memory - Python/Numpy MemoryError

Question

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_DataPatient SPM Segmentation20 pc
t perim erosion flattopSwSim.py", line 121, in __init__
   self.mainSimLoop()

 File "S:3D_Simulation_DataPatient SPM Segmentation20 pc
t perim erosion flattopSwSim.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_DataPatient SPM Segmentation20 pc
t perim erosion flattopconjugate_getb.py", line 47, in solv
e_cg

u = u + alpha*p

MemoryError

u = u + alpha*p is the line of code that fails.

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

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

Thanks

Answer 1

Rewrite to

p *= alpha
u += p

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.

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