pencil.io.pc_hdf5
=================

.. py:module:: pencil.io.pc_hdf5

.. autoapi-nested-parse::

   Contains optional h5 operations with and without hdf5-parallel, for exampe
   to open h5 file with/without MPI using common switches.
   TODO open h5 pencil var object etc, as alternative to var object for
   large datasets with memory limits.



Functions
---------

.. autoapisummary::

   pencil.io.pc_hdf5.open_h5
   pencil.io.pc_hdf5.group_h5
   pencil.io.pc_hdf5.dataset_h5


Module Contents
---------------

.. py:function:: open_h5(filename, status, driver=None, comm=None, overwrite=False, size=1, rank=0, lfs=False, MB=1, count=1)

   This function opens hdf5 file in serial or parallel.

   :keyword filename: relative or absolute path string for name of hdf5 file.
   :keyword status: open state of file 'w': write, 'r': read or 'a'/'r+': append.
   :keyword driver: 'mpio' required for parallel: version but absent for serial.
   :keyword comm: only present for parallel version of h5py.
   :keyword overwrite: flag to replace existing file.
   :keyword rank: processor rank with root = 0.


.. py:function:: group_h5(h5obj, groupname, status='r', delete=False, overwrite=False, rank=0, size=1, comm=None)

   This function adds/removes hdf5 group objects.

   :keyword h5obj: h5 object, may be the file or a sub group within the file
   :keyword groupname: string for name of the group.
   :keyword status: open state of file 'w': write, 'r': read or 'a'/'r+': append.
   :keyword delete: flag to remove existing group from h5 object.
   :keyword overwrite: flag to replace existing group from h5 object.
   :keyword rank: processor rank with root = 0.
   :keyword comm: only present for parallel version of h5py.


.. py:function:: dataset_h5(h5obj, dataname, status='r', data=None, shape=None, dtype=None, overwrite=False, delete=False, rank=0, size=1, comm=None)

   This function adds/removes hdf5 dataset objects.

   :keyword h5obj: h5 object, may be the file or a sub group within the file
   :keyword dataname: string for name of the dataset.
   :keyword status: open state of file 'w': write, 'r': read or 'a'/'r+': append.
   :keyword data: h5 compatible data object; float, integer, string, array
   :keyword shape: data shape tuple of length > 0
   :keyword dtype: h5 compatible data type, eg. np.float64
   :keyword delete: flag to remove existing group from h5 object.
   :keyword overwrite: flag to replace existing group from h5 object.
   :keyword rank: processor rank with root = 0.
   :keyword comm: only present for parallel version of h5py.