[MOAB-dev] version: (1.0rc1/svn r1016) moab compilation errors on BLUES/fusion

[Tim Tautges]

You're linking against a MOAB which uses CGM, which isn't necessary for your use.

- tim

On 07/10/2014 11:03 AM, Vegendla, Surya Narayana Prasad wrote:
> Hi all,
>
> I am having the following moab compilation errors (svn r1016) while compiling on BLUES using moab_conjht example. Please
> let me know  how to avoid these?
>
> Here, attaching makenek and soft file for your reference.
>
> Thanks,
>
> Prasad
>
> mpif77 -f77=ifort -c  -O2 -r8 -fpconstant -fpp -DMOAB -DPTRSIZE8 -DMPI -DLONGINT8 -DUNDERSCORE -DGLOBAL_LONG_LONG
> -I/home/svegendla/nekFiles/moab_conjhtOld -I/home/svegendla/nek5_svn/trunk/nek -I./
> /home/svegendla/nekFiles/moab_conjhtOld/moab_conjht.f -I/home/svegendla/nek5_svn/trunk/nek/3rd_party
> -DUNORDERED_MAP_NS=std::tr1 -DHAVE_UNORDERED_MAP=tr1/unordered_map -DHAVE_UNORDERED_SET=tr1/unordered_set
> -I/soft/netcdf/4.0.1-intel-11-serial/include -I/home/jain/lib/hdf5-1.8.7//include -isystem
> /home/jain/lib/hdf5-1.8.7//include  -DTEMPLATE_SPECIALIZATION -DTEMPLATE_FUNC_SPECIALIZATION -DHAVE_VSNPRINTF
> -D_FILE_OFFSET_BITS=64   -DUSE_MPI -DHDF5_FILE -DHDF5_PARALLEL -DNETCDF_FILE -DCGM
> -I/home/jain/install/opt_moab//include -o obj/moab_conjht.o
>
> mpif77 -f77=ifort -o nek5000  obj/moab_conjht.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/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/dsygv.o obj/ssygv.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/soft/netcdf/4.0.1-intel-11-serial/lib -lnetcdf      -L/home/jain/lib/hdf5-1.8.7//lib
> -L/home/jain/install/opt_cgm13/lib  -L/home/jain/Cubit-13.1//bin -L/home/jain/install/opt_moab//lib
> -L/home/jain/install/opt_moab//lib -liMesh -lMOAB -lnetcdf  -lhdf5 -lgpfs     -lm -L/home/jain/install/opt_cgm13/lib
> -L/home/jain/Cubit-13.1//bin -lcgm  -L/home/jain/Cubit-13.1//bin -lcubiti19 -lcubit_geom -lcubit_util
>
> ld: warning: libgtcAttrib.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libCMLTet.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libcbtverdict.so.1.2, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: liblpsolve55.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkWidgets.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkIO.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtkHybrid.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkVolumeRendering.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath
> or -rpath-link)
>
> ld: warning: libvtkRendering.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkImaging.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkGraphics.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkFiltering.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkCommon.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkDICOMParser.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkftgl.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtkfreetype.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkexoIIc.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkNetCDF.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkverdict.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtksqlite.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkexpat.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libvtkjpeg.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtkpng.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtktiff.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtksys.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtkzlib.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> ld: warning: libvtkNetCDF_cxx.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libmesquite.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or
> -rpath-link)
>
> ld: warning: libSpaACIS.so, needed by /home/jain/Cubit-13.1//bin/libcubiti19.so, not found (try using -rpath or -rpath-link)
>
> /home/jain/lib/hdf5-1.8.7//lib/libhdf5.a(H5Zdeflate.o): In function `H5Z_filter_deflate':
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:110: undefined reference to `inflateInit_'
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:116: undefined reference to `inflate'
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:180: undefined reference to `compress2'
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:135: undefined reference to `inflateEnd'
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:124: undefined reference to `inflateEnd'
>
> /fusion/gpfs/home/jain/hdf5-1.8.7/src/H5Zdeflate.c:157: undefined reference to `inflateEnd'
>
> ld: nek5000: hidden symbol `stat' in /usr/lib64/libc_nonshared.a(stat.oS) is referenced by DSO
>
> ld: final link failed: Nonrepresentable section on output
>
> make: *** [nek5000] Error 1
>

-- 
Timothy J. Tautges
Manager, Directed Meshing, CD-adapco
Phone: 608-354-1459
timothy.tautges at cd-adapco.com