[Numpy-discussion] extension module with swig
Giovanni Samaey
Giovanni.Samaey@cs.kuleuven...
Tue Nov 4 04:10:26 CST 2008
Dear all,
I am unsure about the correct place to put this question -- If this
isn't the correct list, please let me know which place is more
appropriate.
I am trying to build an extension module in python that calls a C
routine that depends on the GNU Scientific Library.
I am using swig to wrap the c-file and the numpy.i file that is
included with numpy for the typemaps. To build the module, I am using
distutils, with a modified version of the setup.py file that was
included with the examples (in order to link against gsl).
Although the build succeeds wtihout problems, I am getting "undefined
symbol" errors from gsl when importing the module in python. I am
attaching the source code of the simplest possible example below
together with the error messages. Note that I am trying to link
against my own gsl in my home directory. There is no system-wide one
available.
I get the feeling that I am doing something silly, but I am unable to
put the finger on it. Any help would be greatly appreciated.
As a c-file I have : test.c
#include <gsl/gsl_rng.h>
#include <gsl/gsl_randist.h>
# include <math.h>
double var;
void test(double *x, double *y, double *z, int n) {
int i;
const gsl_rng_type *T;
gsl_rng *r;
// gsl_rng_env_setup();
// T = gsl_rng_default;
T = gsl_rng_mt19937;
r = gsl_rng_alloc(T);
for (i=0;i<n;i++) {
*(z++)=x[i]+y[i]+var;
}
var += gsl_rng_uniform(r);
}
As a header file : test.h
extern double var;
void test(double *x, double *y, double *z, int n);
The swig interface file: test.i
/* test.i */
%module test
%{
#define SWIG_FILE_WITH_INIT
%}
%include "numpy.i"
%init %{
import_array();
%}
%inline %{
#include "test.h"
%}
%apply (double* IN_ARRAY1, int DIM1) {(double* x, int n1),
(double* y, int n2)}
%apply (double* ARGOUT_ARRAY1, int DIM1) {(double* z, int m)};
%rename (test) my_test;
%inline %{
void my_test(double* x, int n1, double* y, int n2, double* z, int m) {
test(x,y,z,m);
}
%}
%ignore test;
%include "test.h"
The setup.py file is :
#! /usr/bin/env python
# System imports
from distutils.core import *
from distutils import sysconfig
# Third-party modules - we depend on numpy for everything
import numpy
# Obtain the numpy include directory. This logic works across numpy
versions.try:
numpy_include = numpy.get_include()
except AttributeError:
numpy_include = numpy.get_numpy_include()
# dot extension module
_test = Extension("_test",
["test_wrap.c",
"test.c"],
include_dirs = [numpy_include,'/data/home/
u0038151/include'],
library_dirs = ['/data/home/u0038151/lib']
)
# NumyTypemapTests setup
setup(name = ["test"],
description = "test c module swigging",
author = "Giovanni Samaey",
py_modules = ["test"],
ext_modules = [_test ]
)
The error message is the following:
0 u0038151@lo-03-02 dot2 $ python -c "import test"
Traceback (most recent call last):
File "<string>", line 1, in ?
File "test.py", line 7, in ?
import _test
ImportError: ./_test.so: undefined symbol: gsl_rng_mt19937
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