[MOAB-dev] linking against MOAB
tautges at mcs.anl.gov
tautges at mcs.anl.gov
Fri Feb 5 23:06:06 CST 2010
Since those are both coming from Moab_libs_link, though, we should
change how that's constructed.
- tim
On Feb 5, 2010, at 9:03 PM, Jason Kraftcheck <kraftche at cae.wisc.edu>
wrote:
> On 02/05/2010 05:32 PM, iulian at mcs.anl.gov wrote:
>> 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.
>>
>
> Libraries (at least static ones) must be specified in order of
> reverse-dependency. If both libnetcdf and libhdf5_hl depend on
> libhdf5, then the -lhdf5 must appear *after* both -lnetcdf and -
> lhdf5_hl on the link line.
>
> - jason
>
>
>
>
>
>> 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
>
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