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

Sun Dec 1 11:00:34 CST 2013

Thanks, Vijay and Praveen,

Yes, userq2() is a part of Nek-MOAB interface -- see examples/moab_conjht/moab_conjht.usr

I'll discuss the issue of linking with other developers.

Best.
Aleks

----- Original Message -----
From: nek5000-users at lists.mcs.anl.gov
To: "nek5000-users" <nek5000-users at lists.mcs.anl.gov>
Sent: Sunday, December 1, 2013 2:07:59 AM
Subject: Re: [Nek5000-users] nek+moab problem on mac osx 10.9 using macports

That should technically be an easy inclusion to NEK makenek script
using say a LD variable to specify linker separate from compilers. But
will leave that decision to the core NEK devs before I make any
recommendations.

Vijay

On Sun, Dec 1, 2013 at 1:56 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
> Thanks. It compiles now. But I had to manually change the linker in the
> makefile generated by makenek. Is there a way to do this properly without
> having to edit makefile.
>
> Praveen
>
> On 1 Dec 2013 13:09, <nek5000-users at lists.mcs.anl.gov> wrote:
>>
>> > -stdlib=libc++
>>
>> Ah I switched those around. But good that you figured this out.
>>
>> > Undefined symbols for architecture x86_64:
>> >
>> >   "_userq2_", referenced from:
>>
>> userq2 should be part of your problem setup - *.usr file. Make sure
>> this is defined and implemented correctly before appropriate linkage.
>>
>> On Sun, Dec 1, 2013 at 1:24 AM,  <nek5000-users at lists.mcs.anl.gov> wrote:
>> >
>> > 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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>> > Nek5000-users at lists.mcs.anl.gov
>> > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users
>> >
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