Why do I get an error from the HDF5 library when I try to create an HDF5 dataset with one of the dimensions set to 'H5S_UNLIMITED' in MATLAB?

I am trying to create a dataset in the HDF5 format with an unspecified dimension (by using the 'H5S_UNLIMITED' option for one of my dimensions) using the following code:

 

dims       = [60 30 10];
maxdims    = {dims(1), dims(2), 'H5S_UNLIMITED'};
spaceID    = H5S.create_simple(length(dims),fliplr(dims),fliplr(maxdims));

typeID     = H5T.copy ('H5T_NATIVE_DOUBLE');
dset       = H5D.create (fid, 'sourceName', typeID, spaceID, 'H5P_DEFAULT');

However, when I try to run this code, I get the following error:

Error using hdf5lib2

The HDF5 library encountered an error and produced the following stack trace information:

    H5D_contig_construct    extendible contiguous non-external dataset

    H5D_create              unable to construct layout information

    H5O_dset_create         unable to create dataset

    H5O_obj_create          unable to open object

    H5L_link_cb             unable to create object

    H5G_traverse_real       traversal operator failed

    H5G_traverse            internal path traversal failed

    H5L_create_real         can't insert link

    H5L_link_object         unable to create new link to object

    H5D_create_named        unable to create and link to dataset

    H5Dcreate1              unable to create dataset

Error in H5D.create (line 59)

id = H5ML.hdf5lib2('H5Dcreate', varargin{:} );

Error in example2 (line 17)

dset       = H5D.create (fid, '/psfSourceName', typeID, spaceID, 'H5P_DEFAULT'); 

How can I resolve this?

Answer 1

[MathWorks Support Team]

This error occurs because if 'H5S_UNLIMITED' is specified for one of the dataset dimensions, the dataset must be chunked rather than contiguous.  To resolve the error, one can simply define the dataset creation property list to specify that the dataset should be chunked.  For the example in the question, this can be done as follows:

 

dims       = [60 30 10];
maxdims    = {dims(1), dims(2), 'H5S_UNLIMITED'};
spaceID    = H5S.create_simple(length(dims),fliplr(dims),fliplr(maxdims));

typeID     = H5T.copy ('H5T_NATIVE_DOUBLE');
dcpl = H5P.create('H5P_DATASET_CREATE');
chunk_dims = [60 30 10];
h5_chunk_dims = fliplr(chunk_dims);
H5P.set_chunk(dcpl,h5_chunk_dims);
dset       = H5D.create (fid, 'sourceName', typeID, spaceID, dcpl);
For more information, please consult <http://www.hdfgroup.org/HDF5/doc/RM/RM_H5Front.html the API for the HDF5 library>.