Unable to allocate array with shape and data type

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   np zeros  156816  36  53806   dtype  uint8     and while I m getting an error on Ubuntu OS   gt  gt  gt  import numpy as np  gt  gt  gt  np zeros  156816  36  53806   dtype  uint8   Traceback  most recent call last     File   lt stdin gt    line 1  in  lt module gt  numpy core  exceptions MemoryError  Unable to allocate array with shape  156816  36  53806  and data type uint8   I m not getting it on MacOS    gt  gt  gt  import numpy as np   gt  gt  gt  np zeros  156816  36  53806   dtype  uint8   array    0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0              0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0              0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                           0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0              0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0              0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0                         0  0  0       0  0  0            0  0  0       0  0  0            0  0  0       0  0  0     dtype uint8    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   versions   Ubuntu os - gt  ubuntu mate 18 python - gt  3 6 8 numpy - gt  1 17 0  mac os - gt  10 14 6 python - gt  3 6 4 numpy - gt  1 17 0   PS  also failed on Google Colab

User · Answer

I came across this problem on Windows too. The solution for me was to switch from a 32-bit to a 64-bit version of Python. Indeed, a 32-bit software, like a 32-bit CPU, can adress a maximum of 4 GB of RAM (2^32). So if you have more than 4 GB of RAM, a 32-bit version cannot take advantage of it.

With a 64-bit version of Python (the one labeled x86-64 in the download page), the issue disappeared.

You can check which version you have by entering the interpreter. I, with a 64-bit version, now have: Python 3.7.5rc1 (tags/v3.7.5rc1:4082f600a5, Oct 1 2019, 20:28:14) [MSC v.1916 64 bit (AMD64)], where [MSC v.1916 64 bit (AMD64)] means "64-bit Python".

Note : as of the time of this writing (May 2020), matplotlib is not available on python39, so I recommand installing python37, 64 bits.

Sources :

User · Answer

I had this same problem on Window s and came across this solution  So if someone comes across this problem in Windows the solution for me was to increase the pagefile size  as it was a Memory overcommitment problem for me too  Windows 8  On the Keyboard Press the WindowsKey   X then click System in the popup menu Tap or click Advanced system settings  You might be asked for an admin password or to confirm your choice On the Advanced tab  under Performance  tap or click Settings  Tap or click the Advanced tab  and then  under Virtual memory  tap or click Change Clear the Automatically manage paging file size for all drives check box  Under Drive  Volume Label   tap or click the drive that contains the paging file you want to change Tap or click Custom size  enter a new size in megabytes in the initial size  MB  or Maximum size  MB  box  tap or click Set  and then tap or click OK Reboot your system  Windows 10  Press the Windows key Type SystemPropertiesAdvanced Click Run as administrator Under Performance  click Settings Select the Advanced tab Select Change    Uncheck Automatically managing paging file size for all drives Then select Custom size and fill in the appropriate size Press Set then press OK then exit from the Virtual Memory  Performance Options  and System Properties Dialog Reboot your system  Note  I did not have the enough memory on my system for the  282GB in this example but for my particular case this worked  EDIT From here the suggested recommendations for page file size   There is a formula for calculating the correct pagefile size  Initial size is one and a half  1 5  x the amount of total system memory  Maximum size is three  3  x the initial size  So let s say you have 4 GB  1 GB   1 024 MB x 4   4 096 MB  of memory  The initial size would be 1 5 x 4 096   6 144 MB and the maximum size would be 3 x 6 144   18 432 MB   Some things to keep in mind from here   However  this does not take into consideration other important factors and system settings that may be unique to your computer  Again  let Windows choose what to use instead of relying on some arbitrary formula that worked on a different computer   Also   Increasing page file size may help prevent instabilities and crashing in Windows  However  a hard drive read write times are much slower than what they would be if the data were in your computer memory  Having a larger page file is going to add extra work for your hard drive  causing everything else to run slower  Page file size should only be increased when encountering out-of-memory errors  and only as a temporary fix  A better solution is to adding more memory to the computer

User · Answer

Sometimes  this error pops up because of the kernel has reached its limit  Try to restart the kernel redo the necessary steps

User · Answer

In my case  adding a dtype attribute changed dtype of the array to a smaller type from float64 to uint8   decreasing array size enough to not throw MemoryError in Windows 64 bit    from   mask   np zeros edges shape    to  mask   np zeros edges shape dtype  uint8

User · Answer

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   gt  gt  gt  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  gt   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    I tested this myself on a machine with 32 GB of RAM   With overcommit mode 0 I also got a MemoryError  but after changing it back to 1 it works    gt  gt  gt  import numpy as np  gt  gt  gt  a   np zeros  156816  36  53806   dtype  uint8    gt  gt  gt  a nbytes 303755101056   You can then go ahead and write to any location within the array  and the system will only allocate physical pages when you explicitly write to that page   So you can use this  with care  for sparse arrays

User · Answer

change the data type to another one which uses less memory works  For me  I change the data type to numpy uint8  data  label     data  label   astype np uint8

[python] Unable to allocate array with shape and data type

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