[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 8:18 AM, <nek5000-users at lists.mcs.anl.gov> wrote:

> 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
>

Hello Vijay

Here is some information on my mpi which is installed from macports

clang is from xcode.

$ clang -v

Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Target: x86_64-apple-darwin13.0.0

Thread model: posix


$ openmpicc -v

Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Target: x86_64-apple-darwin13.0.0

Thread model: posix


$ openmpic++ -v

Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)

Target: x86_64-apple-darwin13.0.0

Thread model: posix


$ openmpif77 -v

Using built-in specs.

COLLECT_GCC=/opt/local/bin/gfortran-mp-4.8

COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.8.1/lto-wrapper

Target: x86_64-apple-darwin13

Configured with:
/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc48/gcc48/work/gcc-4.8.1/configure
--prefix=/opt/local --build=x86_64-apple-darwin13
--enable-languages=c,c++,objc,obj-c++,lto,fortran,java
--libdir=/opt/local/lib/gcc48 --includedir=/opt/local/include/gcc48
--infodir=/opt/local/share/info --mandir=/opt/local/share/man
--datarootdir=/opt/local/share/gcc-4.8 --with-local-prefix=/opt/local
--with-system-zlib --disable-nls --program-suffix=-mp-4.8
--with-gxx-include-dir=/opt/local/include/gcc48/c++/ --with-gmp=/opt/local
--with-mpfr=/opt/local --with-mpc=/opt/local --with-cloog=/opt/local
--enable-cloog-backend=isl --disable-cloog-version-check
--enable-stage1-checking --disable-multilib --enable-lto
--enable-libstdcxx-time --with-as=/opt/local/bin/as
--with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=
https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc48
4.8.1_3'

Thread model: posix

gcc version 4.8.1 (MacPorts gcc48 4.8.1_3)


I configure moab like this


./configure --prefix=`pwd` \

            --with-mpi \

            --with-hdf5=/opt/local \

            --enable-mbzoltan \

            --with-zoltan=/opt/trilinos-11.4.1-mpi \

            CC=openmpicc CXX=openmpic++ FC=openmpif77 F77=openmpif77


If I add -stdlib=libstdc++ flag it is not recognized


makenek - automatic build tool for Nek5000

generating makefile ...

openmpif77 -c  -O2 -fdefault-real-8 -fdefault-double-8 -x f77-cpp-input
-fcray-pointer -DMOAB -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE
-DGLOBAL_LONG_LONG -I/Users/praveen/rayleigh3
-I/Users/praveen/Applications/nek5_svn/trunk/nek -I./
/Users/praveen/rayleigh3/ray.f
-I/Users/praveen/Applications/nek5_svn/trunk/nek/3rd_party
-I/Users/praveen/Applications/moab/moab-4.6.2/include  -o obj/ray.o

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++ -stdlib=libstdc++

gfortran-mp-4.8: error: unrecognized command line option '-stdlib=libstdc++'

make: *** [nek5000] Error 1


Thanks

praveen
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