[Numpy-discussion] Compiling numpy on Red-Hat Import Error with lapack_lite.so

[Jeffrey Spencer]

I'll answer my own question. It was a mix of using two different fortran 
compilers so specified the option: python setup.py config_fc 
--fcompiler=gfortran build.

All seems to be going well now.


On 07/08/2011 05:35 PM, Jeffrey Spencer wrote:
> That actually makes sense because I am not sure the gnu that it was 
> compiled with but I think it is different. I have since compiled gcc 
> myself, then python, and atlas libraries. Then I tried to install 
> numpy. It go tthrough the install no worries and found the correct 
> libraries. It stuffed when I tried to import it with this error:
>
> >>> import numpy
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/home/jspender/lib/python2.6/site-packages/numpy/__init__.py", 
> line 137, in <module>
>     import add_newdocs
>   File 
> "/home/jspender/lib/python2.6/site-packages/numpy/add_newdocs.py", 
> line 9, in <module>
>     from numpy.lib import add_newdoc
>   File 
> "/home/jspender/lib/python2.6/site-packages/numpy/lib/__init__.py", 
> line 13, in <module>
>     from polynomial import *
>   File 
> "/home/jspender/lib/python2.6/site-packages/numpy/lib/polynomial.py", 
> line 17, in <module>
>     from numpy.linalg import eigvals, lstsq
>   File 
> "/home/jspender/lib/python2.6/site-packages/numpy/linalg/__init__.py", 
> line 48, in <module>
>     from linalg import *
>   File 
> "/home/jspender/lib/python2.6/site-packages/numpy/linalg/linalg.py", 
> line 23, in <module>
>     from numpy.linalg import lapack_lite
> ImportError: 
> /home/jspender/lib/python2.6/site-packages/numpy/linalg/lapack_lite.so: undefined 
> symbol: _gfortran_concat_string
> >>>
>
> Any ideas???
>
> Cheers,
> Jeff
>
> On Fri, Jul 8, 2011 at 12:37 AM, Bruce Southey <bsouthey at gmail.com 
> <mailto:bsouthey at gmail.com>> wrote:
>
>     On 07/07/2011 05:23 AM, Jeffrey Spencer wrote:
>     > The error is below:
>     >
>     > creating build/temp.linux-x86_64-2.6/numpy/core/blasdot
>     > compile options: '-DATLAS_INFO="\"None\"" -Inumpy/core/blasdot
>     > -Inumpy/core/include
>     > -Ibuild/src.linux-x86_64-2.6/numpy/core/include/numpy
>     > -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core
>     > -Inumpy/core/src/npymath -Inumpy/core/src/multiarray
>     > -Inumpy/core/src/umath -Inumpy/core/include
>     > -I/home/jspender/include/python2.6
>     > -Ibuild/src.linux-x86_64-2.6/numpy/core/src/multiarray
>     > -Ibuild/src.linux-x86_64-2.6/numpy/core/src/umath -c'
>     > gcc: numpy/core/blasdot/_dotblas.c
>     > numpy/core/blasdot/_dotblas.c: In function ‘dotblas_matrixproduct’:
>     > numpy/core/blasdot/_dotblas.c:239: warning: comparison of distinct
>     > pointer types lacks a cast
>     > numpy/core/blasdot/_dotblas.c:257: warning: passing argument 3 of
>     > ‘*(PyArray_API + 2240u)’ from incompatible pointer type
>     > numpy/core/blasdot/_dotblas.c:292: warning: passing argument 3 of
>     > ‘*(PyArray_API + 2240u)’ from incompatible pointer type
>     > gcc -pthread -shared
>     > build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o
>     > -L/usr/local/lib -Lbuild/temp.linux-x86_64-2.6 -lf77blas -lcblas
>     -latlas
>     > -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so
>     > /usr/bin/ld: skipping incompatible /usr/local/lib/libf77blas.a when
>     > searching for -lf77blas
>     > /usr/bin/ld: skipping incompatible /usr/local/lib/libf77blas.a when
>     > searching for -lf77blas
>     > /usr/bin/ld: cannot find -lf77blas
>     > collect2: ld returned 1 exit status
>     > /usr/bin/ld: skipping incompatible /usr/local/lib/libf77blas.a when
>     > searching for -lf77blas
>     > /usr/bin/ld: skipping incompatible /usr/local/lib/libf77blas.a when
>     > searching for -lf77blas
>     > /usr/bin/ld: cannot find -lf77blas
>     > collect2: ld returned 1 exit status
>     > error: Command "gcc -pthread -shared
>     > build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o
>     > -L/usr/local/lib -Lbuild/temp.linux-x86_64-2.6 -lf77blas -lcblas
>     -latlas
>     > -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so" failed
>     with exit
>     > status 1
>     >
>     > Any help would be appreciated.
>     >
>     Python is looking for a 64-bit  library as the one in
>     /usr/local/lib/ is
>     either 32-bit or built with a different compiler version. If you have
>     the correct library in another location then you need to point
>     numpy to
>     it or just build everything with the same compiler.
>
>     Bruce
>
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