<div dir="ltr"><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Dec 1, 2013 at 8:18 AM, <span dir="ltr"><<a href="mailto:nek5000-users@lists.mcs.anl.gov" target="_blank">nek5000-users@lists.mcs.anl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div id=":k0" style="overflow:hidden">AFAIK, these routines have not been deprecated in clang. Can you print<br>
out the version of your compilers so that we can see if some<br>
implementation is missing ? clang --version.<br>
<br>
You should also use LDFLAGS+="-stdlib=libstdc++" on the linker command<br>
since OSX Mavericks might have a different behavior by default in<br>
choosing the standard C++ runtime libraries. If that doesn't fix the<br>
undefined errors, let us know the detailed messages.<br>
<br>
Vijay</div></blockquote></div><div class="gmail_extra"><br></div>Hello Vijay</div><div class="gmail_extra"><br></div><div class="gmail_extra">Here is some information on my mpi which is installed from macports</div><div class="gmail_extra">
<br></div><div class="gmail_extra">clang is from xcode.</div><div class="gmail_extra"><br><p style="margin:0px;font-size:11px;font-family:Menlo">$ clang -v</p>
<p style="margin:0px;font-size:11px;font-family:Menlo">Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)</p>
<p style="margin:0px;font-size:11px;font-family:Menlo">Target: x86_64-apple-darwin13.0.0</p>
<p style="margin:0px;font-size:11px;font-family:Menlo">Thread model: posix</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">$ openmpicc -v</p><p style="margin:0px;font-size:11px;font-family:Menlo">
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)</p><p style="margin:0px;font-size:11px;font-family:Menlo">Target: x86_64-apple-darwin13.0.0</p><p style="margin:0px;font-size:11px;font-family:Menlo">
</p><p style="margin:0px;font-size:11px;font-family:Menlo">Thread model: posix</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">$ openmpic++ -v</p><p style="margin:0px;font-size:11px;font-family:Menlo">
Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn)</p><p style="margin:0px;font-size:11px;font-family:Menlo">Target: x86_64-apple-darwin13.0.0</p><p style="margin:0px;font-size:11px;font-family:Menlo">
</p><p style="margin:0px;font-size:11px;font-family:Menlo">Thread model: posix</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">$ openmpif77 -v</p><p style="margin:0px;font-size:11px;font-family:Menlo">
Using built-in specs.</p><p style="margin:0px;font-size:11px;font-family:Menlo">COLLECT_GCC=/opt/local/bin/gfortran-mp-4.8</p><p style="margin:0px;font-size:11px;font-family:Menlo">COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.8.1/lto-wrapper</p>
<p style="margin:0px;font-size:11px;font-family:Menlo">Target: x86_64-apple-darwin13</p><p style="margin:0px;font-size:11px;font-family:Menlo">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=<a href="https://trac.macports.org/newticket">https://trac.macports.org/newticket</a> --with-pkgversion='MacPorts gcc48 4.8.1_3'</p>
<p style="margin:0px;font-size:11px;font-family:Menlo">Thread model: posix</p><p style="margin:0px;font-size:11px;font-family:Menlo">
</p><p style="margin:0px;font-size:11px;font-family:Menlo">gcc version 4.8.1 (MacPorts gcc48 4.8.1_3)</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">
I configure moab like this</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">./configure <span style="color:rgb(213,59,211)">--prefix=`</span><span style="color:rgb(52,189,38)">pwd</span><span style="color:rgb(213,59,211)">`</span> <span style="color:rgb(52,189,38)">\</span></p>
<p style="margin:0px;font-size:11px;font-family:Menlo"> <span style="color:rgb(213,59,211)">--with-mpi</span> <span style="color:rgb(52,189,38)">\</span></p><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(213,59,211)">
<span style="color:rgb(0,0,0)"> </span>--with-hdf5=/opt/local<span style="color:rgb(0,0,0)"> </span><span style="color:rgb(52,189,38)">\</span></p><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(213,59,211)">
<span style="color:rgb(0,0,0)"> </span>--enable-mbzoltan<span style="color:rgb(0,0,0)"> </span><span style="color:rgb(52,189,38)">\</span></p><p style="margin:0px;font-size:11px;font-family:Menlo;color:rgb(213,59,211)">
<span style="color:rgb(0,0,0)"> </span>--with-zoltan=/opt/trilinos-11.4.1-mpi<span style="color:rgb(0,0,0)"> </span><span style="color:rgb(52,189,38)">\</span></p><p style="margin:0px;font-size:11px;font-family:Menlo">
</p><p style="margin:0px;font-size:11px;font-family:Menlo"> <span style="color:rgb(52,187,199)">CC</span>=openmpicc <span style="color:rgb(52,187,199)">CXX</span>=openmpic++ <span style="color:rgb(52,187,199)">FC</span>=openmpif77 <span style="color:rgb(52,187,199)">F77</span>=openmpif77</p>
<p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">If I add -stdlib=libstdc++ flag it is not recognized</p><p style="margin:0px;font-size:11px;font-family:Menlo">
<br></p><p style="margin:0px;font-size:11px;font-family:Menlo">makenek - automatic build tool for Nek5000</p><p style="margin:0px;font-size:11px;font-family:Menlo">generating makefile ...</p><p style="margin:0px;font-size:11px;font-family:Menlo">
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 </p>
<p style="margin:0px;font-size:11px;font-family:Menlo">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++ </p>
<p style="margin:0px;font-size:11px;font-family:Menlo">gfortran-mp-4.8: error: unrecognized command line option '-stdlib=libstdc++'</p><p style="margin:0px;font-size:11px;font-family:Menlo">
</p><p style="margin:0px;font-size:11px;font-family:Menlo">make: *** [nek5000] Error 1</p><p style="margin:0px;font-size:11px;font-family:Menlo"><br></p><p style="margin:0px;font-size:11px;font-family:Menlo">Thanks</p><p style="margin:0px;font-size:11px;font-family:Menlo">
praveen</p></div></div>