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

[Ikuo Cho]

Brad, 

Thank you for the suggestion.
I tried to do
> The workaround is to add CXXFLAGS=-DMPICH_IGNORE_CXX_SEEK to the 
but the same problem arose.

I also tried the option "--enable-hdf5=no" for builfing pylith.
In this case, I could successfully finish the configure script, but
couldn't complete the compilation.

> propagates to PyLith). I will update the installer to do this automatically.
I'm looking forward your updating anyway.

Ikuo

On Mon, 11 Jul 2011 08:18:24 -0700
Brad Aagaard <baagaard at usgs.gov> wrote:

> 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
> > ----------------------------------------------------------
> >
> >
> >
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
> 
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-- 
Cho Ikuo <ikuo-chou at aist.go.jp>