I am having some trouble writing a cython interface to a library. It does
something pretty simple: creates a malloc'ed array of values, passes it to
a external function in the library, and gets a malloc'ed array back.
In the past i made something similar to this work:
#clib homotopyPath
cdef extern from "stdlib.h":
void free(void* ptr)
cdef extern from "homotopyPath.h":
double* homotopyPath (int degree, double *_coef, double _y0R, double
_y0I)
def contpath(deg,values,y0r,y0i):
cdef double* rop
c_values = <double*>sage_malloc(sizeof(double)*len(values))
#cdef int clen = <int> len(values)
for i,v in enumerate(values):
c_values[i] = values[i]
cdef double y0R = y0r
cdef double y0I = y0i
rop = homotopyPath (int(deg), c_values, y0R, y0I)
n=int(rop[0])
l=[0 for i in range(n)]
for i in range(n):
l[i]=(rop[3*i+1],rop[3*i+2],rop[3*i+3])
free(rop)
free(c_values)
return l
But when i try to load it i get the error:
Compiling ./my_library.pyx...
Error compiling cython file:
Error compiling ./my_library.pyx:
running build
running build_ext
building '_home_mmarco_integrado_my_library_pyx_16' extension
gcc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/home/
mmarco/sage/local/include/csage -I/home/mmarco/sage/local/include -I/home/
mmarco/sage/local/include/python2.7 -I/home/mmarco/sage/local/lib/python/
site-packages/numpy/core/include -I/home/mmarco/sage/src/sage/ext -I/home/
mmarco/sage/src -I/home/mmarco/sage/src/sage/gsl -I. -I/home/mmarco/sage/
local/include/python2.7 -c _home_mmarco_integrado_my_library_pyx_16.c -o
build/temp.linux-x86_64-2.7/_home_mmarco_integrado_my_library_pyx_16.o -w -
O2
_home_mmarco_integrado_my_library_pyx_16.c:1183:28: error: redefinition of
'sage_malloc'
static CYTHON_INLINE void *sage_malloc(size_t __pyx_v_n) {
^
In file included from /home/mmarco/sage/local/include/csage/stdsage.h:36:0,
from _home_mmarco_integrado_my_library_pyx_16.c:230:
/home/mmarco/sage/local/include/csage/memory.h:29:21: note: previous
definition of 'sage_malloc' was here
static inline void* sage_malloc(size_t n)
^
_home_mmarco_integrado_my_library_pyx_16.c:1245:28: error: redefinition of
'sage_realloc'
static CYTHON_INLINE void *sage_realloc(void *__pyx_v_ptr, size_t
__pyx_v_size) {
^
In file included from /home/mmarco/sage/local/include/csage/stdsage.h:36:0,
from _home_mmarco_integrado_my_library_pyx_16.c:230:
/home/mmarco/sage/local/include/csage/memory.h:49:21: note: previous
definition of 'sage_realloc' was here
static inline void* sage_realloc(void *ptr, size_t size)
^
_home_mmarco_integrado_my_library_pyx_16.c:1307:28: error: redefinition of
'sage_calloc'
static CYTHON_INLINE void *sage_calloc(size_t __pyx_v_nmemb, size_t
__pyx_v_size) {
^
In file included from /home/mmarco/sage/local/include/csage/stdsage.h:36:0,
from _home_mmarco_integrado_my_library_pyx_16.c:230:
/home/mmarco/sage/local/include/csage/memory.h:36:21: note: previous
definition of 'sage_calloc' was here
static inline void* sage_calloc(size_t nmemb, size_t size)
^
_home_mmarco_integrado_my_library_pyx_16.c:1369:27: error: redefinition of
'sage_free'
static CYTHON_INLINE void sage_free(void *__pyx_v_ptr) {
^
In file included from /home/mmarco/sage/local/include/csage/stdsage.h:36:0,
from _home_mmarco_integrado_my_library_pyx_16.c:230:
/home/mmarco/sage/local/include/csage/memory.h:43:20: note: previous
definition of 'sage_free' was here
static inline void sage_free(void* ptr)
^
error: command 'gcc' failed with exit status 1
I have no idea why it complains about sage_malloc being redefined. Any clue?
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