python - Unable to save DataFrame to HDF5 ("object header message is too large") -


i have dataframe in pandas:

in [7]: my_df out[7]:  <class 'pandas.core.frame.dataframe'> int64index: 34 entries, 0 0 columns: 2661 entries, airplane zoo dtypes: float64(2659), object(2)

when try save disk:

store = pd.hdfstore(p_full_h5) store.append('my_df', my_df)

i get:

  file "h5a.c", line 254, in h5acreate2     unable create attribute   file "h5a.c", line 503, in h5a_create     unable create attribute in object header   file "h5oattribute.c", line 347, in h5o_attr_create     unable create new attribute in header   file "h5omessage.c", line 224, in h5o_msg_append_real     unable create new message   file "h5omessage.c", line 1945, in h5o_msg_alloc     unable allocate space message   file "h5oalloc.c", line 1142, in h5o_alloc     object header message large  end of hdf5 error trace  can't set attribute 'non_index_axes' in node:  /my_df(group) u''.

why?

note: in case matters, dataframe column names simple small strings:

in[12]: max([len(x) x in list(my_df.columns)]) out{12]: 47

this pandas 0.11 , latest stable version of ipython, python , hdf5.

hdf5 has header limit of 64kb metadata of columns. include name, types, etc. when go 2000 columns, run out of space store metadata. fundamental limitation of pytables. don't think make workarounds on side time soon. either have split table or choose storage format.


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