[gpaw-users] HDF5 and parallel calculation support

[Gaël DONVAL]

Hi everyone,

I'm about to install gpaw on our computer cluster.

I'd like to enable the HDF5 support in gpaw since it seems sensible. So,
I began by HDF5 (1.9.141) compilation:

        ./configure --prefix=/u/foo --enable-fortran --enable-cxx
        --enable-production --with-gnu-ld --with-zlib=/u/foo/bar
        --with-szlib=/u/foo/bar
        
I updated my env variables (LD_LIBRARY_PATH, PATH) accordingly.

I altered gpaw's customize.py file:
        libraries = ["hdf5","openblas"]
        library_dirs += ["/u/foo/bar/lib"]
        include_dirs += ["/u/foo/bar/include"]
        
And that's it: I launch python setup.py build_ext.

But I get this:
        build/temp.linux-x86_64-2.7/c/hdf5.o: in the fonction «
        h5p_set_fapl_mpio »:
        c/hdf5.c:(.text+0x1313): undefined reference to «
        H5Pset_fapl_mpio »
        build/temp.linux-x86_64-2.7/c/hdf5.o: in the fonction «
        h5p_set_dxpl_mpio »:
        c/hdf5.c:(.text+0x1357): undefined reference to «
        H5Pset_dxpl_mpio »
        
        [...]
        
        * Using standard lapack
        * Architecture: linux-x86_64
        * Compiling with HDF5
        * Building a custom interpreter
        * linking FAILED!  Only serial version of code will work.

In this case, there is no gpaw-python in ./build/bin*

When hdf5 support is disable, everything compiles just fine:
        * Using standard lapack
        * Architecture: linux-x86_64
        * Building a custom interpreter
and I get gpaw-python.

The question is, is there any support for the HDF5 format in gpaw
without parallel compilation of the HDF5 library? I tried to compile
HDF5 with parallel support but since the FS we used is not parallel yet,
we don't even have the MPI/IO extension compiled in OpenMPI.

Best regards,
Gaël