Hi, h5py requires a shared version of HDF5 (see http://docs.h5py.org/en/latest/build.html#building-against-parallel-hdf5 )
On Tue, Apr 28, 2015 at 08:06:42PM +0200, simona bellavista wrote: > 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! > > > > _______________________________________________ > > Hdf-forum is for HDF software users discussion. > > [email protected] > > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > Twitter: https://twitter.com/hdf5 > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 -- ----------------------------------------------------------- Pierre de Buyl KU Leuven - Institute for Theoretical Physics T +32 16 3 27355 W http://pdebuyl.be/ ----------------------------------------------------------- _______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
