[yt-users] pickling clumps
Charles Hansen
chansen at astro.berkeley.edu
Fri May 28 13:51:56 PDT 2010
cPickle works. I should probably be using that instead of pickle anyway.
I did reload the first time I tried to pickle, but not the second time.
David Collins wrote:
> Hi, Charles--
>
> I save my clumps directly with cPickle, and it works fine. So, in
> principle, at least, it's possible. I do:
>
>
>>>> cPickle.dump(SomeClump,file('ctest.pickle','wb'),protocol=-1)
>>>> c = cPickle.load(file('ctest.pickle','rb'))
>>>>
>
> Using protocol=-1 stores the data in binary, so it's faster on both
> read and write, and smaller by quite a lot.
>
> Have you reloaded anything since you created the object? Pickle tends
> to choke if you've reloaded the module since you've created the
> object.
>
> d.
>
>
> On Fri, May 28, 2010 at 11:49 AM, Matthew Turk <matthewturk at gmail.com> wrote:
>
>> Hi Charles,
>>
>> This feels a bit more like a file system errorl. What happens if you
>> use the cPickle module instead of the Pickle module?
>>
>> -Matt
>>
>> On Fri, May 28, 2010 at 11:46 AM, Charles Hansen
>> <chansen at astro.berkeley.edu> wrote:
>>
>>> sorry, the preceding line was
>>>
>>> outfile = open("dummy.pkl", "wb")
>>>
>>> The type is...
>>>
>>> In [73]: type(outfile)
>>> Out[73]: <type 'file'>
>>>
>>>
>>> Matthew Turk wrote:
>>>
>>>> Hi Charles,
>>>>
>>>> What's "outfile" in this case? Can you send a bit more of your setup
>>>> of the problem, or at least the output of "type(outfile)"?
>>>>
>>>> -Matt
>>>>
>>>> On Fri, May 28, 2010 at 11:32 AM, Charles Hansen
>>>> <chansen at astro.berkeley.edu> wrote:
>>>>
>>>>
>>>>> pf.h.save_object does work as advertised for me. Thanks for the pointer.
>>>>> For what it is worth, clumps do not have the attribute save_object, so
>>>>> masterclump.save_object is not a valid function.
>>>>>
>>>>> I tried pickling again and I can no longer even dump the clumps. I don't
>>>>> know why the dumping 'worked' before and not now, though I have been
>>>>> trying
>>>>> it on more complicated clumps than before. I pasted the error message if
>>>>> you are interested.
>>>>>
>>>>> In [6]: pickle.dump(masterclump, outfile)
>>>>>
>>>>> ---------------------------------------------------------------------------
>>>>> AssertionError Traceback (most recent call
>>>>> last)
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/src/yt-trunk-svn/scripts/iyt in <module>()
>>>>> ----> 1
>>>>> 2
>>>>> 3
>>>>> 4
>>>>> 5
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in dump(obj, file,
>>>>> protocol)
>>>>> 1360
>>>>> 1361 def dump(obj, file, protocol=None):
>>>>> -> 1362 Pickler(file, protocol).dump(obj)
>>>>> 1363
>>>>> 1364 def dumps(obj, protocol=None):
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in dump(self, obj)
>>>>> 222 if self.proto >= 2:
>>>>> 223 self.write(PROTO + chr(self.proto))
>>>>> --> 224 self.save(obj)
>>>>> 225 self.write(STOP)
>>>>> 226
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 329
>>>>> 330 # Save the reduce() output and finally memoize the object
>>>>>
>>>>> --> 331 self.save_reduce(obj=obj, *rv)
>>>>> 332
>>>>> 333 def persistent_id(self, obj):
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_reduce(self,
>>>>> func, args, state, listitems, dictitems, obj)
>>>>> 399 else:
>>>>> 400 save(func)
>>>>> --> 401 save(args)
>>>>> 402 write(REDUCE)
>>>>> 403
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_tuple(self,
>>>>> obj)
>>>>> 560 write(MARK)
>>>>> 561 for element in obj:
>>>>> --> 562 save(element)
>>>>> 563
>>>>> 564 if id(obj) in memo:
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_list(self,
>>>>> obj)
>>>>> 598
>>>>> 599 self.memoize(obj)
>>>>> --> 600 self._batch_appends(iter(obj))
>>>>> 601
>>>>> 602 dispatch[ListType] = save_list
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in
>>>>> _batch_appends(self,
>>>>> items)
>>>>> 613 if not self.bin:
>>>>> 614 for x in items:
>>>>> --> 615 save(x)
>>>>> 616 write(APPEND)
>>>>> 617 return
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 329
>>>>> 330 # Save the reduce() output and finally memoize the object
>>>>>
>>>>> --> 331 self.save_reduce(obj=obj, *rv)
>>>>> 332
>>>>> 333 def persistent_id(self, obj):
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_reduce(self,
>>>>> func, args, state, listitems, dictitems, obj)
>>>>> 399 else:
>>>>> 400 save(func)
>>>>> --> 401 save(args)
>>>>> 402 write(REDUCE)
>>>>> 403
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_tuple(self,
>>>>> obj)
>>>>> 560 write(MARK)
>>>>> 561 for element in obj:
>>>>> --> 562 save(element)
>>>>> 563
>>>>> 564 if id(obj) in memo:
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_list(self,
>>>>> obj)
>>>>> 598
>>>>> 599 self.memoize(obj)
>>>>> --> 600 self._batch_appends(iter(obj))
>>>>> 601
>>>>> 602 dispatch[ListType] = save_list
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in
>>>>> _batch_appends(self,
>>>>> items)
>>>>> 613 if not self.bin:
>>>>> 614 for x in items:
>>>>> --> 615 save(x)
>>>>> 616 write(APPEND)
>>>>> 617 return
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 329
>>>>> 330 # Save the reduce() output and finally memoize the object
>>>>>
>>>>> --> 331 self.save_reduce(obj=obj, *rv)
>>>>> 332
>>>>> 333 def persistent_id(self, obj):
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_reduce(self,
>>>>> func, args, state, listitems, dictitems, obj)
>>>>> 399 else:
>>>>> 400 save(func)
>>>>> --> 401 save(args)
>>>>> 402 write(REDUCE)
>>>>> 403
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_tuple(self,
>>>>> obj)
>>>>> 560 write(MARK)
>>>>> 561 for element in obj:
>>>>> --> 562 save(element)
>>>>> 563
>>>>> 564 if id(obj) in memo:
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 284 f = self.dispatch.get(t)
>>>>> 285 if f:
>>>>> --> 286 f(self, obj) # Call unbound method with explicit self
>>>>> 287 return
>>>>> 288
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_list(self,
>>>>> obj)
>>>>> 598
>>>>> 599 self.memoize(obj)
>>>>> --> 600 self._batch_appends(iter(obj))
>>>>> 601
>>>>> 602 dispatch[ListType] = save_list
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in
>>>>> _batch_appends(self,
>>>>> items)
>>>>> 613 if not self.bin:
>>>>> 614 for x in items:
>>>>> --> 615 save(x)
>>>>> 616 write(APPEND)
>>>>> 617 return
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save(self, obj)
>>>>> 329
>>>>> 330 # Save the reduce() output and finally memoize the object
>>>>>
>>>>> --> 331 self.save_reduce(obj=obj, *rv)
>>>>> 332
>>>>> 333 def persistent_id(self, obj):
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in save_reduce(self,
>>>>> func, args, state, listitems, dictitems, obj)
>>>>> 403
>>>>> 404 if obj is not None:
>>>>> --> 405 self.memoize(obj)
>>>>> 406
>>>>> 407 # More new special cases (that work with older protocols as
>>>>>
>>>>>
>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in memoize(self,
>>>>> obj)
>>>>> 242 if self.fast:
>>>>> 243 return
>>>>> --> 244 assert id(obj) not in self.memo
>>>>> 245 memo_len = len(self.memo)
>>>>> 246 self.write(self.put(memo_len))
>>>>>
>>>>> AssertionError:
>>>>>
>>>>>
>>>>>
>>>>> Matthew Turk wrote:
>>>>>
>>>>>
>>>>>> Hi Britton, Charles,
>>>>>>
>>>>>> Britton is correct, YT has its own routine for pickling. This is a
>>>>>> couple step process, because specifically the pickling of parameter
>>>>>> files is somewhat ill-defined as a problem. When you initialize a
>>>>>> parameter file, it's given a (likely) unique hash that corresponds to
>>>>>> its location, some of its contents, last modified time (or in Enzo's
>>>>>> case, the CurrentTimeIdentifier in the parameter file) and this is
>>>>>> stored in ~/.yt/parameter_files.csv. By this mechanism, one can store
>>>>>> the pointer to a parameter file that exists on disk with a
>>>>>> bidirectional hash. When a new parameter file is opened, it checks to
>>>>>> see if the path location in the .csv file needs to be updated, and if
>>>>>> so, it does.
>>>>>>
>>>>>> So when pickling a YT object, it stores the minimum set of information
>>>>>> necessary to recreate that object. For a sphere, region, etc etc,
>>>>>> this is really just the necessary arguments to recreate the empty
>>>>>> object, along with the hash of the parameter file that it belongs to.
>>>>>> So the actual information necessary to pickle simple objects is very
>>>>>> small: hash, arguments. (Called "_con_args" in the source, for
>>>>>> Constructor Arguments.) When this is unpickled, the parameter file is
>>>>>> recreated (or grabbed from in memory, if it has already been
>>>>>> instantiated) and then the object is recreated.
>>>>>>
>>>>>> For more complicated objects, like Clumps and ExtractedSets, we have
>>>>>> to store more information -- because the constructor arguments are
>>>>>> much larger and more complicated. But the basic idea is the same.
>>>>>>
>>>>>> When using save_object, the same pickling routine gets called, but
>>>>>> instead of being loosely affiliated and put into a separate file, it
>>>>>> gets stored as a dataset in a the corresponding .yt file, which is
>>>>>> itself an HDF5 file. So the results should be the same, except
>>>>>> save_object and load_object remove the extra file from the equation.
>>>>>>
>>>>>> The error you're seeing above seems to be related to an incompletely
>>>>>> saved or corrupted file; can you replicate this in a very simple,
>>>>>> quick fashion? I would suggest getting a clump that is very, very
>>>>>> small, taken from a small data region, and seeing if that will pickle
>>>>>> and unpickle correctly. If it does, then we know that perhaps the
>>>>>> previous pickle file was corrupted, or that something is wrong with
>>>>>> the yt pickling protocol. If it doesn't work, then we *know*
>>>>>> something is wrong with the yt pickling protocol.
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Matt
>>>>>>
>>>>>> On Thu, May 27, 2010 at 6:43 PM, Britton Smith <brittonsmith at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hi Chris,
>>>>>>>
>>>>>>> YT has its own routine designed to pickle data objects for saving and
>>>>>>> reloading. For a given pf, you can do pf.h.save_object(object, name)
>>>>>>> and
>>>>>>> the object will be saved to the .yt file associated with the dataset.
>>>>>>> You
>>>>>>> can then get it back with object = pf.h.load_object(name). I have used
>>>>>>> this
>>>>>>> successfully to save the mast_clump structure from clump finding.
>>>>>>>
>>>>>>> Britton
>>>>>>>
>>>>>>> On Thu, May 27, 2010 at 9:26 PM, Charles Hansen
>>>>>>> <chansen at astro.berkeley.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> The find_clumps function is working correctly for me I believe, but
>>>>>>>> the
>>>>>>>> analysis takes a very long time and I'd like to save the master_clump
>>>>>>>> object
>>>>>>>> (from
>>>>>>>>
>>>>>>>> http://yt.enzotools.org/doc/cookbook/recipes.html#cookbook-find-clumps)
>>>>>>>> for
>>>>>>>> further analysis. I've tried pickling master_clump. It dumps
>>>>>>>> correctly,
>>>>>>>> but gives an EOF error (below) on loading. Is there another way to
>>>>>>>> save
>>>>>>>> master_clump?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> Charles
>>>>>>>>
>>>>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in load(file)
>>>>>>>> 1368
>>>>>>>> 1369 def load(file):
>>>>>>>> -> 1370 return Unpickler(file).load()
>>>>>>>> 1371
>>>>>>>> 1372 def loads(str):
>>>>>>>>
>>>>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in load(self)
>>>>>>>> 856 while 1:
>>>>>>>> 857 key = read(1)
>>>>>>>> --> 858 dispatch[key](self)
>>>>>>>> 859 except _Stop, stopinst:
>>>>>>>> 860 return stopinst.value
>>>>>>>>
>>>>>>>> /nics/c/home/chansen/lib/yt/lib/python2.6/pickle.pyc in load_eof(self)
>>>>>>>> 878
>>>>>>>> 879 def load_eof(self):
>>>>>>>> --> 880 raise EOFError
>>>>>>>> 881 dispatch[''] = load_eof
>>>>>>>> 882
>>>>>>>>
>>>>>>>> EOFError:
>>>>>>>>
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