[Numpy-discussion] extension module with swig
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
#include
# include
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", line 1, in ?
File "test.py", line 7, in ?
import _test
ImportError: ./_test.so: undefined symbol: gsl_rng_mt19937
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Re: [Numpy-discussion] extension module with swig
And, additionally setting the environment variable LD_LIBRARY_PATH to
start with /data/home/u0038151/lib instead of ending with it, it picks
up my own gsl, and gives the error message
0 [EMAIL PROTECTED] dot2 $ python -c "import dot"
Traceback (most recent call last):
File "", line 1, in ?
File "dot.py", line 7, in ?
import _dot
ImportError: /data/home/u0038151/lib/libgsl.so.0: undefined symbol:
cblas_ctrmv
Again something different...
Giovanni
On 04 Nov 2008, at 11:46, Giovanni Samaey wrote:
> Hi Matthieu,
>
> thank you for your prompt reply.
>
> On 04 Nov 2008, at 11:24, Matthieu Brucher wrote:
>
>>> # 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']
>>> )
>
> This is where is specify the directory where my header files are, as
> well as the directory of the library. If I add, from your
> suggestion libraries = ['gsl'] to that list, it tries to pick up a
> gsl that is installed in /usr/lib (but there are no headers there.)
> Then I get the message:
>
> python -c "import dot"
> Traceback (most recent call last):
> File "", line 1, in ?
> File "dot.py", line 7, in ?
>import _dot
> ImportError: /usr/lib/libgsl.so.0: undefined symbol: cblas_dsdot
>
> So it finds the gsl symbols in the system library (not mine),
> probably combined with my headers, and then has a different error.
>
> Giovanni
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Re: [Numpy-discussion] extension module with swig
> # 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 [EMAIL PROTECTED] dot2 $ python -c "import test"
> Traceback (most recent call last):
> File "", line 1, in ?
> File "test.py", line 7, in ?
> import _test
> ImportError: ./_test.so: undefined symbol: gsl_rng_mt19937
Hi,
Where did you add the gsl library when building the extension ? I
think the Extension class is missing an argument (library = ["gsl"] or
something like that)
Matthieu
--
Information System Engineer, Ph.D.
Website: http://matthieu-brucher.developpez.com/
Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
LinkedIn: http://www.linkedin.com/in/matthieubrucher
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Re: [Numpy-discussion] extension module with swig
Giovanni Samaey wrote: > changing the library path and explicitly adding libraries =['gsl', > 'gslcblas'] did the trick ! one other suggestion: if you want this to run any other machine, you might want to build gsl as a static lib, so it will get linked directly into your extension, and your extension will no longer rely on having it installed. -Chris -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R(206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception [EMAIL PROTECTED] ___ Numpy-discussion mailing list Numpy-discussion@scipy.org http://projects.scipy.org/mailman/listinfo/numpy-discussion
Re: [Numpy-discussion] extension module with swig
Thanks,
changing the library path and explicitly adding libraries =['gsl',
'gslcblas'] did the trick !
Thank you so much !
Giovanni
On 04 Nov 2008, at 12:09, Matthieu Brucher wrote:
> The issue with the LD_LIBRARY_PATH would come up in any case. You have
> to put your gsl library folder before the system one if you want your
> gsl library to be used.
>
> For the cblas issue, it seems from Google you have to link against a
> CBLAS library as well to use the GSL (for instance blas or atlas
> shoule be enough).
>
> Matthieu
>
> 2008/11/4 Giovanni Samaey <[EMAIL PROTECTED]>:
>> And, additionally setting the environment variable LD_LIBRARY_PATH to
>> start with /data/home/u0038151/lib instead of ending with it, it
>> picks
>> up my own gsl, and gives the error message
>>
>> 0 [EMAIL PROTECTED] dot2 $ python -c "import dot"
>> Traceback (most recent call last):
>> File "", line 1, in ?
>> File "dot.py", line 7, in ?
>> import _dot
>> ImportError: /data/home/u0038151/lib/libgsl.so.0: undefined symbol:
>> cblas_ctrmv
>>
>> Again something different...
>>
>> Giovanni
>>
>> On 04 Nov 2008, at 11:46, Giovanni Samaey wrote:
>>
>>> Hi Matthieu,
>>>
>>> thank you for your prompt reply.
>>>
>>> On 04 Nov 2008, at 11:24, Matthieu Brucher wrote:
>>>
> # 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']
>)
>>>
>>> This is where is specify the directory where my header files are, as
>>> well as the directory of the library. If I add, from your
>>> suggestion libraries = ['gsl'] to that list, it tries to pick up a
>>> gsl that is installed in /usr/lib (but there are no headers there.)
>>> Then I get the message:
>>>
>>> python -c "import dot"
>>> Traceback (most recent call last):
>>> File "", line 1, in ?
>>> File "dot.py", line 7, in ?
>>> import _dot
>>> ImportError: /usr/lib/libgsl.so.0: undefined symbol: cblas_dsdot
>>>
>>> So it finds the gsl symbols in the system library (not mine),
>>> probably combined with my headers, and then has a different error.
>>>
>>> Giovanni
>>
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>>
>
>
>
> --
> Information System Engineer, Ph.D.
> Website: http://matthieu-brucher.developpez.com/
> Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
> LinkedIn: http://www.linkedin.com/in/matthieubrucher
> ___
> Numpy-discussion mailing list
> Numpy-discussion@scipy.org
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Re: [Numpy-discussion] extension module with swig
Hi Matthieu,
thank you for your prompt reply.
On 04 Nov 2008, at 11:24, Matthieu Brucher wrote:
>> # 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']
>> )
This is where is specify the directory where my header files are, as
well as the directory of the library. If I add, from your suggestion
libraries = ['gsl'] to that list, it tries to pick up a gsl that is
installed in /usr/lib (but there are no headers there.)
Then I get the message:
python -c "import dot"
Traceback (most recent call last):
File "", line 1, in ?
File "dot.py", line 7, in ?
import _dot
ImportError: /usr/lib/libgsl.so.0: undefined symbol: cblas_dsdot
So it finds the gsl symbols in the system library (not mine), probably
combined with my headers, and then has a different error.
Giovanni
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Re: [Numpy-discussion] extension module with swig
The issue with the LD_LIBRARY_PATH would come up in any case. You have
to put your gsl library folder before the system one if you want your
gsl library to be used.
For the cblas issue, it seems from Google you have to link against a
CBLAS library as well to use the GSL (for instance blas or atlas
shoule be enough).
Matthieu
2008/11/4 Giovanni Samaey <[EMAIL PROTECTED]>:
> And, additionally setting the environment variable LD_LIBRARY_PATH to
> start with /data/home/u0038151/lib instead of ending with it, it picks
> up my own gsl, and gives the error message
>
> 0 [EMAIL PROTECTED] dot2 $ python -c "import dot"
> Traceback (most recent call last):
> File "", line 1, in ?
> File "dot.py", line 7, in ?
>import _dot
> ImportError: /data/home/u0038151/lib/libgsl.so.0: undefined symbol:
> cblas_ctrmv
>
> Again something different...
>
> Giovanni
>
> On 04 Nov 2008, at 11:46, Giovanni Samaey wrote:
>
>> Hi Matthieu,
>>
>> thank you for your prompt reply.
>>
>> On 04 Nov 2008, at 11:24, Matthieu Brucher wrote:
>>
# 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']
)
>>
>> This is where is specify the directory where my header files are, as
>> well as the directory of the library. If I add, from your
>> suggestion libraries = ['gsl'] to that list, it tries to pick up a
>> gsl that is installed in /usr/lib (but there are no headers there.)
>> Then I get the message:
>>
>> python -c "import dot"
>> Traceback (most recent call last):
>> File "", line 1, in ?
>> File "dot.py", line 7, in ?
>>import _dot
>> ImportError: /usr/lib/libgsl.so.0: undefined symbol: cblas_dsdot
>>
>> So it finds the gsl symbols in the system library (not mine),
>> probably combined with my headers, and then has a different error.
>>
>> Giovanni
>
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> Numpy-discussion mailing list
> Numpy-discussion@scipy.org
> http://projects.scipy.org/mailman/listinfo/numpy-discussion
>
--
Information System Engineer, Ph.D.
Website: http://matthieu-brucher.developpez.com/
Blogs: http://matt.eifelle.com and http://blog.developpez.com/?blog=92
LinkedIn: http://www.linkedin.com/in/matthieubrucher
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