[Trilinos-Users] Trilinos 10.0.1: problems in configuring EpetraExt with HDF5.

[Daniele Avitabile]

Hi all,

I am converting my codes from Trilinos 9 to Trilinos 10 on a Mac (Leopard).
Here is my do-configure file

------------------------------------------------------------------------------------------------------------------------------------
export TRILINOS_HOME=..
EXTRA_ARGS=$@
cmake \
  -D CMAKE_INSTALL_PREFIX:PATH=/usr/local/trilinos/trilinos-10.0.1/MAC_MPI/
\
  -D CMAKE_C_COMPILER:FILEPATH=/usr/local/bin/mpicc \
       -D CMAKE_C_FLAGS:STRING=-O3 -ftree-vectorize \
  -D CMAKE_CXX_COMPILER:FILEPATH=/usr/local/bin/mpic++ \
       -D CMAKE_CXX_FLAGS:STRING=-O3 -ftree-vectorize \
  -D CMAKE_Fortran_COMPILER:FILEPATH=/usr/local/bin/mpif90 \
       -D CMAKE_F_FLAGS:STRING=-O3 -ftree-vectorize \
  -D TPL_ENABLE_BLAS:BOOL=ON \
      -D BLAS_LIBRARY_NAMES:STRING=blasMACOSX \
      -D BLAS_LIBRARY_DIRS:FILEPATH=/usr/local/blas/BLAS \
  -D TPL_ENABLE_LAPACK:BOOL=ON \
      -D LAPACK_LIBRARY_NAMES:STRING=lapackMACOSX \
      -D LAPACK_LIBRARY_DIRS:FILEPATH=/usr/local/lapack/lapack-3.2.1 \
  -D TPL_ENABLE_MPI:BOOL=ON \
      -D MPI_BASE_DIR:PATH=/usr/local \
      -D MPI_C_COMPILER:FILEPATH=/usr/local/bin/mpicc \
      -D MPI_CXX_COMPILER:FILEPATH=/usr/local/bin/mpic++ \
      -D MPI_Fortran_COMPILER:FILEPATH=/usr/local/bin/mpif90 \
  -D Trilinos_ENABLE_Tpetra:BOOL=ON \
  -D Trilinos_ENABLE_Epetra:BOOL=ON \
  -D Trilinos_ENABLE_EpetraExt:BOOL=ON \
      -D TPL_ENABLE_HDF5:BOOL=ON \
      -D EpetraExt_USING_HDF5:BOOL=ON \
      -D HDF5_LIBRARY_NAMES:STRING=hdf5 \
      -D HDF5_LIBRARY_DIRS:FILEPATH=/usr/local/hdf5/hdf5-1.6.9/hdf5/lib \
      -D HDF5_INCLUDE_DIRS:FILEPATH=/usr/local/hdf5/hdf5-1.6.9/hdf5/include
\
  -D Trilinos_ENABLE_Komplex:BOOL=ON \
  -D Trilinos_ENABLE_Thyra:BOOL=ON \
  -D Trilinos_ENABLE_NOX:BOOL=ON \
      -D NOX_ENABLE_LOCA:BOOL=ON \
  -D Trilinos_ENABLE_AztecOO:BOOL=ON \
  -D Trilinos_ENABLE_Amesos:BOOL=ON \
  -D AMESOS_ENABLE_SuperLUDist:BOOL=ON \
  -D AMESOS_ENABLE_ParMETIS:BOOL=ON \
  -D Trilinos_ENABLE_Ifpack:BOOL=ON \
  -D Trilinos_ENABLE_ML:BOOL=ON \
  -D Trilinos_ENABLE_Anasazi:BOOL=ON \
  -D Trilinos_ENABLE_Teuchos:BOOL=ON \
      -D TEUCHOS_ENABLE_COMPLEX:BOOL=ON \
  -D Trilinos_ENABLE_Triutils:BOOL=ON \
  -D Trilinos_ENABLE_Galeri:BOOL=ON \
  -D Trilinos_ENABLE_TESTS:BOOL=OFF \
  -D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \
  -D DART_TESTING_TIMEOUT:STRING=600 \
  -D
Trilinos_EXTRA_LINK_FLAGS:STRING="/usr/local/parmetis/ParMetis-3.1/libmetis.a
/usr/local/parmetis/ParMetis-3.1/libparmetis.a
/usr/local/superludist/SuperLU_DIST_2.3/lib/libsuperlu_dist_2.3.a
/usr/local/lib/libgfortran.a
/usr/local/mumps/MUMPS_4.7.3/lib/libdmumpsMACOSX.a
/usr/local/mumps/MUMPS_4.7.3/lib/libpordMACOSX.a
/usr/local/scalapack/scalapack-1.8.0/libscalapack.a /usr/local/lib/libmpi.a
/usr/local/lib/libmpi_f77.a /usr/local/lib/libmpi_cxx.a
/usr/local/lib/libmpi_f90.a /usr/local/blacs/BLACS/LIB/blacs_MPI-MACOSX-0.a
/usr/local/blacs/BLACS/LIB/blacsF77init_MPI-MACOSX-0.a
/usr/local/blacs/BLACS/LIB/blacsCinit_MPI-MACOSX-0.a" \
  $EXTRA_ARGS \
  ${TRILINOS_HOME}
--------------------------------------------------------------------------------------------------------------------------------

I am aware that the last few lines, where I set
-D Trilinos_EXTRA_LINK_FLAGS:STRING, are a sort of blasphemy. I will amend
them soon.

My problem concerns EpetraExt and HDF5. Please note that:

1) I am absolutely sure that my folder /usr/local/hdf5/hdf5-1.6.9/hdf5/lib
contains the file libhdf5
2) I am also sure that my folder /usr/local/hdf5/hdf5-1.6.9/hdf5/include
contains the file hdf5.h
3) When I run do-configure, I receive no complaint

Now, when I run make, I receive the following error

-------------------------------------------------------------------------
In file included from
/usr/local/trilinos/trilinos-10.0.1/packages/epetraext/src/inout/EpetraExt_HDF5.cpp:28:
/usr/local/trilinos/trilinos-10.0.1/packages/epetraext/src/inout/EpetraExt_HDF5.h:35:18:
error: hdf5.h: No such file or directory
----------------------------------------------------------------------------

Here are my questions:

a) How come the hdf5 header is not included? I manage to solve this problem
by specifying

-----------------------------------------------------------------------------------------------------------------------------------------
-D CMAKE_C_FLAGS:STRING=-O3 -ftree-vectorize
-I/usr/local/hdf5/hdf5-1.6.9/hdf5/include
-L/usr/local/hdf5/hdf5-1.6.9/hdf5/lib
 -D CMAKE_CXX_FLAGS:STRING=-O3 -ftree-vectorize
-I/usr/local/hdf5/hdf5-1.6.9/hdf5/include
-L/usr/local/hdf5/hdf5-1.6.9/hdf5/lib
--------------------------------------------------------------------------------------------------------------------------------------------

but I don't quite like this solution.

b) I would have thought that hdf5 were considered TPLs. If I look at the
output of my do-configure, I read

-----------------------------------------------------------------------------------------------------------------------------------------------
Final set of enabled TPLs:  MPI BLAS LAPACK 3

Final set of non-enabled TPLs:  TBB Pthread ARPREC QD Boost Scotch METIS
ParMETIS PaToH CppUnit ADOLC TVMET MF ExodusII Nemesis ZoltanTpl y12m
SuperLUDist SuperLU Zlib UMFPACK MA28 AMD PETSC HYPRE BLACS SCALAPACK MUMPS
Oski TAUCS ForUQTK Dakota 32
------------------------------------------------------------------------------------------------------------------------------------------------

Thanks a lot for your help!

Daniele
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