I usually find these problems by searching for "error" in the output, in your case the complete problem is at the bottom of the log.  The relocation errors you're seeing are happening because the build process is trying to link in Atlas libraries (located here: /home/hxc249/lib/atlas/lib/) that were not compiled with -fPIC . Are you building ATLAS from source?  If so, then you follow the instructions to recompile ATLAS with -fPIC enabled here: http://math-atlas.sourceforge.net/atlas_install/atlas_install.html#SECTION00043000000000000000


creating build/temp.linux-x86_64-2.6/numpy/core/blasdot
compile options: '-DATLAS_INFO="\"3.9.83\"" -Inumpy/core/blasdot -I/home/hxc249/lib/atlas/include -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/usr/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 ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type


numpy/core/blasdot/_dotblas.c:257: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’

numpy/core/blasdot/_dotblas.c:292: warning: passing argument 3 of ‘(struct PyObject * (*)(struct PyObject *, struct PyObject *, struct PyArrayObject *))*(PyArray_API + 2240u)’ from incompatible pointer type

numpy/core/blasdot/_dotblas.c:292: note: expected ‘struct PyArrayObject *’ but argument is of type ‘struct PyObject *’
gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so


/usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC


/home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value

collect2: ld returned 1 exit status
/usr/bin/ld: /home/hxc249/lib/atlas/lib/libptcblas.a(cblas_dptgemm.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared object; recompile with -fPIC


/home/hxc249/lib/atlas/lib/libptcblas.a: could not read symbols: Bad value

collect2: ld returned 1 exit status
error: Command "gcc -pthread -shared build/temp.linux-x86_64-2.6/numpy/core/blasdot/_dotblas.o -L/home/hxc249/lib/atlas/lib -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6 -lptf77blas -lptcblas -latlas -lpython2.6 -o build/lib.linux-x86_64-2.6/numpy/core/_dotblas.so" failed with exit status 1

On Fri, Jul 6, 2012 at 6:00 AM, Hung-Hsuan Chen <hhchen@psu.edu> wrote:
Link is a great suggestion!  I was hesitating about whether or not to
paste such a long output.

The site.cfg file is shown in the following link.
https://gist.github.com/3059209

The output message for
$ python setup.py build --fcompiler=gnu95
can be found at the URL.
https://gist.github.com/3059320

Any suggestion is appreciated.

On Fri, Jul 6, 2012 at 5:21 AM, Paul Anton Letnes
<paul.anton.letnes@gmail.com> wrote:
>>
>> However, I got the following error message:
>> error: Command "/usr/bin/g77 -g -Wall -g -Wall -shared
>> build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/scipy/integrate/vodemodule.o
>> build/temp.linux-x86_64-2.6/build/src.linux-x86_64-2.6/fortranobject.o
>> -L/home/username/lib/ -L/usr/lib64 -Lbuild/temp.linux-x86_64-2.6
>> -lodepack -llinpack_lite -lmach -lblas -lpython2.6 -lg2c -o
>> build/lib.linux-x86_64-2.6/scipy/integrate/vode.so" failed with exit
>> status
>
> I'm sure there must have been more output? It does say that the command "failed", but not _why_ it failed. I suggest posting the entire output either in an email, or on a webpage (gist.github.com, for instance) and giving the link. It's very very hard to debug a build without the build log, so I'd suggest always giving it in the first instance.
>
> Paul
> _______________________________________________
> NumPy-Discussion mailing list
> NumPy-Discussion@scipy.org
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