[ Python 常見問題 ] Unable to allocate array with shape and data type

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Question
I'm facing an issue with allocating huge arrays in numpy on Ubuntu 18 while not facing the same issue on MacOS. I am trying to allocate memory for a numpy array with shape (156816, 36, 53806) with:

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1. np.zeros((156816, 36, 53806), dtype='uint8')  

and while I'm getting an error on Ubuntu OS

>>> import numpy as np
>>> np.zeros((156816, 36, 53806), dtype='uint8')
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
numpy.core._exceptions.MemoryError: Unable to allocate array with shape (156816, 36, 53806)

I've read somewhere that np.zeros shouldn't be really allocating the whole memory needed for the array, but only for the non-zero elements. Even though the Ubuntu machine has 64gb of memory, while my MacBook Pro has only 16gb.

HowTo
This is likely due to your system's overcommit handling mode.

In the default mode, 0,

Heuristic overcommit handling. Obvious overcommits of address space are refused. Used for a typical system. It ensures a seriously wild allocation fails while allowing overcommit to reduce swap usage. root is allowed to allocate slightly more memory in this mode. This is the default.

The exact heuristic used is not well explained here, but this is discussed more on Linux over commit heuristic and on this page.

You can check your current overcommit mode by running

$ cat /proc/sys/vm/overcommit_memory
0

In this case you're allocating

>>> 156816 * 36 * 53806 / 1024.0**3
282.8939827680588

~282 GB, and the kernel is saying well obviously there's no way I'm going to be able to commit that many physical pages to this, and it refuses the allocation.

If (as root) you run:

$ echo 1 > /proc/sys/vm/overcommit_memory

This will enable "always overcommit" mode, and you'll find that indeed the system will allow you to make the allocation no matter how large it is (within 64-bit memory addressing at least).