[yt-users] pickle
Elizabeth Tasker
tasker at astro1.sci.hokudai.ac.jp
Thu Dec 1 14:41:48 PST 2011
Hi Matt,
The odd thing is that if I use exactly the same .yt program, on the same machine with the same pickle file, it works fine with the older version of yt.
I will check the unique identifier though. I'm using an old version of Enzo, so it's possible something got changed :/
Elizabeth
On 2011-12-02, at 12:31 AM, Matthew Turk wrote:
> Hi Elizabeth,
>
> The hashes don't match, so it thinks you're loading a pickle for a
> file it doesn't have in memory. So, two possibilities:
>
> 1) The pickles were generated from a different static output than the
> one you are pf = load()ing earlier. If you load() the one that
> generated them, this will work.
>
> 2) The hash for your parameter file changed. The hash is generated by
> taking the md5sum of the following three items:
>
> basename
> current_time (for enzo this is InitialTime in the parameter file)
> unique_identifier
>
> The third one is the important one that you should check, and the one
> that has the most possibility of variation. I assume you're running
> Enzo. If your simulation has the parameter CurrentTimeIdentifier
> (which was added to the LCA enzo 1.5, and has persisted since then)
> this is used. If it does not, then the modification time of the
> parameter file is used. This can be changed if you edit or copy
> (without using -p) the file.
>
> -Matt
>
> On Thu, Dec 1, 2011 at 10:03 AM, Elizabeth Tasker
> <tasker at astro1.sci.hokudai.ac.jp> wrote:
>> Tis:
>>
>> In [1]: pf._hash()
>> Out[1]: '283b7c4d88671dbff7acf083098da6ae'
>>
>> E.
>>
>>
>> On 2011-12-01, at 11:57 PM, Matthew Turk wrote:
>>
>>> 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
>>>>>>>>> _______________________________________________
>>>>>>>>> yt-users mailing list
>>>>>>>>> yt-users at lists.spacepope.org
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