[Numpy-discussion] Numpy Installation Problem on Redhat Linux

[Aron Ahmadia]

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 at 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 at 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 at scipy.org
> > http://mail.scipy.org/mailman/listinfo/numpy-discussion
> _______________________________________________
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