[MOAB-dev] undefined reference to `H5Tarray_create2

[de Almeida, Valmor F.]

Got it. If a package is in the usual place don't need to tell
./configure.

That was indeed the problem. The /usr/local/hdf5 I installed is v1.8.1
but I need to keep another version, hdf5-1.6.4, on the system so other
packages don't break. The configure was getting confused.

Thanks,

--
Valmor

> -----Original Message-----
> From: Jason Kraftcheck [mailto:kraftche at cae.wisc.edu]
> Sent: Wednesday, June 11, 2008 11:13 AM
> To: de Almeida, Valmor F.
> Cc: Tim Tautges; MOAB-dev at mcs.anl.gov
> Subject: Re: [MOAB-dev] undefined reference to `H5Tarray_create2
> 
> de Almeida, Valmor F. wrote:
> > Tim,
> >
> > I am trying to compile MOAB without imesh enabled, and with parallel
> > hdf5 enabled. Here is the configure
> >
> > ./configure --prefix=$HOME/projects/scidac/itaps/moab-usr
> > --enable-doxygen=/usr/bin   --with-mpi=/usr/local/ompi_gnu
--with-zlib=/
> > --with-szip=/ --with-hdf5=/usr/local/hdf5 --with-netcdf=/usr/lib
> >
> 
> You should not need to specify paths such as /usr/bin and /usr/lib.
The
> configure script will look in the normal places automatically.  The
> following should be sufficient:
>   ./configure --prefix=$HOME/projects/scidac/itaps/moab-usr \
>               --enable-doxygen \
>               --with-mpi=/usr/local/ompi_gnu \
>               --with-hdf5=/usr/local/hdf5
> 
> > At the end of this e-mail is the end of the compilation output.
> >
> > I can get a successful MOAB compilation if I use hdf5 without
parallel
> > support but not otherwise.
> >
> > When I built hdf5 with parallel support, I could not enable the c++
> > interface because it is incompatible with parallel support. So I am
> > guessing that MOAB is using the hdf5 c++ interface. Is this correct?
If
> > so, this interface is not available when hdf5 is built with parallel
> > support.
> 
> MOAB uses only the C interface (for both parallel and serial hdf5.)
The
> problem is most likely that your parallel HDF5 is 1.8.x and the serial
is
> 1.6.x.  During your parallel build you are using the 1.8.x headers and
> trying to link the 1.6.x library.  From your configure line:
>   --with-hdf5=/usr/local/hdf5
> From the failing link line:
>   /usr/lib/libhdf5.so
> 
> This is most likely a side effect of the unnecessary /usr/lib entry
for
> other configure options, which is apparently causing -L/usr/lib to be
> listed
> before -L/usr/local/hdf5/lib on the link line.
> 
> - jason