Python Memory Error Large Array
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Python Memory Error Numpy
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creating huge matrix up vote 2 down vote favorite 3 I am using numpy and trying to create a huge matrix. While doing this, I receive a memory error Because the matrix is not important, I will just show the way how
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to easily reproduce the error. a = 10000000000 data = np.array([float('nan')] * a) not surprisingly, this throws me MemoryError There are two things I would like to tell: I really need to create and to use a big matrix I think I have enough RAM to handle this matrix (I have 24 Gb or RAM) Is there an easy way to handle big matrices in numpy? Just to be on the safe side, I previously read these posts (which sounds similar): Python Numpy Very Large Matrices how to solve memory error in python Python/Numpy MemoryError Processing a very very big data set in python - memory error P.S. apparently I have some problems with multiplication and division of numbers, which made me think that I have enough memory. So I think it is time for me to go to sleep, review math and may be to buy some memory. May be during this time some genius might come up with idea how to actually create this matrix using only 24 Gb of Ram. Why I need this big matrix I am not going to do any manipulations with this matrix. All I need to do with it is to save it into pytables. python memory numpy share|improve this question edited Sep 30 '13 at 1:18 asked Sep 30 '13 at 0:53 Salvador Dali 50.5k41232311 2 How do you expect to fit 10 billion floats in 24 GB? If a float were 2.4 bytes, and 100% of your RAM were devoted to holding this array - sure ;-) –Tim Peters Sep 30 '13 at 0:56 What do you need to do with this matrix? That might give an insight to a workaround. –Rohit Sep 30 '13 at 1:14 cant you save it piece by piece? n work on partitions of your data? –usethedeathstar Sep 30 '13 at 7:20 Also, The way you create it first creates a python list of that size. Now the float is always the same object, but the list itself will have the same size as the resulting arra
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the company Business Learn more about hiring developers or memory error pandas posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss python huge matrix Join the Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like you, helping each other. Join them; it only numpy very large arrays takes a minute: Sign up Python/Numpy MemoryError up vote 10 down vote favorite 7 Basically, I am getting a memory error in python when trying to perform an algebraic operation on a numpy matrix. The variable u, is a large http://stackoverflow.com/questions/19085012/numpy-memory-error-creating-huge-matrix matrix of double (in the failing case its a 288x288x156 matrix of doubles. I only get this error in this huge case, but I am able to do this on other large matrices, just not this big). Here is the Python error: Traceback (most recent call last): File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc t perim erosion flattop\SwSim.py", line 121, in __init__ self.mainSimLoop() File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc t perim erosion flattop\SwSim.py", line 309, in mainSimLoop u = solver.solve_cg(u,b,tensors,param,fdHold,resid) # Solve the left http://stackoverflow.com/questions/4318615/python-numpy-memoryerror hand si de of the equation Au=b with conjugate gradient method to approximate u File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc t perim erosion flattop\conjugate_getb.py", line 47, in solv e_cg u = u + alpha*p MemoryError u = u + alpha*p is the line of code that fails. alpha is just a double, while u and r are the large matrices described above (both of the same size). I don't know that much about memory errors especially in Python. Any insight/tips into solving this would be very appreciated! Thanks python memory numpy scipy share|improve this question edited Mar 24 '15 at 23:45 ali_m 28.3k662114 asked Nov 30 '10 at 21:03 tylerthemiler 85331435 add a comment| 3 Answers 3 active oldest votes up vote 23 down vote accepted Rewrite to p *= alpha u += p and this will use much less memory. Whereas p = p*alpha allocates a whole new matrix for the result of p*alpha and then discards the old p; p*= alpha does the same thing in place. In general, with big matrices, try to use op= assignment. share|improve this answer answered Nov 30 '10 at 22:22 luispedro 4,29932246 This is very helpful, I didn't know this. –tylerthemiler Nov 30 '10 at 22:36 add a comment| up vote 5 down vote Another tip I have found to avoid memory errors is to manually control garbage collection. When objects are deleted or go our of scope, the memory used
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta http://stackoverflow.com/questions/27416311/python-numpy-array-memory-error-in-loop Discuss the workings and policies of this site About Us Learn https://www.kaggle.com/c/word2vec-nlp-tutorial/forums/t/13144/have-memoryerror-when-train-data-features-toarray more about Stack Overflow the company Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 6.2 million programmers, just like memory error you, helping each other. Join them; it only takes a minute: Sign up python numpy array memory error in loop up vote 0 down vote favorite I'm experiencing a very weird problem when using a large numpy array. Here's the basic context. I have about 15 lists of paired objects which I am constructing adjacency matrices for. python memory error Each adjacency matrix is about 4000 x 4000 (square matrix where the diagonal means the object is paired with itself) so it's big but not too big. Here's the basic setup of my code: def createAdjacencyMatrix(pairedObjectList, objectIndexList): N = len(objectIndexList) adj = numpy.zeros((N,N)) for i in range(0, len(pairedObjectList): #put a 1 in the correct row/column position for the pair etc. return adj In my script I call this function about 15 times, one for each paired object list. However every time I run it I get this error: adj = np.zeros((N,N)) MemoryError I really don't understand where the memory error is coming from. Even though I'm making this big matrix, it only exists within the scope of that function, so shouldn't it be cleared from memory every time the function is finished? Not to mention, if the same variable is hanging around in memory, then shouldn't it just overwrite those memory positions? Any help understanding this much appreciated. EDIT : Here's the full output of the traceback T
of Popcorn Tue 9 Dec 2014 – Tue 30 Jun 2015 (16 months ago) Dashboard ▼ Home Data Make a submission Information Description Evaluation Rules Part 1: For Beginners - Bag of Words Part 2: Word Vectors Part 3: More Fun With Word Vectors Part 4: Comparing deep and non-deep learning methods Setting Up Your System What is Deep Learning? Forum Leaderboard Competition Forum All Forums » Bag of Words Meets Bags of Popcorn have "MemoryError" when "train_data_features.toarray()" Start Watching « Prev Topic » Next Topic 1 vote Hi all, I run the code on my PC(windows7 x64, 12G RAM),but I met the MemoryError whenrun "train_data_features.toarray()" version of scipy on my PC is 0.14.0 the message as following: Traceback (most recent call last): File "D:/kaggleData/BagOfWords/BagOfWords.py", line 66, in train_data_features = train_data_features.toarray() File "C:\Python27\lib\site-packages\scipy\sparse\compressed.py", line 901, in toarray return self.tocoo(copy=False).toarray(order=order, out=out) File "C:\Python27\lib\site-packages\scipy\sparse\coo.py", line 269, in toarray B = self._process_toarray_args(order, out) File "C:\Python27\lib\site-packages\scipy\sparse\base.py", line 789, in _process_toarray_args return np.zeros(self.shape, dtype=self.dtype, order=order)MemoryError what should I do to solve this problem? Thanks! #1 | Posted 19 months ago Permalink wen xue Posts 2 | Votes 1 Joined 10 Jun '13 | Email User 0 votes It seems that you have this error when vectorizing the reviews using bag of words. If that's the case, you might try using less features so that less ram is used. #2 | Posted 19 months ago Permalink Skabed Posts 4 | Votes 4 Joined 15 Dec '13 | Email User 0 votes Skabed wrote: It seems that you have this error when vectorizing the reviews using bag of words. If that's the case, you might try using less features so that less ram is used. I decreased the number of max feature to 1000 and no MemoryError anymore. Thanks for your advice. #3 | Posted 19 months ago Permalink wen xue Posts 2 | Votes 1 Joined 10 Jun '13 | Email User 0 votes Skabed wrote: It seems that yo