I have rebuild HDF5 (static) with MPI. I still get the same error. Could it
be due to some directory missing from path (example: LIBRARY_PATH, PATH,
etc)
By the way: I have looked into the hdf5 libraries (with 'nm
/clusterdata/afylot/local/lib/*.a | grep H5Pget_fapl_mpio') and I cannot
find it anywhere
I report the complete error for clarity:
In [3]: import h5py
---------------------------------------------------------------------------
ImportError Traceback (most recent call
last)
<ipython-input-3-e81388eeaef8> in <module>()
----> 1 import h5py
/clusterdata/afylot/local/lib64/python3.4/site-packages/h5py-2.5.0-py3.4-linux-x86_64.egg/h5py/__init__.py
in <module>()
21 _errors.silence_errors()
22
---> 23 from . import _conv
24 _conv.register_converters()
25
/clusterdata/afylot/h5py/h5r.pxd in init h5py._conv
(/clusterdata/afylot/download/h5py-2.5.0/h5py/_conv.c:7274)()
/clusterdata/afylot/h5py/_objects.pxd in init h5py.h5r
(/clusterdata/afylot/download/h5py-2.5.0/h5py/h5r.c:3184)()
/clusterdata/afylot/h5py/_objects.pyx in init h5py._objects
(/clusterdata/afylot/download/h5py-2.5.0/h5py/_objects.c:7285)()
ImportError:
/clusterdata/afylot/local/lib64/python3.4/site-packages/h5py-2.5.0-py3.4-linux-x86_64.egg/h5py/
defs.cpython-34m.so: undefined symbol: H5Pget_fapl_mpio
2015-04-28 17:55 GMT+02:00 Pierre de Buyl <[email protected]>:
> Hi,
>
> Is your HDF5 library built with MPI? This is the first thing to check.
>
> On Tue, Apr 28, 2015 at 05:43:44PM +0200, simona bellavista wrote:
> > I have installed h5py 2.5.0 with mpi switched on.
> >
> > I used:
> >
> > export CC=mpicc
> > python3 setup.py configure --mpi
> > python3 setup.py build
> > python3 setup.py install --prefix=/clusterdata/afylot/local/
> >
> > (python3 is alias for python 3.4)
> > When I import h5py from ipython3 I get
> >
> > ImportError:
> >
> /clusterdata/afylot/local/lib64/python3.4/site-packages/h5py-2.5.0-py3.4-linux-x86_64.egg/h5py/
> > defs.cpython-34m.so: undefined symbol: H5Pget_fapl_mpio
> >
> > I have checked is mpi is enable by running configure:
> >
> > python3 setup.py configure
> > --hdf5=/clusterdata/afylot/local/hdf5-1.8.14/hdf5/lib/ --mpi
> >
> > running configure
> > Autodetected HDF5 1.8.14
> >
> >
> ********************************************************************************
> > Summary of the h5py configuration
> >
> > Path to HDF5: '/clusterdata/afylot/local/hdf5-1.8.14/hdf5/lib/'
> > HDF5 Version: '1.8.14'
> > MPI Enabled: True
> > Rebuild Required: False
> >
> >
> >
> ********************************************************************************
> >
> >
> > Any idea welcome!
>
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