undefined symbol when importing module compiled with weave

[lcharlin]

I've been using scipy's weave to speed up some numerically-intensive routines. I have a problem importing an extension created through weave.

Specifically, while weave successfully imports (and runs) the module it has compiled I cannot import the module outside of weave. Importing from a python prompt results in "undefined symbol" error. The exact error message is pasted below.

I can fix the error by passing an extra library to the linker at compile time (in this case gslcblas as the libraries arguments to weave.inline() ). However I wonder how weave is able to import the module without problems? I think this is related to a bigger performance issue I care about.

The python version I use in both cases is the same (the environment, as far as I can tell, is also exactly the same).

Thanks!

Importing the module from a Python prompt fails:
$ python2.7

import sc_e6d71e9b4074eed34d1cb1112482ee6212
Traceback (most recent call last):
File "", line 1, in
ImportError: /usr/lib64/libgsl.so.0: undefined symbol: cblas_ctrmv

Compilation log:
<weave: compiling>
running build_ext
running build_src
build_src
building extension "sc_e6d71e9b4074eed34d1cb1112482ee6213" sources
build_src: building npy-pkg config files
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
building 'sc_e6d71e9b4074eed34d1cb1112482ee6213' extension
compiling C++ sources
C compiler: g++ -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC

compile options: '-I/usr/local/python/2.7/scipy-mkl/0.14.0/lib64/python2.7/site-packages/scipy/weave -I/usr/local/python/2.7/scipy-mkl/0.14.0/lib64/python2.7/site-packages/scipy/weave/scxx -I/usr/local/python/2.7/numpy-mkl/1.8.1/lib64/python2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c'
extra options: '-march=native -fopenmp -O3 -lpthread'
g++: .cache/scipy/python27_compiled/sc_e6d71e9b4074eed34d1cb1112482ee6213.cpp
In file included from /usr/local/python/2.7/numpy-mkl/1.8.1/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
from /usr/local/python/2.7/numpy-mkl/1.8.1/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
from /usr/local/python/2.7/numpy-mkl/1.8.1/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from .cache/scipy/python27_compiled/sc_e6d71e9b4074eed34d1cb1112482ee6213.cpp:22:
/usr/local/python/2.7/numpy-mkl/1.8.1/lib64/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
g++: /usr/local/python/2.7/scipy-mkl/0.14.0/lib64/python2.7/site-packages/scipy/weave/scxx/weave_imp.cpp
g++ -pthread -shared /tmp/scipy-lcharlin-TBGEf5/python27_intermediate/compiler_fd2a2fbe93416fc0ff84072f09de2daf/.cache/scipy/python27_compiled/sc_e6d71e9b4074eed34d1cb1112482ee6213.o /tmp/scipy-lcharlin-TBGEf5/python27_intermediate/compiler_fd2a2fbe93416fc0ff84072f09de2daf/usr/local/python/2.7/scipy-mkl/0.14.0/lib64/python2.7/site-packages/scipy/weave/scxx/weave_imp.o -L/usr/lib64 -lgomp -lgsl -lpython2.7 -o .cache/scipy/python27_compiled/sc_e6d71e9b4074eed34d1cb1112482ee6213.so

[rgommers]

Not sure. The compile part of inline is quite complex, but the import at the end is simple:

    sys.path.insert(0,storage_dir)
    exec('import ' + module_name)
    func = eval(module_name+'.compiled_func')

[person142]

Closing since weave is no longer a part of SciPy. This issue is now tracked at scipy/weave#7.