I recently tried to build SciPy 0.10.1 on a system with both the GNU and Intel compilers. Everything went find except that import scipy bombed out with:

ImportError: /opt/scipy/0.10.1/lib/python2.7/site-packages/scipy/
sparse/sparsetools/_csr.so: undefined symbol: _ZNSt8ios_base4InitD1Ev

The fix is to add “-lstdc++” to the link flags. I found a post on the SciPy mailing list where someone had the same problem and asked “Could someone please advise me how to ensure that the “-lstdc++” is successfully passed to the linker as and when I build scipy.”

The answer is to use the build_ext target to enable the link flag:

python setup.py config --compiler=intel --cc=icc --fcompiler=intelem build_ext -lstdc++
python setup.py config --compiler=intel --fcompiler=intelem install --prefix=/opt/scipy/0.10.1

Archived Comments

Date: 2012-07-26 11:00:02 UTC

Author: Charles

Thank you for this reposting. It was extremely useful (e.g. solved my problem)!