import h5py: undefined symbol: H5Pget_fapl_mpio

afylot · April 28, 2015, 3:43pm

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!

Pierre_de_Buyl · April 28, 2015, 3:55pm

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!

afylot · April 28, 2015, 6:06pm

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 <pierre.debuyl@chem.kuleuven.be>:

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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

Pierre_de_Buyl · April 28, 2015, 6:17pm

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 <pierre.debuyl@chem.kuleuven.be>:

> 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.
> Hdf-forum@lists.hdfgroup.org
> http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> Twitter: https://twitter.com/hdf5
>

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
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/
-----------------------------------------------------------

afylot · April 28, 2015, 9:20pm

thank you, solved

···

2015-04-28 20:17 GMT+02:00 Pierre de Buyl <pierre.debuyl@chem.kuleuven.be>:

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 <
pierre.debuyl@chem.kuleuven.be>:
>
> > 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.
> > Hdf-forum@lists.hdfgroup.org
> >
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
> > Twitter: https://twitter.com/hdf5
> >

> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@lists.hdfgroup.org
> 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.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5