HDF5 file reading error: "Attribute 'block2_items_variety' does not exist in node:/data"

Code Sample, a copy-pastable example if possible

# Your code here
data.to_hdf('data.h5',mode='w',format='f')

data = pd.read_hdf('data.h5')
####Traceback

AttributeError                            Traceback (most recent call last)
<ipython-input-5-13fe6d5eccfa> in <module>()
----> 1 ndata = pd.read_hdf('cleaned_data_v1.h5')

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_hdf(path_or_buf, key, mode, **kwargs)
    368                                      'contains multiple datasets.')
    369             key = candidate_only_group._v_pathname
--> 370         return store.select(key, auto_close=auto_close, **kwargs)
    371     except:
    372         # if there is an error, close the store

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in select(self, key, where, start, stop, columns, iterator, chunksize, auto_close, **kwargs)
    715                            chunksize=chunksize, auto_close=auto_close)
    716 
--> 717         return it.get_result()
    718 
    719     def select_as_coordinates(

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in get_result(self, coordinates)
   1455 
   1456         # directly return the result
-> 1457         results = self.func(self.start, self.stop, where)
   1458         self.close()
   1459         return results

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in func(_start, _stop, _where)
    708             return s.read(start=_start, stop=_stop,
    709                           where=_where,
--> 710                           columns=columns, **kwargs)
    711 
    712         # create the iterator

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read(self, start, stop, **kwargs)
   2893         for i in range(self.nblocks):
   2894 
-> 2895             blk_items = self.read_index('block%d_items' % i)
   2896             values = self.read_array('block%d_values' % i,
   2897                                      start=_start, stop=_stop)

/opt/conda/lib/python3.6/site-packages/pandas/io/pytables.py in read_index(self, key, **kwargs)
   2475 
   2476     def read_index(self, key, **kwargs):
-> 2477         variety = _ensure_decoded(getattr(self.attrs, '%s_variety' % key))
   2478 
   2479         if variety == u('multi'):

/opt/conda/lib/python3.6/site-packages/tables/attributeset.py in __getattr__(self, name)
    290         if not name in self._v_attrnames:
    291             raise AttributeError("Attribute '%s' does not exist in node: "
--> 292                                  "'%s'" % (name, self._v__nodepath))
    293 
    294         # Read the attribute from disk. This is an optimization to read

AttributeError: Attribute 'block2_items_variety' does not exist in node: '/cleaned_data'

#### Problem description
We are working remotely on a Jupyter notebook on a server doing some 
data preprocessing, having loaded an unprocessed .h5 file that was created 
using the pd.to_hdf() command we then did a number of preprocessing operations
 and added some new columns to dataframe.

Next we saved the data using data.to_hdf command and generated the file data.h5. after 
that we used the command read_hdf to read the file but we get the error:
 "Attribute 'block2_items_variety' does not exist in node: /cleaned_data".


#### Expected Output
reading the file successfully.

#### Output of ``pd.show_versions()``


[paste the output of ``pd.show_versions()`` here below this line]
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.3.final.0
python-bits: 64
OS: Linux
OS-release: 4.5.7-docker-4
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8

pandas: 0.21.0
pytest: 3.3.1
pip: 9.0.1
setuptools: 36.6.0
Cython: 0.25.2
numpy: 1.12.1
scipy: 0.19.1
pyarrow: None
xarray: None
IPython: 6.2.1
sphinx: None
patsy: 0.4.1
dateutil: 2.6.1
pytz: 2017.3
blosc: None
bottleneck: None
tables: 3.4.2
numexpr: 2.6.2
feather: None
matplotlib: 2.0.2
openpyxl: None
xlrd: 1.0.0
xlwt: None
xlsxwriter: None
lxml: None
bs4: 4.5.3
html5lib: 0.999999999
sqlalchemy: 1.1.13
pymysql: None
psycopg2: None
jinja2: 2.9.6
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None

[AiAlex]

Got this error AttributeError: Attribute 'block1_items_variety' does not exist in node: '/dataset'

on Pandas 0.25.3 Python 3.6.3 :: Anaconda, Inc.

[JanKalin]

The problem apparently only occurs on 32-bit Python. With 64-bit running inside a 64-bit virtual machine the conversion goes well:

Y:\>c:\Users\jank\test\dws2hdf5.py Ravbarkomanda_2018_04_04_132938.dxd --fields
1 @rename.opt
2018-07-04 09:53:22.973000 1/1 Ravbarkomanda_2018_04_04_132938.dxd, a_2018_04_04
_13_29_40_110000, T_2018_04_04_13_29_40_110000, done

Y:\>python
Python 2.7.15 (v2.7.15:ca079a3ea3, Apr 30 2018, 16:30:26) [MSC v.1500 64 bit (AM
D64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import pandas as pd
>>> pd.show_versions()

INSTALLED VERSIONS
------------------
commit: None
python: 2.7.15.final.0
python-bits: 64
OS: Windows
OS-release: 7
machine: AMD64
processor: Intel64 Family 6 Model 26 Stepping 5, GenuineIntel
byteorder: little
LC_ALL: None
LANG: None
LOCALE: None.None

pandas: 0.23.1
pytest: None
pip: 10.0.1
setuptools: 39.0.1
Cython: None
numpy: 1.14.5
scipy: None
pyarrow: None
xarray: None
IPython: 5.7.0
sphinx: 1.7.5
patsy: None
dateutil: 2.7.3
pytz: 2018.5
blosc: None
bottleneck: None
tables: None
numexpr: 2.6.5
feather: None
matplotlib: None
openpyxl: None
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: 1.0.1
sqlalchemy: None
pymysql: None
psycopg2: None
jinja2: 2.10
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None