[Trilinos-Users] Compilation with hdf5 TPL fails

[Nico Schlömer]

Hi Martin,

I had a similar issue before and it was indeed caused by the fact that
Trilinos requires HDF5 1.6.* to work.

Btw, the HDF group announced that the current version of the HDF5
library, 1.6.10, will be the last for 1.6:

========================= *snip* =========================
The latest formal release of HDF5 1.6, version 1.6.10, can be obtained
from this page. This release contains bug fixes and changes since the
last release.
Please note that this is the *LAST* release of HDF5 1.6.
Users should plan to move to the HDF5 1.8 release
<http://www.hdfgroup.org/HDF5/release/obtain5.html>. Please refer to the
What's New in 1.8
<http://www.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew180.html> document for
the changes in the HDF5 1.8 release.
========================= *snap* =========================

(from <http://www.hdfgroup.org/HDF5/release/obtain516.html>).
Mike, is anyone on top of that already?

Cheers,
Nico






On 05/21/2010 12:30 PM, Michel Kern wrote:
> This is likely due to a mismatch between the hdf5 version installed on
> your system and the one used by Trilinos.
> The hdf5 API changed between version 1.6 and 1.8.
> If I'm right (yes, it does happen once in a while:), Trilinos uses
> 1.6, whereas you have 1.8 installed.
> A workaround is to add a CPP flag -DH5_USE_16_API, which gets you back
> the 1.6 API.
>
> Hope this helps,
> Michel
>
> Le 21/05/2010 12:15, Martin Vymazal a écrit :
>> Hello trilinos users&  developers,
>>
>>    I'd like to compile trilinos with hdf5 support, but the compilation
>> fails with this error:
>>
>> In file included from
>> /data/repository/trilinos/trilinos-10.2.1-Source/packages/epetraext/src/inout/EpetraExt_HDF5.cpp:28:0:
>>
>> /data/repository/trilinos/trilinos-10.2.1-Source/packages/epetraext/src/inout/EpetraExt_HDF5.h:
>> In member function ?void EpetraExt::HDF5::CreateGroup(const
>> std::string&)?:
>> /data/repository/trilinos/trilinos-10.2.1-Source/packages/epetraext/src/inout/EpetraExt_HDF5.h:333:64:
>> error: too few arguments to function ?hid_t H5Gcreate2(hid_t, const
>> char*, hid_t, hid_t,
>> hid_t)?
>> /usr/include/H5Gpublic.h:75:14: note: declared here
>> /data/repository/trilinos/trilinos-10.2.1-Source/packages/epetraext/src/inout/EpetraExt_HDF5.cpp:
>> In function ?void WriteParameterListRecursive(const
>> Teuchos::ParameterList&,
>> hid_t)?:
>>
>> I configure trilinos with the following script:
>>
>> #!/bin/bash
>>
>> EXTRA_ARGS=$@
>>
>> cd build
>>
>> cmake \
>>     -D CMAKE_BUILD_TYPE:STRING=RELEASE \
>>     -D Trilinos_ENABLE_ML:BOOL=ON \
>>     -D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON \
>>     -D Trilinos_ENABLE_TESTS:BOOL=ON \
>>     -D Trilinos_ENABLE_Anasazi:BOOL=ON \
>>     -D Trilinos_Anasazi_ENABLE_TESTS:BOOL=ON \
>>     -D Trilinos_Anasazi_ENABLE_EXAMPLES:BOOL=ON \
>>     -D Trilinos_Anasazi_ENABLE_Epetra:BOOL=ON \
>>     -D Trilinos_ENABLE_Zoltan:BOOL=ON \
>>     -D Zoltan_ENABLE_MPI:BOOL=ON \
>>     -D EpetraExt_ENABLE_Zoltan:BOOL=ON \
>>     -D EpetraExt_BUILD_Zoltan:BOOL=ON \
>>     -D EpetraExt_BUILD_PETSC:BOOL=ON \
>>     -D EpetraExt_BUILD_UMFPACK:BOOL=ON \
>>     -D EpetraExt_ENABLE_AMD:BOOL=ON \
>>     -D HDF_INCLUDE_DIRS:PATH=/usr/include \
>>     -D HDF_LIBRARY_DIRS:PATH=/usr/lib \
>>     -D EpetraExt_ENABLE_HDF5:BOOL=ON \
>>     -D ML_ENABLE_Aztec:BOOL=ON \
>>     -D ML_ENABLE_MPI:BOOL=ON \
>>     -D ML_ENABLE_Zoltan:BOOL=ON \
>>     -D DART_TESTING_TIMEOUT:STRING=600 \
>>     -D TPL_ENABLE_MPI:BOOL=ON \
>>     -D CMAKE_INSTALL_PREFIX:PATH=$HOME/libs/trilinos \
>>     $EXTRA_ARGS \
>>     ${TRILINOS_HOME}
>>
>> I'm sorry if this question was answered in the past, but your system
>> denies me the access to the mailing list archives (I tried different
>> browsers, had password reminder sent to me too).
>>
>> I'll be grateful for any suggestions conerning the compilation error.
>>
>> Best regards,
>>
>>     Martin Vymazal
>>
>> P.S The error is the same with trilinos 10.2.0 and 10.2.1
>>
>>
>>
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>
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