obj/induct.o obj/perturb.o obj/navier5.o obj/navier6.o
> obj/navier7.o obj/navier8.o obj/fast3d.o obj/fasts.o obj/calcz.o obj/byte.o
> obj/chelpers.o obj/byte_mpi.o obj/postpro.o obj/cvode_driver.o
> obj/nek_comm.o obj/init_plugin.o obj/setprop.o obj/qthermal.o
> obj/cvode_aux.o obj/makeq_aux.o obj/papi.o obj/ssygv.o obj/dsygv.o
> obj/nek_in_situ.o obj/mxm_std.o obj/blas.o obj/moab.o obj/imeshutil.o
> obj/imeshcutil.o obj/comm_mpi.o obj/singlmesh.o obj/jl_gs.o obj/jl_sort.o
> obj/jl_sarray_transfer.o obj/jl_sarray_sort.o obj/jl_gs_local.o
> obj/jl_crystal.o obj/jl_comm.o obj/jl_tensor.o obj/jl_fail.o
> obj/jl_fcrystal.o obj/jl_findpts.o obj/jl_findpts_local.o obj/jl_obbox.o
> obj/jl_poly.o obj/jl_lob_bnd.o obj/jl_findpts_el_3.o obj/jl_findpts_el_2.o
> obj/jl_sparse_cholesky.o obj/jl_xxt.o obj/jl_fcrs.o  -L/opt/local/lib
> -L/Users/praveen/Applications/moab/moab-4.6.2/lib
> -L/Users/praveen/Applications/moab/moab-4.6.2/lib -liMesh -lMOAB -lnetcdf
> -lhdf5     -lm  -L/opt/local/lib
> -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1
> -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi
> -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm  -L/opt/local/lib
> -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1
> -L/opt/local/lib/gcc48/gcc/x86_64-apple-darwin13/4.8.1/../../.. -lmpi_usempi
> -lmpi_mpifh -lmpi -lgfortran -lquadmath -lm  -lmpi_cxx -lstdc++
>
> Undefined symbols for architecture x86_64:
>
>   "std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >::find_last_of(char const*, unsigned long,
> unsigned long) const", referenced from:
>
>
> moab::ReaderWriterSet::get_file_extension_reader(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&) const in
> libMOAB.a(ReaderWriterSet.o)
>
>
> moab::ReaderWriterSet::extension_from_filename(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&) in
> libMOAB.a(ReaderWriterSet.o)
>
>
> moab::ReaderWriterSet::get_file_extension_writer(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&) const in
> libMOAB.a(ReaderWriterSet.o)
>
>       moab::WriteAns::write_file(char const*, bool, moab::FileOptions
> const&, unsigned long const*, int,
> std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > > const&,
> moab::TagInfo* const*, int, int) in libMOAB.a(WriteAns.o)
>
>   "std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >::find_first_of(char const*, unsigned long,
> unsigned long) const", referenced from:
>
>       moab::ReadABAQUS::tokenize(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
> std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > >&, char const*)
> in libMOAB.a(ReadABAQUS.o)
>
>   "std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >::find_last_not_of(char const*, unsigned long,
> unsigned long) const", referenced from:
>
>       _imesh_load_ in libiMesh.a(iMesh_MOAB.o)
>
>       _imesh_save_ in libiMesh.a(iMesh_MOAB.o)
>
>       _imesh_createtagwithoptions_ in libiMesh.a(iMesh_MOAB.o)
>
>       _imesh_gettaghandle_ in libiMesh.a(iMesh_MOAB.o)
>
>   "std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >::find_first_not_of(char const*, unsigned long,
> unsigned long) const", referenced from:
>
>       moab::ReadABAQUS::tokenize(std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > const&,
> std::__1::vector<std::__1::basic_string<char, std::__1::char_traits<char>,
> std::__1::allocator<char> >,
> std::__1::allocator<std::__1::basic_string<char,
> std::__1::char_traits<char>, std::__1::allocator<char> > > >&, char const*)
> in libMOAB.a(ReadABAQUS.o)
>
>
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