Unable to load a previously dumped pickle file of large size in Python
networkx, numpy, pickle, python
Solution
How about save & load the numpy array by `numpy.save()` & `np.load()`?
You can save the pickled list and the numpy array to the same file:
import numpy as np
import cPickle
data = np.random.rand(50000000)
f = open('foo.pck', 'wb')
cPickle.dump([1,2,3], f, protocol=2)
np.save(f, data)
f.close()
to read the data:
import cPickle
import numpy as np
f= open('foo.pck', 'rb')
v = cPickle.load(f)
data = np.load(f)
print data.shape, data
Problem
I used cPickle and protocol version 2 to dump some computation results. The code looks like this: ``` > f = open('foo.pck', 'w') > cPickle.dump(var, f, protocol=2) > f.close() ``` The variable var is a tuple of length two. The type of var[0] is a list and var[1] is a numpy.ndarray. The above code segment successfully generated a file with large size (~1.7G). However, when I tried to load the variable from foo.pck, I got the following error. ``` ValueError Traceback (most recent call last) /home/user_account/tmp/<ipython-input-3-fd3ecce18dcd> in <module>() ----> 1 v = cPickle.load(f) ValueError: buffer size does not match array size ``` The loading codes looks like the following. ``` > f= open('foo.pck', 'r') > v = cPickle.load(f) ``` I also tried to use pickle (instead of cPickle) to load the variable, but got a similar error msg as follows. ``` ValueError Traceback (most recent call last) /home/user_account/tmp/<ipython-input-3-aa6586c8e4bf> in <module>() ----> 1 v = pickle.load(f) /usr/lib64/python2.6/pickle.pyc in load(file) 1368 1369 def load(file): -> 1370 return Unpickler(file).load() 1371 1372 def loads(str): /usr/lib64/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 /usr/lib64/python2.6/pickle.pyc in load_build(self) 1215 setstate = getattr(inst, "__setstate__", None) 1216 if setstate: -> 1217 setstate(state) 1218 return 1219 slotstate = None ValueError: buffer size does not match array size ``` I tried the same code segments to a much smaller size data and it worked fine. So my best guess is that I reached the loading size limitation of pickle (or cPickle). However, it is strange to dump successfully (with large size variable) but failed to load. If this is indeed a loading size limitation problem, how should I bypass it? If not, what can be the possible cause of the problem? Any suggestion is appreciated. Thanks!