Saturday, 24 December 2022

Memory efficient dot product between a sparse matrix and a non-sparse numpy matrix

I have gone through similar questions that has been asked before (for example [1] [2]). However, none of them completely relevant for my problem.

I am trying to calculate a dot product between two large matrices and I have some memory constraint that I have to meet.

I have a numpy sparse matrix, which is a shape of (10000,600000). For example,

from scipy import sparse as sps
x = sps.random(m=10000, n=600000, density=0.1).toarray()

The second numpy matrix is of size (600000, 256), which consists of only (-1, 1).

import numpy as np
y = np.random.choice([-1,1], size=(600000, 256))

I need dot product of x and y at lowest possible memory required. Speed is not the primary concern.

Here is what I have tried so far:

Scipy Sparse Format:

Naturally, I converted the numpy sparse matrix to scipy csr_matrix. However, task is still getting killed due to memory issue. There is no error, I just get killed on the terminal.

from scipy import sparse as sps
sparse_x = sps.csr_matrix(x, copy=False)
z = sparse_x.dot(y)
# killed

Decreasing dtype precision + Scipy Sparse Format:

from scipy import sparse as sps

x = x.astype("float16", copy=False)
y = y.astype("int8", copy=False)

sparse_x = sps.csr_matrix(x, copy=False)
z = sparse_x.dot(y)
# Increases the memory requirement for some reason and dies 

np.einsum

Not sure if it helps/works with sparse matrix. Found something interesting in this answer. However, following doesn't help either:

z = np.einsum('ij,jk->ik', x, y)
# similar memory requirement as the scipy sparse dot

Suggestions?

If you have any suggestions to improve any of these. Please let me know. Further, I am thinking in the following directions:

  1. It would be great If I can get rid of dot product itself somehow. My second matrix (i.e. y is randomly generated and it just has [-1, 1]. I am hoping if there is way I could take advantage of its features.

  2. May be diving dot product into several small dot product and then, aggregate.



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