[Trilinos-Users] Cannot compile trilinos with hdf5 support

[Perschbacher, Brent M]

Hi Martin,
  Trilinos 10.6 only supports version 1.6 for hdf5. That has been addressed
and the next release will support version 1.8. I don't know why your 1.8
build of hdf5 with the 1.6 api failed though. I don't recall if using that
option required changes in the host code I vaguely recall something about
macros though. I really only glanced at it since we were moving to the newer
api so I could be completely wrong on that point.

I believe there are a couple potential fixes. I seem to recall that HDF5's
configure would only build the mpi symbols if you configured it with your
mpi compilers and you pass it the --enable-parallel option. That alone might
solver your issue since you were also configuring with the 1.6 api, however
your best bet would be to get a copy of  version 1.6.10 which is what we had
been testing against and use that. It is still available on the HDF5 website
at http://www.hdfgroup.org/ftp/HDF5/prev-releases/. You will still have to
build with your mpi compilers as above though.

Brent






On 7/28/11 3:55 PM, "Martin Vymazal" <martin.vymazal at vki.ac.be> wrote:

> Dear Trilinos developers,
> 
>   I would like to use Trilinos with hdf5 support. I compiled and
> installed hdf-1.8.6 in my ~/local/hdf5, but I cannot compile trilinos.
> I'm getting this error:
> 
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp: In member function ?void
> EpetraExt::HDF5::Create(std::string)?:
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp:247: error: ?H5Pset_fapl_mpio? was not declared in this
> scope
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp:249: error: ?H5Pset_fapl_mpio? was not declared in this
> scope
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp: In member function ?void EpetraExt::HDF5::Write(const std::string&,
> const Epetra_MultiVector&,
> bool)?:
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp:944: error: ?H5Pset_dxpl_mpio? was not declared in this
> scope
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp: In member function ?void EpetraExt::HDF5::Read(const std::string&,
> Epetra_MultiVector*&, bool, const
> int&)?:
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp:1038: error: ?H5Pset_dxpl_mpio? was not declared in this
> scope
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp: In member function ?void EpetraExt::HDF5::Write(const std::string&,
> const std::string&, int, int, int, const
> void*)?:
> /home/martin/trilinos-10.6.1-source/packages/epetraext/src/inout/EpetraExt_HDF
> 5.cpp:1583: error: ?H5Pset_dxpl_mpio? was not declared in this
> scope
> 
> I set the path to hdf5 with:
>    -D HDF5_INCLUDE_DIRS:PATH=$HOME/local/hdf5/include \
>    -D HDF5_LIBRARY_DIRS:PATH=$HOME/local/hdf5/lib \
> 
> Looking to CMakeCache.txt, I have:
> 
> TPL_HDF5_INCLUDE_DIRS:PATH=/home/martin/local/hdf5/include
> TPL_HDF5_LIBRARIES:FILEPATH=/home/martin/local/hdf5/lib/libhdf5.so
> 
> which is correct.
> 
> I also did 'grep -iRn H5Pset_dxpl_mpio ./*' in
> /home/martin/local/hdf5. I got this:
> ./include/H5FDmpio.h:53:H5_DLL herr_t H5Pset_dxpl_mpio(hid_t dxpl_id,
> H5FD_mpio_xfer_t xfer_mode);
> 
> I compiled hdf5 with the version 1.6 API. It is strange that the
> trilinos compilation fails, since I used exactly the same cmake
> configuration for trilinos and hdf5 in another machine, where
> everything worked perfectly. Could you please help me?
> 
>   Thank you very much,
> 
>    Martin Vymazal
> 
> 
> 
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