[yt-users] unpickle / load problems

[Matthew Turk]

Hi Elizabeth,

Okay -- cool.  I think I will work around the h5py thing for now.  But
it is worrisome; I think save_object is currently broken as h5py
changed how it deals with VLEN strings between 2.0 and 2.1.

I've reproduced it by using Pickle by itself.  More as I get it.

-Matt

On Fri, Mar 15, 2013 at 11:25 AM, Elizabeth Tasker
<tasker at astro1.sci.hokudai.ac.jp> wrote:
> Hi Matt,
>
> According to the directory I have in yt, an older version:
>
> /Users/Elizabeth/yt/src/h5py-2.0.1/
>
> Elizabeth
>
> On Mar 15, 2013, at 10:04 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>
>> Hi Elizabeth,
>>
>> On Wed, Mar 13, 2013 at 4:45 PM, Elizabeth Tasker
>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>> Hi Matt,
>>>
>>> So ironically, it took me a long time to find the right combination to make this break in the test script! The fatal combination seems to be an extract region from a boolean object.
>>>
>>> This is the script I used:
>>>
>>> http://paste.yt-project.org/show/3228/
>>>
>>> It should work with any data set.
>>>
>>> It creates 6 saved objects. Objects 1-4 work fine but 5 and 6 have the attribute error.
>>
>> I'm getting h5py errors when I even run the script.  Which version of
>> h5py are you on?
>>
>>>>> h5py.version.version
>> '2.1.0'
>>
>>
>>>
>>> Elizabeth
>>>
>>>
>>> On Mar 13, 2013, at 3:08 PM, Matthew Turk <matthewturk at gmail.com> wrote:
>>>
>>>> Hi Elizabeth,
>>>>
>>>> Okay, this seems like it's bumped up against a problem with the way yt
>>>> handles pickles.  At some point in the reconstruction, data objects
>>>> aren't getting separated from their parameter files.
>>>>
>>>> Any chance you could make something that reproduces this on one of the
>>>> workshop datasets?
>>>>
>>>> http://yt-project.org/data/
>>>>
>>>> -Matt
>>>>
>>>> On Wed, Mar 13, 2013 at 3:03 PM, Elizabeth Tasker
>>>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>>> Hi,
>>>>>
>>>>> I'm struggling to unpickle / load_object a previously pickled / save_object.
>>>>>
>>>>> I've done:
>>>>>
>>>>> pf.h.save_object(allclouds, "clouds_pyfindclouds2_yt")
>>>>>
>>>>> but when I do:
>>>>>
>>>>> clouds = pf.h.load_object("clouds_pyfindclouds2_yt")
>>>>>
>>>>> I get:
>>>>>
>>>>> AttributeError                            Traceback (most recent call last)
>>>>> /Users/Elizabeth/yt/src/yt-hg/scripts/iyt in <module>()
>>>>> ----> 1 execfile("cloud_surfacedensity_b.py")
>>>>>
>>>>> /Users/Elizabeth/yt/src/yt-hg/scripts/iyt in <module>()
>>>>>    13 #file.close()
>>>>>    14
>>>>> ---> 15 clouds = pf.h.load_object("clouds_pyfindclouds2_yt")
>>>>>
>>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/hierarchy.pyc in load_object(self, name)
>>>>>   328         if obj is None:
>>>>>   329             return
>>>>> --> 330         obj = cPickle.loads(obj.value)
>>>>>   331         if iterable(obj) and len(obj) == 2:
>>>>>   332             obj = obj[1] # Just the object, not the pf
>>>>>
>>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs)
>>>>>  4623     pf = pfs.get_pf_hash(pfid)
>>>>>  4624     cls = getattr(pf.h, dtype)
>>>>> -> 4625     obj = cls(*new_args)
>>>>>  4626     obj.field_parameters.update(field_parameters)
>>>>>  4627     return pf, obj
>>>>>
>>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in __init__(self, regions, fields, pf, **kwargs)
>>>>>  4046         self._all_overlap = []
>>>>>  4047         self._cut_masks = {}
>>>>> -> 4048         self._get_all_regions()
>>>>>  4049         self._make_overlaps()
>>>>>  4050         self._get_list_of_grids()
>>>>>
>>>>> /Users/Elizabeth/yt/src/yt-hg/yt/data_objects/data_containers.pyc in _get_all_regions(self)
>>>>>  4057             self._all_regions.append(item)
>>>>>  4058             # So cut_masks don't get messed up.
>>>>> -> 4059             item._boolean_touched = True
>>>>>  4060         self._all_regions = np.unique(self._all_regions)
>>>>>  4061
>>>>>
>>>>> AttributeError: ("'tuple' object has no attribute '_boolean_touched'", <function _reconstruct_object at 0x101dcd578>, ('73850deee907adf5217f43156c5057cd', 'boolean', [(GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240, AMRCylinder (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240): center=[ 16.  16.  16.], _norm_vec=[ 0.  0.  1.], _radius=7.5, _height=0.100000208264), 'NOT', (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240, AMRCylinder (GR_Enzo2_128amr5_zeus_turb_psupp_rr_0240): center=[ 16.  16.  16.], _norm_vec=[ 0.  0.  1.], _radius=4.5, _height=0.100000208264)], {'bulk_velocity': array([ 0.,  0.,  0.]), 'center': array([ 0.5,  0.5,  0.5]), 'normal': array([ 0.,  0.,  1.])}))
>>>>>
>>>>>
>>>>>
>>>>> This is all on the same computer.
>>>>>
>>>>> Elizabeth
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