python(3)-h5py not mpi-aware

Lars Bungum lars at bungum.no
Thu Jun 30 14:17:31 UTC 2016


Dear all,

running this script:

import mpi4py
from mpi4py import MPI
import h5py

rank = MPI.COMM_WORLD.rank  # The process ID (integer 0-3 for 4-process run)

print(rank)
f = h5py.File('parallel_test.hdf5', 'w', driver='mpio', comm=MPI.COMM_WORLD)

dset = f.create_dataset('test', (4,), dtype='i')
dset[rank] = rank

f.close()

yields this result, for both python versions for as well 14.04 as 16.04 
(Kubuntu):

$ mpirun -np 4 python3 multiproc_hdf5_mpi4py.py
Traceback (most recent call last):
   File "multiproc_hdf5_mpi4py.py", line 1, in <module>
     import mpi4py
ImportError: No module named 'mpi4py'
Traceback (most recent call last):
   File "multiproc_hdf5_mpi4py.py", line 1, in <module>
     import mpi4py
ImportError: No module named 'mpi4py'
Traceback (most recent call last):
   File "multiproc_hdf5_mpi4py.py", line 1, in <module>
     import mpi4py
ImportError: No module named 'mpi4py'
Traceback (most recent call last):
   File "multiproc_hdf5_mpi4py.py", line 1, in <module>
     import mpi4py
ImportError: No module named 'mpi4py'
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, 
thus causing
the job to be terminated. The first process to do so was:

   Process name: [[43945,1],1]
   Exit code:    1


I have googled it, and it seems  that the package must be rebuilt, with 
the correct options referring it to the installation of mpi.  I tried 
rebuilding the package myself, but was not (yet) able to figure out 
where to actually change that settings.  (debian/rules? how?).

Perhaps you could fix this in the central repository as package maintainers?

Kind regards,
Lars B










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