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

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

On Sun, Dec 1, 2013 at 12:36 PM, <nek5000-users at lists.mcs.anl.gov> wrote:

> Praveen,
>
> The linker with mpif77 cannot handle -stdlib since it should be passed
> to a clang compiler and not gfortran. Try changing the linker from
> mpif77 to mpicxx.
>
> I dont have a configuration setup with this combination of
> OpenMPI+clang to test currently. I have mpich3+clang3.4 on a ubuntu
> system and can try to check if NEK builds cleanly there after
> upgrading my gfortran. If there are clang issues, it should show up
> there too.
>
> Vijay
>

Hello Vijay

It seems that I have to use

-stdlib=libc++

I manually changed the linker command in makefile. I dont get the c++
errors but something else

openmpic++ -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++ -stdlib=libc++

Undefined symbols for architecture x86_64:

  "_userq2_", referenced from:

      _setqvol_ in conduct.o

      _makeuq_ in conduct.o

ld: symbol(s) not found for architecture x86_64

clang: error: linker command failed with exit code 1 (use -v to see
invocation)

make: *** [nek5000] Error 1


Thanks

praveen
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