[yt-users] pickle
Matthew Turk
matthewturk at gmail.com
Thu Dec 1 06:57:58 PST 2011
Hi Elizabeth,
What is the output of pf._hash() ?
-Matt
On Thu, Dec 1, 2011 at 9:32 AM, Elizabeth Tasker
<tasker at astro1.sci.hokudai.ac.jp> wrote:
> Sorry, still no luck!
>
> The current version of the code is:
>
> ---
> c1a446be3a7a (yt) tip
> ---
>
>
> unpickle core data
> ---------------------------------------------------------------------------
> KeyError Traceback (most recent call last)
>
> /home/taskere/yt-2/src/yt-hg/scripts/iyt in <module>()
> 199
> 200 file = open('cores.pickle','rb')
> --> 201 allcloudcores = cPickle.load(file)
> 202 file.close()
> 203
>
> /home/taskere/yt-2/src/yt-hg/yt/data_objects/data_containers.pyc in _reconstruct_object(*args, **kwargs)
> 3640 else: new_args.append(arg)
> 3641 pfs = ParameterFileStore()
> -> 3642 pf = pfs.get_pf_hash(pfid)
> 3643 cls = getattr(pf.h, dtype)
> 3644 obj = cls(*new_args)
>
> /home/taskere/yt-2/src/yt-hg/yt/utilities/parameter_file_storage.pyc in get_pf_hash(self, hash)
> 109 def get_pf_hash(self, hash):
> 110 """ This returns a parameter file based on a hash. """
> --> 111 return self._convert_pf(self._records[hash])
> 112
> 113 def get_pf_ctid(self, ctid):
>
> KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function _reconstruct_object at 0xa8cd848>, ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16., 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]), {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16., 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector': array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1238, 0.1476, 0.1714, 0.1952, 0.219 ,
> 0.2428, 0.2666, 0.2904, 0.3142, 0.33
>
>
>
> Unless I need to re-pickle first?
>
> Elizabeth
>
>
>
>
> On 2011-12-01, at 8:20 PM, Matthew Turk wrote:
>
>> Thanks, Elizabeth. The move to in-memory brought up a funny bug where
>> the initialization process was reseting the list of known parameter
>> hashes. This is fixed in c1a446be3a7a.
>>
>> Also, save_object won't work except on yt objects; the result of
>> extract_connected_sets is a tuple of values and python objects.
>> Pickle will, tho.
>>
>> On Thu, Dec 1, 2011 at 4:33 AM, Elizabeth Tasker
>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>> I also tried switching out pickle for the yt method of storing
>>> objects. Unfortunately, it doesn't seem to save the object I want. I
>>> tried:
>>>
>>> contours = dd.extract_connected_sets("NegEscapeVelocity", 1, 30.0,
>>> maxv, log_space=False)
>>> contours.save_object("cloudcores", "storedcores.cpkl")
>>>
>>> In [1]: contours.save_object("cloudcores", "storedcores.cpkl")
>>> ---------------------------------------------------------------------------
>>> AttributeError Traceback (most recent call last)
>>>
>>> /home/tasker/yt/src/yt-hg/scripts/iyt in <module>()
>>> ----> 1
>>> 2
>>> 3
>>> 4
>>> 5
>>>
>>> AttributeError: 'tuple' object has no attribute 'save_object'
>>>
>>> The alternative method --of saving it via the hierarchy-- is slightly
>>> less good since I'm running multiple yt scripts on the same data set.
>>> (As least, when I tried to load the values back in, it produced an
>>> empty set which I presume was because I'd inadvertently overwritten
>>> the .yt file?).
>>>
>>> If I could get one of these working again, then I'd be super happy. I
>>> don't need the all :)
>>>
>>> Elizabeth
>>>
>>>
>>> On 1 December 2011 12:35, Elizabeth Tasker
>>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>> Hi Matt,
>>>>
>>>> Sorry, that still doesn't work.... unless I've misunderstood your
>>>> suggestion? The code is here:
>>>>
>>>> http://paste.yt-project.org/show/1974/
>>>>
>>>> Pickle + unpickle on a pile of properties I calculate from the
>>>> connected sets is fine, but pickling the connected sets themselves is
>>>> a problem. Could it be the later pickle doesn't require the parameter
>>>> file? Or is it possible there is an unrelated write error happening?
>>>>
>>>> Elizabeth
>>>>
>>>> On 30 November 2011 23:43, Matthew Turk <matthewturk at gmail.com> wrote:
>>>>> Hi Elizabeth,
>>>>>
>>>>> We recently changed the mechanism of storing parameter files to be
>>>>> off-by-default, which means that rather than dumping them to a .csv
>>>>> file, they only stay in memory. This functionality can be turned back
>>>>> on (this change is documented in the development documentation.) Can
>>>>> you try:
>>>>>
>>>>> 1) Loading your parameter file, *then* loading your pickle. I am
>>>>> optimistic this will fix it.
>>>>> 2) If it doesn't, at the very top of your python script, put this:
>>>>>
>>>>> from yt.config import ytcfg; ytcfg["yt","storeparameterfiles"] = "True"
>>>>>
>>>>> -Matt
>>>>>
>>>>> On Wed, Nov 30, 2011 at 4:46 AM, Elizabeth Tasker
>>>>> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>>>>>> Hi,
>>>>>>
>>>>>> A bigger problem....
>>>>>>
>>>>>> The lastest version of yt
>>>>>>
>>>>>> The current version of the code is:
>>>>>>
>>>>>> ---
>>>>>> a519b8754ba8 (yt) tip
>>>>>> ---
>>>>>>
>>>>>>
>>>>>> has problems with pickle. If I pickle a data set and then try and
>>>>>> unpickle it, I see:
>>>>>>
>>>>>> unpickle core data
>>>>>> ---------------------------------------------------------------------------
>>>>>> KeyError Traceback (most recent call last)
>>>>>>
>>>>>> /home/tasker/yt/src/yt-hg/scripts/iyt in <module>()
>>>>>> 338
>>>>>> 339 #file = open('cores.pickle','rb')
>>>>>> --> 340 allcloudcores = cPickle.load(file('cores.pickle', 'rb'))
>>>>>> 341 file.close()
>>>>>> 342
>>>>>>
>>>>>> /home/tasker/yt/src/yt-hg/yt/data_objects/data_containers.pyc in
>>>>>> _reconstruct_object(*args, **kwargs)
>>>>>> 3676 else: new_args.append(arg)
>>>>>> 3677 pfs = ParameterFileStore()
>>>>>> -> 3678 pf = pfs.get_pf_hash(pfid)
>>>>>> 3679 cls = getattr(pf.h, dtype)
>>>>>> 3680 obj = cls(*new_args)
>>>>>>
>>>>>> /home/tasker/yt/src/yt-hg/yt/utilities/parameter_file_storage.pyc in
>>>>>> get_pf_hash(self, hash)
>>>>>> 106 def get_pf_hash(self, hash):
>>>>>> 107 """ This returns a parameter file based on a hash. """
>>>>>> --> 108 return self._convert_pf(self._records[hash])
>>>>>> 109
>>>>>> 110 def get_pf_ctid(self, ctid):
>>>>>>
>>>>>> KeyError: (('283b7c4d88671dbff7acf083098da6ae',), <function
>>>>>> _reconstruct_object at 0x272c938>,
>>>>>> ('283b7c4d88671dbff7acf083098da6ae', 'region', array([ 16., 16.,
>>>>>> 16.]), array([ 0., 0., 0.]), array([ 32., 32., 32.]),
>>>>>> {'disk_center': array([16, 16, 16]), 'center': array([ 16., 16.,
>>>>>> 16.]), 'bulk_velocity': array([ 0., 0., 0.]), 'disk_vector':
>>>>>> array([0, 0, 1]), 'disk_radius': array([ 0.1 , 0.1358, 0.1716,
>>>>>> 0.2074, 0.2432, 0.279 ,
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> The fact it mentions the field parameters in the last line, might mean
>>>>>> it's an error introduced because of the corrections to them (that I
>>>>>> have been demanding!)?
>>>>>>
>>>>>> The script I have works fine (pickles and all) on yt version:
>>>>>>
>>>>>> ---
>>>>>> 16e8d749a806 (yt) tip
>>>>>> ---
>>>>>>
>>>>>>
>>>>>> Elizabeth
>>>>>> _______________________________________________
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