====== h5py ======


===== Installation guide =====

Running

<code bash>
pip install h5py
</code>

gives the error message

<code>
h5py/defs.c:8:22: fatal error: pyconfig.h: No such file or directory
</code>

this was due to the ''python development'' package not being installed.

Subsequently running

<code bash>
pip install h5py
</code>

throws the error message

<code>
/usr/include/H5public.h:57:20: fatal error: mpi.h: No such file or directory
</code>

this was due to ''pip'' not finding the mpi package. It can be resolved by specifying the ''CFLAGS'' shell variable.

Eventually running

<code bash>
env CFLAGS=-I/usr/lib/openmpi/include pip install h5py
</code>

did the trick.

An alternative could be

<code bash>
pip install --global-option "env CFLAGS=-I/usr/lib/openmpi/include" h5py
</code>

The alternative did not work for me (Manuel, python2, @ww8stud6)
 --- //[[manuel.leimberger@ww.stud.uni-erlangen.de|Manuel Leimberger]] 2014/08/28 11:19//

===== Installing H5py Parallel HDF5 (Recommended) =====
Required is a HDF5 library compiled with MPI. Ask your admin or compile it yourself.
If that's the case, execute this is in your bash: 
<code bash>
export CC=mpicc
export HDF5_MPI="ON"
pip install h5py --no-binary=h5py h5py
</code>
If it has finished without any (major) complaints, test it with this script:
<code bash>
from mpi4py import MPI
import h5py

rank = MPI.COMM_WORLD.Get_rank()
N = MPI.COMM_WORLD.Get_size()

f = h5py.File('parallel.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)
dset = f.create_dataset('test', (N,), dtype='i')
dset[rank] = rank
f.close()
</code> 
by executing: 
</code>
If it has finished without any (major) complaints, test it with this script:
<code bash>
mpiexec -n <number of processors on your computer> python test-h5py-parallel.py
</code>
You should have now a hdf5 file of the name "parallel.hdf5" with one dataset inside with the number of processors in c-indexing in sequential order. So for four processors the entries are 0,1,2,3.