[CIG-SHORT] pylith installer problem with related to hdf5.h

[Brad Aagaard]

Ikuo-

This is an mpich related error.
http://wiki.mcs.anl.gov/mpich2/index.php/Frequently_Asked_Questions#Q:_I_get_compile_errors_saying_.22SEEK_SET_is_.23defined_but_must_not_be_for_the_C.2B.2B_binding_of_MPI.22.

The workaround is to add CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK to the 
configure argument to HDF5 (we already do this for PETSc which 
propagates to PyLith). I will update the installer to do this automatically.

Brad



On 07/10/2011 09:36 PM, Ikuo Cho wrote:
> Dear PyLith developers;
>
> I've been trying to install PyLith 1.6 by the installer
> pylith-installer.1.6.0-1.
> Following the instruction, I ran the configure script by typing the command as
>
> $HOME/src/pylith/pylith-installer-1.6.0-1/configure \
>      --with-fortran=no \
>      --disable-numpy \
>      --disable-proj4 \
>      --disable-netcdf \
>      --with-petsc_options="--with-clanguage=C++ --with-mpi-dir=$pylithdir --with-mpi=1 --with-fc=gfortran --with-shared-libraries" \
>      --with-make-threads=8 \
>      --prefix=$HOME/pylith
>
> after separately installing mpich2, python, netcdf, numpy, proj, and
> petsc(-dev-pylith-1.6.0) .
>
> Afetr all, the configuration for PyLith failed with the message:
>
> ...
> checking hdf5.h usability... no
> checking hdf5.h presence... yes
> configure: WARNING: hdf5.h: present but cannot be compiled
> configure: WARNING: hdf5.h:     check for missing prerequisite headers?
> configure: WARNING: hdf5.h: see the Autoconf documentation
> configure: WARNING: hdf5.h:     section "Present But Cannot Be Compiled"
> configure: WARNING: hdf5.h: proceeding with the compiler's result
> configure: WARNING:     ## ---------------------------------------- ##
> configure: WARNING:     ## Report this to cig-short at geodynamics.org ##
> configure: WARNING:     ## ---------------------------------------- ##
> checking for hdf5.h... no
> configure: error: HDF5 header not found; try CPPFLAGS="-I<hdf5 include dir>"
>
> I checked the existence of the file hdf5.h in the directory
> $HOME/pylith/include. I don't know what was wrong.
>
> The attached file was generated in the directory
> build/pylith/pylith-build/config.log
>
> Ikuo Cho
>
> ----------------------------------------------------------
> Ikuo Cho  ( ikuo-chou at aist.go.jp )
> Geological Survey of Japan,
> National Institute of Advanced Industrial Science and Technology
> Tsukuba Central 7, Tsukuba 305-8567 Japan
> Tel +81-29-861-3891, Fax +81-29-855-1298
> ----------------------------------------------------------
>
>
>
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