[Trilinos-Users] [EXTERNAL] EpetraExt_HDF5

[Perschbacher, Brent M]

Minh Do,
  If you only set EpetraExt_USING_HDF5 to on then you haven't actually
enabled the TPL HDF5, but instead only told EpetraExt to expect HDF5.
Without actually enabling HDF5 though the libraries are never linked and
you will get linker errors like the ones you are seeing. To properly
enable HDF5 you will want to use the configure option:

-DTPL_ENABLE_HDF5=ON

This should find your HDF5 since it is in a system library path, however
if it does not you can tell the configure where to find HDF5 with the
following configure options:

-DHDF5_LIBRARY_DIRS=/usr/lib
-DHDF5_INCLUDE_DIRS=/usr/include

You should also remove the line "-D EpetraExt_USING_HDF5:BOOL=ON \" from
your configure script as that is not needed. EpetraExt will default to
using HDF5 when it is enabled and won't use it when it is disabled.
Setting this directly is generally only useful to disable a package's
usage of a TPL when the TPL is enabled.

Brent

On 8/22/13 10:23 PM, "Minh Do-Quang" <minh at mech.kth.se> wrote:

>Hi,
>
>I would like to config Trilinos with EpetraExt_HDF5, but I the compiler
>cant not link with HDF5 library. The error is:
>
>Linking CXX shared library libtpetraext.so
>[ 44%] Built target tpetraext
>[ 46%] Built target epetraext
>Linking CXX executable EpetraExt_Permutation_test.exe
>../../src/libepetraext.so.11.4.1: undefined reference to
>`H5P_CLS_FILE_ACCESS_g'
>../../src/libepetraext.so.11.4.1: undefined reference to `H5Dread'
>../../src/libepetraext.so.11.4.1: undefined reference to `H5Pclose'
>../../src/libepetraext.so.11.4.1: undefined reference to
>`H5Sget_simple_extent_ndims'
>../../src/libepetraext.so.11.4.1: undefined reference to
>`H5Pset_dxpl_mpio'
>../../src/libepetraext.so.11.4.1: undefined reference to
>`H5Screate_simple'
>
>When I do the configuration, I have used the options:
> -D Trilinos_ENABLE_EpetraExt:BOOL=ON \
> -D EpetraExt_USING_HDF5:BOOL=ON \
>
>My HDF5 libraries are located at /usr/lib as a default
>
>Any help would be appreciated,
>Regards,
>/ Minh Do
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