[MOAB-dev] linking against MOAB

Fri Feb 5 17:32:41 CST 2010

Hello,
I have a beginner's question on how to link against MOAB :(

I don't use autotools, and I can't understand the error I am getting.
It seems it is a problem with the version for hdf5 library.  

my makefile is below, and the error I am getting is after that.

Thanks,
Iulian

CXX=/homes/sharp/3rdparty/mpich2/mpich2-1.1.1p1/gcc/bin/mpicxx

.SUFFIXES: .cxx .cc .fd

.cc.o:
        $(CXX) $(CFLAGS) -c $<

.cxx.o:
        $(CXX) $(CFLAGS) -c $<

.C.o:
        $(CXX) $(CFLAGS) -c $<

.fd.c:
        fdesign -c $<

.fd.h:
        fdesign -c $<

GFX2_FLAGS = -m486 -DGFX_NO_BOOL -DGFX_DEF_FMATH -Wno-deprecated

include /homes/iulian/lib/MOAB/lib/moab.make

OPTFLAGS = -O2 $(GFX2_FLAGS)
FEATURES =

CFLAGS = $(MOAB_INCLUDES) $(OPTFLAGS)
LFLAGS = $(LIBDIR) $(OPTFLAGS)

CORE_SRCS = cmdline.cxx avars.cxx decimate.cxx quadrics.cxx \
            AdjPrims.cxx AdjModel.cxx Nvars.cxx Mat4.cxx timing.cxx \
            smf.cxx smfstate.cxx 3D.cxx heap.cxx \
            ProxGrid.cxx futils.cxx ProjectH.cxx

QSLIM_SRCS = qslim.cxx $(CORE_SRCS)
QSLIM_OBJS = $(QSLIM_SRCS:.cxx=.o)

qslim : $(QSLIM_OBJS)
        $(CXX) -o qslim $(QSLIM_OBJS) -lm $(MOAB_LIBS_LINK)

clean:
        -$(CLEAN)

error in compiling
...
/homes/sharp/3rdparty/mpich2/mpich2-1.1.1p1/gcc/bin/mpicxx -o qslim qslim.o cmdline.o avars.o decimate.o quadrics.o AdjPrims.o AdjMo
del.o Nvars.o Mat4.o timing.o smf.o smfstate.o 3D.o heap.o ProxGrid.o futils.o ProjectH.o -lm -L/homes/sharp/3rdparty/netcdf/netcdf-
4.0.1/parallel/gcc/lib    -L/homes/sharp/3rdparty/zlib/zlib-1.2.3/gcc/lib -L/homes/sharp/3rdparty/szip/szip-2.1/gcc/lib  -L/homes/sh
arp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib -L/homes/iulian/lib/CGM/lib  -L/homes/sharp/3rdparty/OCC/OpenCASCADE6.3.0/gcc/lib -L/h
omes/iulian/lib/MOAB/lib -lMOAB -lm -lhdf5  -lsz -lz -lnetcdf_c++ -lnetcdf -lhdf5_hl -lcgm  -lTKMath -lTKXSBase -lTKernel -lTKShHeal
ing -lTKBRep -lTKG3d -lTKBO -lTKFeat -lTKFillet -lTKG2d -lTKOffset -lTKBool -lTKGeomAlgo -lTKGeomBase -lTKPrim -lTKTopAlgo -lTKHLR -
lTKIGES -lTKMesh -lTKPrim -lTKSTEP209 -lTKSTEPAttr -lTKSTEPBase -lTKSTEP -lTKSTL -lTKTopAlgo -lTKXSBase -lTKLCAF -lTKBinL -ldl
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `get_netcdf_type':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1220: undefined reference to `H5Tget_native_type'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `nc4_open_var_grp2':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:175: undefined reference to `H5Dopen1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `nc4_open_var_grp':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:152: undefined reference to `H5Dopen1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `get_hdf_typeid':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:379: undefined reference to `H5Tset_strpad'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `pg_att_grpa':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1751: undefined reference to `H5Tset_strpad'
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1694: undefined reference to `H5Tget_native_type'
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1674: undefined reference to `H5Tget_native_type'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `read_dataset':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:4343: undefined reference to `H5Dopen1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `read_type':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1828: undefined reference to `H5Tget_native_type'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `read_var':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:4158: undefined reference to `H5Tget_native_type'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `commit_type':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:2129: undefined reference to `H5Tcommit1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `write_dim':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:2579: undefined reference to `H5Dextend'
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:2518: undefined reference to `H5Dcreate1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `var_create_dataset':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1528: undefined reference to `H5Dcreate1'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `nc4_get_vara':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:1077: undefined reference to `H5Tget_native_type'
/homes/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/gcc/lib/libnetcdf.a(nc4hdf.o): In function `nc4_put_vara':
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:819: undefined reference to `H5Tget_native_type'
/homes/smithrm/sharp/3rdparty/netcdf/netcdf-4.0.1/parallel/src/libsrc4/nc4hdf.c:792: undefined reference to `H5Dextend'
/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib/libhdf5_hl.a(H5LT.o): In function `H5LTmake_dataset_string':
H5LT.c:(.text+0x136a): undefined reference to `H5Tset_strpad'
/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib/libhdf5_hl.a(H5LT.o): In function `H5LTset_attribute_string':
H5LT.c:(.text+0x1976): undefined reference to `H5Tset_strpad'
/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib/libhdf5_hl.a(H5LT.o): In function `H5LT_set_attribute_string':
H5LT.c:(.text+0x1b12): undefined reference to `H5Tset_strpad'
/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib/libhdf5_hl.a(H5LT.o): In function `H5LT_dtype_to_text':
H5LT.c:(.text+0x2b09): undefined reference to `H5Tget_strpad'
H5LT.c:(.text+0x2b1b): undefined reference to `H5Tget_cset'
H5LT.c:(.text+0x30f4): undefined reference to `H5Tset_cset'
H5LT.c:(.text+0x3106): undefined reference to `H5Tset_strpad'
H5LT.c:(.text+0x32f0): undefined reference to `H5Tset_cset'
H5LT.c:(.text+0x3314): undefined reference to `H5Tset_strpad'
/homes/sharp/3rdparty/hdf5/hdf5-1.8.3/parallel/gcc/lib/libhdf5_hl.a(H5LTparse.o): In function `H5LTyyparse':
H5LTparse.c:(.text+0xc96): undefined reference to `H5Tset_strpad'
H5LTparse.c:(.text+0xca3): undefined reference to `H5Tset_cset'
H5LTparse.c:(.text+0xdcf): undefined reference to `H5Tget_native_type'
collect2: ld returned 1 exit status
make: *** [qslim] Error 1