Python/Numpy MemoryError [英] Python/Numpy MemoryError

问题描述

基本上，尝试在numpy矩阵上执行代数运算时，我在python中遇到内存错误.变量u是一个大的double矩阵(在失败的情况下，它是288x288x156的double矩阵.在这种情况下，我只会出现此错误，但是我可以在其他大型矩阵上执行此操作，但不是那么大) ).这是Python错误:

Basically, I am getting a memory error in python when trying to perform an algebraic operation on a numpy matrix. The variable u, is a large matrix of double (in the failing case its a 288x288x156 matrix of doubles. I only get this error in this huge case, but I am able to do this on other large matrices, just not this big). Here is the Python error:

 Traceback (most recent call last):

 File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc
t perim erosion flattop\SwSim.py", line 121, in __init__
   self.mainSimLoop()

 File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc
t perim erosion flattop\SwSim.py", line 309, in mainSimLoop
   u = solver.solve_cg(u,b,tensors,param,fdHold,resid) # Solve the left hand si
de of the equation Au=b with conjugate gradient method to approximate u

 File "S:\3D_Simulation_Data\Patient SPM Segmentation\20 pc
t perim erosion flattop\conjugate_getb.py", line 47, in solv
e_cg

u = u + alpha*p

MemoryError

u = u + alpha*p是失败的代码行.

alpha只是双精度，而u和r是上述大型矩阵(大小相同).

alpha is just a double, while u and r are the large matrices described above (both of the same size).

我对内存错误了解不多，尤其是在Python中.任何有识之士/解决这个问题的技巧将不胜感激！

I don't know that much about memory errors especially in Python. Any insight/tips into solving this would be very appreciated!

谢谢

推荐答案

重写为

p *= alpha
u += p

，这将使用更少的内存.而p = p*alpha为p*alpha的结果分配一个全新的矩阵，然后丢弃旧的p； p*= alpha就地做同样的事情.

and this will use much less memory. Whereas p = p*alpha allocates a whole new matrix for the result of p*alpha and then discards the old p; p*= alpha does the same thing in place.

通常，对于大型矩阵，请尝试使用op=分配.

In general, with big matrices, try to use op= assignment.

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