[MOAB-dev] undefined reference to `H5Tarray_create2
de Almeida, Valmor F.
dealmeidav at ornl.gov
Tue Jun 10 19:15:21 CDT 2008
Tim,
I am trying to compile MOAB without imesh enabled, and with parallel
hdf5 enabled. Here is the configure
./configure --prefix=$HOME/projects/scidac/itaps/moab-usr
--enable-doxygen=/usr/bin --with-mpi=/usr/local/ompi_gnu --with-zlib=/
--with-szip=/ --with-hdf5=/usr/local/hdf5 --with-netcdf=/usr/lib
At the end of this e-mail is the end of the compilation output.
I can get a successful MOAB compilation if I use hdf5 without parallel
support but not otherwise.
When I built hdf5 with parallel support, I could not enable the c++
interface because it is incompatible with parallel support. So I am
guessing that MOAB is using the hdf5 c++ interface. Is this correct? If
so, this interface is not available when hdf5 is built with parallel
support.
Please advise. Thanks,
--
Valmor
/usr/local/ompi_gnu/bin/mpicxx -Wall -pipe -O2 -DNDEBUG -o mbconvert
convert.o -L/usr/lib -L//lib -L/usr/local/hdf5_gnu/lib
../../.libs/libMOAB.a /usr/lib/libnetcdf_c++.so /usr/lib/libnetcdf.so
/usr/lib/libhdf5.so -lssl -lcrypto -lz
/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib/libmpi_cxx.so
/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib/libmpi.so
/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib/libopen-rte.so
/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib/libopen-pal.so -lm
-Wl,--rpath -Wl,/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib
-Wl,--rpath -Wl,/usr/local/packages/openmpi-1.2.6_gcc-4.1.2/lib
../../.libs/libMOAB.a(ReadHDF5.o): In function `ReadHDF5::read_tag(char
const*)':
ReadHDF5.cpp:(.text+0x447d): undefined reference to `H5Tarray_create2'
../../.libs/libMOAB.a(WriteHDF5.o): In function
`WriteHDF5::write_sparse_tag(WriteHDF5::SparseTag const&)':
WriteHDF5.cpp:(.text+0x2835): undefined reference to `H5Tarray_create2'
../../.libs/libMOAB.a(adjacency.o): In function `mhdf_haveAdjacency':
adjacency.c:(.text+0x28f): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(file.o): In function `mhdf_readHistory':
file.c:(.text+0x76): undefined reference to `H5Gopen2'
file.c:(.text+0xb6): undefined reference to `H5Dopen2'
../../.libs/libMOAB.a(file.o): In function `mhdf_writeHistory':
file.c:(.text+0x3d5): undefined reference to `H5Dcreate2'
../../.libs/libMOAB.a(file.o): In function `get_max_id':
file.c:(.text+0x57f): undefined reference to `H5Gopen2'
file.c:(.text+0x5ab): undefined reference to `H5Dopen2'
../../.libs/libMOAB.a(file.o): In function `mhdf_getElemHandles':
file.c:(.text+0x867): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(file.o): In function `make_hdf_group':
file.c:(.text+0xa93): undefined reference to `H5Gcreate2'
../../.libs/libMOAB.a(file.o): In function `mhdf_addElement':
file.c:(.text+0xc90): undefined reference to `H5Gcreate2'
file.c:(.text+0xcc5): undefined reference to `H5Gcreate2'
../../.libs/libMOAB.a(file.o): In function `mhdf_openFileWithOpt':
file.c:(.text+0x10e8): undefined reference to `H5Gopen2'
file.c:(.text+0x1112): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(file.o): In function `mhdf_createFile':
file.c:(.text+0x1501): undefined reference to `H5Gopen2'
file.c:(.text+0x160d): undefined reference to `H5Tcommit2'
../../.libs/libMOAB.a(sets.o): In function `mhdf_haveSets':
sets.c:(.text+0x10d6): undefined reference to `H5Gopen2'
sets.c:(.text+0x1117): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `get_tag':
tags.c:(.text+0x3a2): undefined reference to `H5Gopen2'
tags.c:(.text+0x3c1): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_createVarLenTagData':
tags.c:(.text+0x640): undefined reference to `H5Topen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_createSparseTagData':
tags.c:(.text+0x7e6): undefined reference to `H5Topen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_openDenseTagData':
tags.c:(.text+0x963): undefined reference to `H5Gopen2'
tags.c:(.text+0xa36): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_createDenseTagData':
tags.c:(.text+0xb03): undefined reference to `H5Gopen2'
tags.c:(.text+0xb85): undefined reference to `H5Gopen2'
tags.c:(.text+0xba4): undefined reference to `H5Gopen2'
tags.c:(.text+0xbcd): undefined reference to `H5Topen2'
tags.c:(.text+0xc67): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_haveDenseTag':
tags.c:(.text+0xdd3): undefined reference to `H5Gopen2'
tags.c:(.text+0xe33): undefined reference to `H5Gopen2'
tags.c:(.text+0xeb8): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function
`get_attrib_array_length_name':
tags.c:(.text+0xffb): undefined reference to `H5Tget_array_dims2'
../../.libs/libMOAB.a(tags.o): In function `read_tag_attrib_data':
tags.c:(.text+0x1124): undefined reference to `H5Tarray_create2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_getTagInfo':
tags.c:(.text+0x1401): undefined reference to `H5Topen2'
tags.c:(.text+0x16e6): undefined reference to `H5Tget_array_dims2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_getNumberTags':
tags.c:(.text+0x18a6): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `mhdf_getTagNames':
tags.c:(.text+0x1977): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(tags.o): In function `store_tag_val_in_attrib':
tags.c:(.text+0x1c20): undefined reference to `H5Tarray_create2'
../../.libs/libMOAB.a(tags.o): In function `create_tag_common':
tags.c:(.text+0x1d2d): undefined reference to `H5Gopen2'
tags.c:(.text+0x1d71): undefined reference to `H5Gcreate2'
tags.c:(.text+0x1e8d): undefined reference to `H5Tarray_create2'
tags.c:(.text+0x1edd): undefined reference to `H5Tcommit2'
tags.c:(.text+0x236f): undefined reference to `H5Tarray_create2'
../../.libs/libMOAB.a(util.o): In function `mhdf_write_max_id':
util.c:(.text+0x1a8): undefined reference to `H5Gopen2'
util.c:(.text+0x269): undefined reference to `H5Acreate2'
../../.libs/libMOAB.a(util.o): In function `mhdf_create_scalar_attrib':
util.c:(.text+0x326): undefined reference to `H5Acreate2'
../../.libs/libMOAB.a(util.o): In function `get_elem_type_enum':
util.c:(.text+0x3e0): undefined reference to `H5Topen2'
../../.libs/libMOAB.a(util.o): In function `mhdf_open_table':
util.c:(.text+0x63d): undefined reference to `H5Dopen2'
../../.libs/libMOAB.a(util.o): In function `mhdf_create_table':
util.c:(.text+0x79b): undefined reference to `H5Dcreate2'
../../.libs/libMOAB.a(util.o): In function `mhdf_find_attribute':
util.c:(.text+0xfc5): undefined reference to `H5Aiterate2'
../../.libs/libMOAB.a(util.o): In function `mhdf_open_table2':
util.c:(.text+0x112d): undefined reference to `H5Dopen2'
../../.libs/libMOAB.a(util.o): In function
`mhdf_elem_group_from_handle':
util.c:(.text+0x1548): undefined reference to `H5Gopen2'
../../.libs/libMOAB.a(WriteHDF5Parallel.o): In function
`WriteHDF5Parallel::create_file(char const*, bool,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > >&, int, bool)':
WriteHDF5Parallel.cpp:(.text+0x6c7b): undefined reference to
`H5Pset_fapl_mpio'
collect2: ld returned 1 exit status
make[3]: *** [mbconvert] Error 1
make[3]: Leaving directory
`/home/dealmeida/projects/scidac/itaps/moab-dev/tools/converter'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory
`/home/dealmeida/projects/scidac/itaps/moab-dev/tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/home/dealmeida/projects/scidac/itaps/moab-dev'
make: *** [all] Error 2
> -----Original Message-----
> From: Tim Tautges [mailto:tautges at mcs.anl.gov]
> Sent: Tuesday, June 10, 2008 12:28 PM
> To: de Almeida, Valmor F.
> Cc: MOAB-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] error: The package name "iMesh_SIDL" is
illegal
> because it has an underbar (_)
>
> MOAB's only compatible right now with SIDL 0.10.12. There are
specific
> changes required to go to 1.x that we haven't made yet. I'll put the
> question to the ITAPS group in general (if you're interested in doing
> that I'd very much welcome that too). We've gone to a common
> implementation of the SIDL interface on top of our C interface, but
> right now that implementation is supposed to be ours.
>
> - tim
>
> de Almeida, Valmor F. wrote:
> > This is a more involved config build
> >
> > ./configure --prefix=$HOME/projects/scidac/itaps/moab-usr
> > --enable-doxygen=/usr/bin --enable-imesh
--with-mpi=/usr/local/ompi_gnu
> > --with-zlib=/ --with-szip=/ --with-hdf5=/usr/lib
--with-netcdf=/usr/lib
> > --with-babel=/usr/local/cca-tools
> >
> > The configure went fine I think. Here is where make stopped:
> >
> >
> > ***********************************************
> > ...snip...
> >
> > make[4]: Leaving directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev/tools/iMesh'
> > Making all in SIDL
> > make[4]: Entering directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev/tools/iMesh/SIDL'
> > test -d mserver || /bin/mkdir -p mserver || exit 1
> > /usr/local/cca-tools/bin/babel -sC++ ./iBase.sidl ./iMesh.sidl
> > ./iMesh_SIDL.sidl -o mserver
> > - #1----------------------------------------
> >
/home/dealmeida/projects/scidac/itaps/moab-dev/tools/iMesh/SIDL/iMesh_SI
> > DL.sidl:4: error: The package name "iMesh_SIDL" is illegal because
it
> > has an underbar (_).
> > package iMesh_SIDL version 0.002 {
> > ^^^^^^^^^^
> > make[4]: *** [mserver/babel.make] Error 88
> > make[4]: Leaving directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev/tools/iMesh/SIDL'
> > make[3]: *** [all-recursive] Error 1
> > make[3]: Leaving directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev/tools/iMesh'
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev/tools'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory
> > `/home/dealmeida/projects/scidac/itaps/moab-dev'
> > make: *** [all] Error 2
> > ***********************************************
> >
> > Here is babel's version
> >
> > ->babel --version
> > Babel version 1.0.8
> >
> > Is this a matter of upgrading babel or another issue?
> >
> > Thanks,
> >
> > --
> > Valmor
> >
> >
> >
> >
>
> --
> ================================================================
> "You will keep in perfect peace him whose mind is
> steadfast, because he trusts in you." Isaiah 26:3
>
> Tim Tautges Argonne National Laboratory
> (tautges at mcs.anl.gov) (telecommuting from UW-Madison)
> phone: (608) 263-8485 1500 Engineering Dr.
> fax: (608) 263-4499 Madison, WI 53706
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