[Numpy-discussion] Numpy Installation Problem on Redhat Linux

Hung-Hsuan Chen hhchen@psu....
Fri Jul 6 10:28:42 CDT 2012


Thank you.  This is very helpful!

On Fri, Jul 6, 2012 at 6:23 AM, Aron Ahmadia <aron@ahmadia.net> wrote:
> 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
>> > _______________________________________________
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>
>
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