Memory usage - coords waste
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Description
Dear developers,
Description
In my code, I'm using sparse for handling large data ( > 10 GB). I noticed a larger memory usage by the sparse library than I expected. Comparing 2D matrix with scipy.sparse I realized that sparse is using a significantly larger amount of memory than scipy.sparse. Below you can find the memory consumption of the small example code included at the bottom (obtained with the memory_profiler library)
Line # Mem usage Increment Line Contents
================================================
7 99.5 MiB 99.5 MiB @profile
8 def check_conv(N1, N2, N3):
9 226.4 MiB 126.9 MiB A = sp.random(N1, N2, density=0.12, format="coo")
10
11 447.0 MiB 220.6 MiB B = sparse.COO.from_scipy_sparse(A)
12 636.3 MiB 189.3 MiB return B.reshape((N3, N2, N2))
We see a usage of 220 MB by sparse.COO while scipy.sparse uses only 127 MB.
Investigating the memory usage in sparse.COO, I found a large amount of memory used by the lines
246 415.6 MiB 126.1 MiB self.coords = self.coords.astype(np.intp, copy=False)
and
276 510.1 MiB 94.3 MiB self._sort_indices()
If I comment line 246 in the file sparse/_coo/core.py then the memory usage is significantly smaller.
Line # Mem usage Increment Line Contents
================================================
7 99.2 MiB 99.2 MiB @profile
8 def check_conv(N1, N2, N3):
9 226.3 MiB 127.1 MiB A = sp.random(N1, N2, density=0.12, format="coo")
10
11 383.8 MiB 157.5 MiB B = sparse.COO.from_scipy_sparse(A)
12 573.1 MiB 189.2 MiB return B.reshape((N3, N2, N2))
A gain of around 60 MB. My question is, why line 246 in sparse/_coo/core.py seems to copy the memory, while copy=False and how can I avoid it?
Also, do there is a way to avoid the sorting of index in line 276 when converting the matrix from scipy.sparse?
Example Code
from __future__ import division
import numpy as np
import scipy.sparse as sp
import sparse
from memory_profiler import profile
@profile
def check_conv(N1, N2, N3):
A = sp.random(N1, N2, density=0.12, format="coo")
B = sparse.COO.from_scipy_sparse(A)
return B.reshape((N3, N2, N2))
check_conv(453264, 152, 2982)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with sparse/_coo/core.py around the coords astype call at line 246 and _sort_indices at line 276, then reproduce the reported memory profile using the example with scipy.sparse and sparse.COO.from_scipy_sparse. Determine whether the conversions create avoidable copies or sorting work, and consider the issue complete when the conversion preserves correctness with the reported memory overhead addressed or the behavior is clearly documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- numpy, python
- Domain
- performance
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100