I've been dealing with issues like this, on this one system, for a year now. At one point, I had a working combination of python, numpy, and scipy. I tried so many things that I can't really remember how I got to that point. I think I used gcc to build scipy 0.6 because I couldn't get it to work with icc, and I linked it with the Intel MKL successfully. However, when I upgraded to scipy-0.7.0 I am again facing this problem. The latest thing I tried was to build both Numpy and Scipy with the Intel C and Fortran compilers (icc and ifort). Numpy builds fine and passes all its unit tests. Scipy builds without errors or warnings, but I still have problems when trying to import any Scipy module that depends on "sparse." Build command: python setup.py config --compiler=intel --fcompiler=intelem install --prefix=/home/cfinch 2>&1 > scipy_build_log.txt Results:

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from scipy import sparse Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/cfinch/lib/python2.5/site-packages/scipy/sparse/__init__.py", line 6, in <module> from csr import * File "/home/cfinch/lib/python2.5/site-packages/scipy/sparse/csr.py", line 12, in <module> from sparsetools import csr_tocsc, csr_tobsr, csr_count_blocks, \ File "/home/cfinch/lib/python2.5/site-packages/scipy/sparse/sparsetools/__init__.py", line 4, in <module> from csr import * File "/home/cfinch/lib/python2.5/site-packages/scipy/sparse/sparsetools/csr.py", line 7, in <module> import _csr ImportError: /home/cfinch/lib/python2.5/site-packages/scipy/sparse/sparsetools/_csr.so: undefined symbol: _ZNSt8ios_base4InitD1Ev

When I use nm to look at the symbols in _csr.so, I see that these are undefined, along with several dozen other Python-related symbols: ... 00000000000d2810 W _ZNSt6vectorIxSaIxEE6resizeEmx 00000000000d2fdc W _ZNSt6vectorIySaIyEE6resizeEmy U _ZNSt8ios_base4InitC1Ev U _ZNSt8ios_base4InitD1Ev I have no idea what this symbol is, or where it's supposed to come from. Has anyone seen an error like this before? I am going to see what kind of support I can get from Intel. Craig ----- Original Message ---- From: Craig Finch <oanjao@yahoo.com> To: David Cournapeau <cournape@gmail.com>; SciPy Users List <scipy-user@scipy.org> Sent: Sunday, July 5, 2009 2:30:18 PM Subject: Re: [SciPy-user] Scipy weave errors: undefined symbols when importing compiled extension By "build log" I assume you mean the output to stderr and stdout when when building Scipy. It's a huge amount of output, and I'm not sure exactly what to look for. Do you want me to post a particular section? Below is the output from sections where g++ is called. It seems to be linked with g++ everywhere. One more potential problem area: I'm linking with the Intel Math Kernel Library (MKL) which was almost certainly built with Intel compilers. Could that be causing this problem? Craig ----------------------- building 'scipy.interpolate._interpolate' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC compile options: '-Iscipy/interpolate/src -I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/interpolate/src/_interpolate.cpp g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/interpolate/src/_interpolate.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/interpolate/_interpolate.so ----------------------- building 'scipy.sparse.sparsetools._csr' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC creating build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools compile options: '-I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/sparse/sparsetools/csr_wrap.cxx g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools/csr_wrap.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/sparse/sparsetools/_csr.so building 'scipy.sparse.sparsetools._csc' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC compile options: '-I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/sparse/sparsetools/csc_wrap.cxx g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools/csc_wrap.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/sparse/sparsetools/_csc.so building 'scipy.sparse.sparsetools._coo' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC compile options: '-I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/sparse/sparsetools/coo_wrap.cxx g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools/coo_wrap.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/sparse/sparsetools/_coo.so building 'scipy.sparse.sparsetools._bsr' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC compile options: '-I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/sparse/sparsetools/bsr_wrap.cxx g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools/bsr_wrap.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/sparse/sparsetools/_bsr.so building 'scipy.sparse.sparsetools._dia' extension compiling C++ sources C compiler: g++ -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -fPIC compile options: '-I/home/cfinch/lib/python2.5/site-packages/numpy/core/include -I/home/cfinch/include/python2.5 -c' g++: scipy/sparse/sparsetools/dia_wrap.cxx g++ -pthread -shared build/temp.linux-x86_64-2.5/scipy/sparse/sparsetools/dia_wrap.o -Lbuild/temp.linux-x86_64-2.5 -o build/lib.linux-x86_64-2.5/scipy/sparse/sparsetools/_dia.so ----------------------- ----- Original Message ---- From: David Cournapeau <cournape@gmail.com> To: Craig Finch <cfinch@ieee.org>; SciPy Users List <scipy-user@scipy.org> Sent: Friday, July 3, 2009 10:21:28 PM Subject: Re: [SciPy-user] Scipy weave errors: undefined symbols when importing compiled extension On Sat, Jul 4, 2009 at 3:38 AM, Craig Finch<oanjao@yahoo.com> wrote:

ImportError: /home/cfinch/lib/python2.5/site-packages/scipy/sparse/sparsetools/_csr.so: undefined symbol: __gxx_personality_v0

As far as I know, everything Python-related on this machine has now been built with GNU tools, but something is still broken. One more thing--Python, Numpy, and Scipy are all locally installed in my /home/cfinch directory because the system Python is frozen at 2.4.

This is still a C++ problem, I have sometimes noticed this problem on some machines. Normally this is caused by a C++ object file being linked with gcc (instead of g++). Can you post the build log of scipy ? David