How to declare 2D list in Cython

Question

I'm trying to compile this kind of code:

def my_func(double c, int m):
    cdef double f[m][m]

    f = [[c for x in range(m)] for y in range(m)]
    ...

which raises:

Error compiling Cython file:
------------------------------------------------------------
def grow(double alpha, double beta, double gamma, int m, int s):
    cdef double f[m][m]
                     ^
------------------------------------------------------------
test.pyx:6:22: Not allowed in a constant expression

after which I assume I can't use variable at the pointed place and I try with numeric value:

def my_func(double c, int m):
    cdef double f[500][500]

    f = [[c for x in range(500)] for y in range(500)]
    ...

but then I get:

Error compiling Cython file:
------------------------------------------------------------
    f = [[beta for x in range(500)] for y in range(500)]
     ^
------------------------------------------------------------
test.pyx:13:6: Assignment to non-lvalue 'f'

So, I'm wondering how to declare and make 2D list in cython code. I couldn't find this kind of example in documentation of googling for "cython 2D list"

Answer 1

Do not use list comprehension in Cython. There are not speedups as they create regular python list. Wiki says, that you should use dynamic allocation in Cython as follow:

from libc.stdlib cimport malloc, free

def my_func(double c, int m):
    cdef int x
    cdef int y
    cdef double *my_array = <double *>malloc(m * m * sizeof(double))

    try:

        for y in range(m):
            for x in range(m):
                #Row major array access
                my_array[ x + y * m ] = c

        #do some thing with my_array

    finally:
       free( my_array )

But if you need to have a python object of a 2D array, its recommended to use NumPy.

Answer 2

cdef double f[500][500]

This is declaring a C array of 500 C arrays of 500 doubles. That's 500 * 500 packed double values (stored on the stack in this case, unless Cython does something funky) without any indirection, which aids performance and cache utilization, but obviously adds severe restrictions. Maybe you want this, but you should learn enough C to know what that means first. By the way, one restriction is that the size must be a compile-time constant (depending on the C version; C99 and C10 allow it), which is what the first error message is about.

If you do use arrays, you don't initialize f the way you did, because that doesn't make any sense. f is already 500x500 double variables, and arrays as a whole can't be assigned to (which is what the latter error message is trying to tell you). In particular, list comprehension creates a fully-blown Python list object (which you could also use from Cython, see below) containing fully-blown "boxed" Python objects (float objects, in this case). A list is not compatible with a C array. Use a nested for loop with item assignment for the initialization. Lastly, such an array takes 500 * 500 * 8 byte, which is almost 2 MiB. On some systems, that's larger than the entire stack, and on all other systems, it's such a large portion of the stack that it's a bad idea. You should heap-allocate that array.

If you use a Python list, be warned that you won't get much improvement in performance and memory use (assuming your code will mostly be manipulating that list), though you may gain back some convenience in return. You could just leave off the cdef, or use list as the type (object should work too, but you gain nothing from it, so you might as well omit it).

A NumPy array may be faster, more memory-efficient, and more convenient to use. If you can implement the performance-critical parts of your algorithm in terms of NumPy's operations, you may gain the desired speedup without using Cython at all.