Parallel io from the docs

[roybens]

1) Bug

If you are reporting a bug please provide the following:

Steps to Reproduce

Trying to run the code from the docs for parallel io: https://pynwb.readthedocs.io/en/latest/tutorials/general/advanced_hdf5_io.html?highlight=mpi#parallel-i-o-using-mpi

here is writenwb.py :

from mpi4py import MPI
import numpy as np
from dateutil import tz
from pynwb import NWBHDF5IO, NWBFile, TimeSeries
from datetime import datetime
from hdmf.data_utils import DataChunkIterator

start_time = datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz('US/Pacific'))
fname = 'test_parallel_pynwb.nwb'
rank = MPI.COMM_WORLD.rank  # The process ID (integer 0-3 for 4-process run)

# Create file on one rank. Here we only instantiate the dataset we want to
# write in parallel but we do not write any data
if rank == 0:
    nwbfile = NWBFile('aa', 'aa', start_time)
    data = DataChunkIterator(data=None, maxshape=(4,), dtype=np.dtype('int'))

    nwbfile.add_acquisition(TimeSeries('ts_name', description='desc', data=data,
                                       rate=100., unit='m'))
    with NWBHDF5IO(fname, 'w') as io:
        io.write(nwbfile)

# write to dataset in parallel
with NWBHDF5IO(fname, 'a', comm=MPI.COMM_WORLD) as io:
    nwbfile = io.read()
    print(rank)
    nwbfile.acquisition['ts_name'].data[rank] = rank
and in read i replace the last 4 lines with:
 read from dataset in parallel
with NWBHDF5IO(fname, 'r', comm=MPI.COMM_WORLD) as io:
    print(io.read().acquisition['ts_name'].data[rank])

after running:
(.env) roybens@nid00227:~/tests> srun -n 3  python ./writenwb.py
0
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
0
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
0
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
(.env) roybens@nid00227:~/tests> vi writenwb.py
(.env) roybens@nid00227:~/tests> srun -n 3  python ./writenwb.py
0
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
0
/global/homes/r/roybens/.conda/envs/.env/lib/python3.6/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.
  from ._conv import register_converters as _register_converters
0

ranks are always 0 when reading getting similiar errors

Provide a minimal code snippet here to reproduce this error.

Environment

Please describe your environment according to the following bullet points.

• Python Executable: Conda
• Python Version: Python 3.6
• Operating System: Linux
• **Pynwb Version:1.0.2 (latest from github)

2) Feature Request

If you are requesting a feature please provide the following:

Problem/Use Case

Briefly describe the needed feature as well as the reasoning behind it

Checklist

• [ ] Have you ensured the feature or change was not already reported ?
• [ ] Have you included a brief and descriptive title?
• [ ] Have you included a clear description of the problem you are trying to solve?
• [ ] Have you included a minimal code snippet that reproduces the issue you are encountering?
• [ ] Have you checked our Contributing document?