Pytables fails to create hdf5 table

[dershow]

I first tried to create an hdf5 table using pandas. But, that failed. So, I went to pytables instead, and that also fails with a similar error. I'm using py27-tables @3.2.2_2 which is using hdf5 @1.10.0_1 Here is a simple example, grabbed from the pytables web page

>>> import tables
>>> from tables import *
>>> h5file = open_file("tutorial1.h5", mode = "w", title = "Test file")
>>> group = h5file.create_group("/", 'detector', 'Detector information')
>>> class Particle(IsDescription):
...     name      = StringCol(16)
...     idnumber  = Int64Col()      #
...     ADCcount  = UInt16Col()     # Unsigned
... 
>>> table = h5file.create_table(group, 'readout', Particle, "Readout example")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/file.py", line 1060, in create_table
    chunkshape=chunkshape, byteorder=byteorder)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/table.py", line 873, in __init__
    byteorder, _log)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/leaf.py", line 262, in __init__
    super(Leaf, self).__init__(parentnode, name, _log)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/node.py", line 270, in __init__
    self._v_objectid = self._g_create()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/tables/table.py", line 1066, in _g_create
    self._v_new_title, self.filters.complib or '', obversion)
  File "tables/tableextension.pyx", line 222, in tables.tableextension.Table._create_table (tables/tableextension.c:3322)
tables.exceptions.HDF5ExtError: HDF5 error back trace

  File "H5A.c", line 265, in H5Acreate2
    not a location
  File "H5Gloc.c", line 253, in H5G_loc
    invalid object ID

End of HDF5 error back trace

Can't set attribute 'CLASS' in table:
 readout.

[dershow]

It looks like this #51923 is probably the same problem, although that bug is written for py27-pyne.

[ryandesign (Ryan Carsten Schmidt)]

You mean #51139?

[dershow]

Yes.

[mamoll (Mark Moll)]

py-tables apparently doesn't work with hdf5 1.10. I have attached a patched Portfile. It requires hdf5 to be deactivated during the build, which seems a little kludgey. Can anyone think of a better solution?

[dershow]

There is a separate port from hdf5, called hdf5-18 @1.8.16_5. I have that installed as well as hdf5. Apparently, it was installed by netcdf. Perhaps it is possible to either use that port for py-tables, or to use whatever technique was used to build that, as it seems to work?

[mamoll (Mark Moll)]

Yes, the patched Portfile requires hdf5-18. The issue is that at build time, hdf5 needs to be deactivated. It'd be nice it this was not necessary.

[dershow]

I tried to deactivate and then used the attached file and it does work for me.

[mamoll (Mark Moll)]

Fixed in r150948.