[SciPy-User] Hi I have a quastion to weave

SungHwan Choi sunghwanchoi91@gmail....
Wed Aug 22 09:56:31 CDT 2012


Hi I am Sunghwan Choi
Now, I am interested on weave. First of all, I have c code to be wrapped by
python.

tmp.c file

#include<xc.h>
#include<stdio.h>
int main(){
        int np =3;
        int return_val;
        xc_func_type func;
        xc_func_init(&func, XC_GGA_X_B88, XC_UNPOLARIZED);
        xc_func_end(&func);
        return_val=np+131;
        printf("%d", return_val);
}

gcc -o exe tmp.c
-L/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs/ -lxc -lm
./exe

above code is my target code and now,

from scipy.weave import inline
np=3
code=\
        """
        xc_func_type func;
        xc_func_init(&func, XC_GGA_X_B88, XC_UNPOLARIZED);
        xc_func_end(&func);
        return_val=np+131;
        """
print inline(code,['np'],include_dirs =
["/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/"],library_dirs=["/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs"],libraries=["m","xc"],headers=["<xc.h>","<stdio.h>"],compiler='gcc')
print np

This is my solution but it give me a error

In file included from
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1975:0,
                 from
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:15,
                 from
/home/shchoi/.python27_compiled/sc_a383cf366f9347f9b6ff017e9aab78882.cpp:22:
/usr/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_deprecated_api.h:11:2:
warning: #warning "Using deprecated NumPy API, disable it by #defining
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/usr/bin/ld:
/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs/libxc.a(libxc_la-functionals.o):
relocation R_X86_64_32 against `xc_functional_keys' can not be used when
making a shared object; recompile with -fPIC
/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs/libxc.a:
could not read symbols: Bad value
collect2: ld returned 1 exit status
/usr/bin/ld:
/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs/libxc.a(libxc_la-functionals.o):
relocation R_X86_64_32 against `xc_functional_keys' can not be used when
making a shared object; recompile with -fPIC
/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs/libxc.a:
could not read symbols: Bad value
collect2: ld returned 1 exit status
Traceback (most recent call last):
  File "tmp.py", line 12, in <module>
    print inline(code,['np'],include_dirs =
["/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/"],library_dirs=["/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs"],libraries=["m","xc"],headers=["<xc.h>","<stdio.h>"],compiler='gcc')
  File "/usr/lib64/python2.7/site-packages/scipy/weave/inline_tools.py",
line 355, in inline
    **kw)
  File "/usr/lib64/python2.7/site-packages/scipy/weave/inline_tools.py",
line 482, in compile_function
    verbose=verbose, **kw)
  File "/usr/lib64/python2.7/site-packages/scipy/weave/ext_tools.py", line
367, in compile
    verbose = verbose, **kw)
  File "/usr/lib64/python2.7/site-packages/scipy/weave/build_tools.py",
line 272, in build_extension
    setup(name = module_name, ext_modules = [ext],verbose=verb)
  File "/usr/lib64/python2.7/site-packages/numpy/distutils/core.py", line
186, in setup
    return old_setup(**new_attr)
  File "/usr/lib64/python2.7/distutils/core.py", line 169, in setup
    raise SystemExit, "error: " + str(msg)
scipy.weave.build_tools.CompileError: error: Command "g++ -pthread -shared
/tmp/shchoi/python27_intermediate/compiler_81874d258832299909898bc232bd652b/home/shchoi/.python27_compiled/sc_a383cf366f9347f9b6ff017e9aab78882.o
/tmp/shchoi/python27_intermediate/compiler_81874d258832299909898bc232bd652b/usr/lib64/python2.7/site-packages/scipy/weave/scxx/weave_imp.o
-L/home/shchoi/git/LagChem/LagChem/Basic/XCs/libxc-1.2.0/src/.libs
-L/usr/lib64 -lm -lxc -lpython2.7 -o
/home/shchoi/.python27_compiled/sc_a383cf366f9347f9b6ff017e9aab78882.so"
failed with exit status 1

I have tried to solve for a while but now I give up. please help me anyone~
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