[MOAB-dev] Re: undefined reference to `H5Tarray_create2
Tim Tautges
tautges at mcs.anl.gov
Tue Jun 10 20:19:08 CDT 2008
First, what version of hdf5 do you have? I've successfully built with
1.6.5 and 1.8.1. MOAB only uses the C interface for HDF5, so you're ok
that way.
I've seen some oddities with the hdf5 stuff not getting completely
cleaned out after compiling serially then doing a make clean and
re-configuring to compile in parallel. Try doing a make distclean, and
if you've installed, delete the lib and include directories there. Then
try rebuilding with parallel support turned on.
- tim
de Almeida, Valmor F. wrote:
> 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
>
>
>
--
================================================================
"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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