Save Large Scipy Sparse Matrix

3
votes

I am trying to cPickle a large scipy sparse matrix for later use. I am getting this error:

  File "tfidf_scikit.py", line 44, in <module>
    pickle.dump([trainID, trainX, trainY], fout, protocol=-1)
SystemError: error return without exception set

trainX is the large sparse matrix, the other two are lists 6mil elements long. 

In [1]: trainX
Out[1]:
<6034195x755258 sparse matrix of type '<type 'numpy.float64'>'
    with 286674296 stored elements in Compressed Sparse Row format>

At this point, Python RAM usage is 4.6GB and I have 16GB of RAM on my laptop.

I think I'm running into a known memory bug for cPickle where it doesn't work with objects that are too big. I tried marshal as well but I don't think it works for scipy matrices. Can someone offer a solution and preferably an example on how to load and save this?

Python 2.7.5

Mac OS 10.9

Thank you.

2
pythonscipysparse-matrixpickle
possible duplicate of Save / load scipy sparse csr_matrix in portable data format – YXD
I have the same problem with sparse matrices and pickle, do not think that this is a duplicate question of the one linked. – Ekgren

2 Answers

1
votes

I had this problem with a multi-gigabyte Numpy matrix (Ubuntu 12.04 with Python 2.7.3 - seems to be this issue: https://github.com/numpy/numpy/issues/2396 ).

I've solved it using numpy.savetxt() / numpy.loadtxt(). The matrix is compressed adding a .gz file extension when saving.

Since I too had just a single matrix I did not investigate the use of HDF5.

0
votes

Both numpy.savetxt (only for arrays, not sparse matrices) and sklearn.externals.joblib.dump (pickling, slow as hell and blew up memory usage) didn't work for me on Python 2.7.

Instead, I used scipy.sparse.save_npz and it worked just fine. Keep in mind that it only works for csc, csr, bsr, dia or coo matrices.