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I am trying to convert some Python / Numpy code to Cython for speed up. Here is my code: 

cimport numpy as np
import numpy as np
from numpy import *
import pylab as pl
from pylab import * 
from scipy import integrate

def myc_rb_e2f(np.ndarray[double,ndim=1] y = np.zeros(7),double t, double k,double d):

    M = y[0]
    E = y[1]
    CD = y[2]
    CE = y[3]
    R = y[4]
    RP = y[5] 
    RE = y[6]

    cdef double S = 0.01
    if t > 300.0:
        S = 5.0
    #if t > 400
        #S = 0.01

    cdef double t1 = k[0]*S/(k[7]+S)
    cdef double t2 = k[1]*(M/(k[14]+M))*(E/(k[15]+E))
    cdef double t3 = k[5]*M/(k[14]+M)
    cdef double t4 = k[11]*CD*RE/(k[16]+RE)
    cdef double t5 = k[12]*CE*RE/(k[17]+RE)
    cdef double t6 = k[2]*M/(k[14]+M)
    cdef double t7 = k[3]*S/(k[7]+S)
    cdef double t8 = k[6]*E/(k[15]+E)
    cdef double t9 = k[13]*RP/(k[18]+RP)
    cdef double t10 = k[9]*CD*R/(k[16]+R)
    cdef double t11 = k[10]*CE*R/(k[17]+R)

    dM = t1-d[0]*M
    dE = t2+t3+t4+t5-k[8]*R*E-d[1]*E
    dCD = t6+t7-d[2]*CD
    dCE = t8-d[3]*CE
    dR = k[4]+t9-k[8]*R*E-t10-t11-d[4]*R
    dRP = t10+t11+t4+t5-t9-d[5]*RP
    dRE = k[8]*R*E-t4-t5-d[6]*RE

    dy = [dM,dE,dCD,dCE,dR,dRP,dRE]

    return dy

cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
cdef int i

for i in range (0,5000):
    k[0] = 1.+0.1*randn(1)
    k[1] = 0.15+0.05*randn(1)
    k[2] = 0.2+0.05*randn(1)
    k[3] = 0.2+0.05*randn(1)
    k[4] = 0.35+0.05*randn(1)
    k[5] = 0.001+0.0001*randn(1)
    k[6] = 0.5+0.05*randn(1)
    k[7] = 0.3+0.05*randn(1)
    k[8] = 30.+5.*randn(1)
    k[9] = 18.+3.*randn(1)
    k[10] = 18.+3.*randn(1)
    k[11] = 18.+3.*randn(1)
    k[12] = 18.+3.*randn(1)
    k[13] = 3.6+0.5*randn(1)
    k[14] = 0.15+0.05*randn(1)
    k[15] = 0.15+0.05*randn(1)
    k[16] = 0.92+0.1*randn(1)
    k[17] = 0.92+0.1*randn(1)
    k[18] = 0.01+0.001*randn(1)
    d[0] = 0.7+0.05*randn(1)
    d[1] = 0.25+0.025*randn(1)
    d[2] = 1.5+0.05*randn(1)
    d[3] = 1.5+0.05*randn(1)
    d[4] = 0.06+0.01*randn(1)
    d[5] = 0.06+0.01*randn(1)
    d[6] = 0.03+0.005*randn(1)
    r = integrate.odeint(myc_rb_e2f,y0,t,args=(k,d))
    E_simulated[:,i] = r[:,1]

for i in range(0,10000):
    E_avg[i] = sum(E_simulated[i,:])/5000.

pl.plot(t,E_avg,'-ro')
pl.show()

I get a slew of errors when trying to compile: 

Error compiling Cython file:
------------------------------------------------------------
...

        dy = [dM,dE,dCD,dCE,dR,dRP,dRE]

        return dy

cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:48:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...

cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:52:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:53:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:54:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:55:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:56:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:57:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:1:0: Buffer vars not allowed in module scope
An exception has occurred, use %tb to see the full traceback.

SystemExit: error: command 'gcc' failed with exit status 1


%run setup.py build_ext --inplace
running build_ext
cythoning myc_rb_e2f_pyx.pyx to myc_rb_e2f_pyx.c
building 'myc_rb_e2f_pyx' extension
C:\Python27\Scripts\gcc.exe -mno-cygwin -mdll -O -Wall -DMS_WIN64 -IC:\Python27\lib\site-packages\numpy\core\include -IC:\Python27\include -IC:\Python27\PC -c myc_rb_e2f_pyx.c -o build\temp.win-amd64-2.7\Release\myc_rb_e2f_pyx.o

Error compiling Cython file:
------------------------------------------------------------
...

        dy = [dM,dE,dCD,dCE,dR,dRP,dRE]

        return dy

cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:48:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...

cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:52:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] t = np.zeros(10000)
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:53:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
t = np.linspace(0.,3000.,10000.)

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:54:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...

# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:55:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
# Initial concentrations of [M,E,CD,CE,R,RP,RE]
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:56:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cdef np.ndarray[double,ndim=1] y0 = np.array([0.,0.,0.,0.,0.4,0.,0.25])
cdef np.ndarray[double,ndim=2] E_simulated = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=2] r = np.zeros([10000,5000])
cdef np.ndarray[double,ndim=1] E_avg = np.zeros([10000])
cdef np.ndarray[double,ndim=1] k = np.zeros([19])
cdef np.ndarray[double,ndim=1] d = np.zeros([7])
                              ^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:57:31: Buffer types only allowed as function local variables

Error compiling Cython file:
------------------------------------------------------------
...
cimport numpy as np
^
------------------------------------------------------------

myc_rb_e2f_pyx.pyx:1:0: Buffer vars not allowed in module scope
An exception has occurred, use %tb to see the full traceback.

SystemExit: error: command 'gcc' failed with exit status 1

Can anyone help me with where I'm going wrong in declaring arrays?

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1 Answer 1

Reset to default
6

The error message is pretty clear: buffer-typed variables are not allowed at toplevel. Put all the code starting from the declaration of t in a function, say main, and call that.

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4 Comments

Can you link to any documentation relating to this limitation?
@pelson: The Cython docs are, unfortunately, never up to date. You can easily try this for yourself, though, which will give the error message that the OP encountered, even in the most recent version of Cython.
Ok, cheers. I'm getting the same error, only for methods in a class (no main level stuff). I'll post a question on here shortly I think.
@pelson: You mean as a cdef class member? I tried that only yesterday and it's not supported :(

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